Identification of long noncoding RNA expression profile in oxaliplatin-resistant hepatocellular carcinoma cells

Identification of long noncoding RNA expression profile in oxaliplatinresistant hepatocellular carcinoma cells Xin Yin, Su-Su Zheng, ...

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Identification of long noncoding RNA expression profile in oxaliplatinresistant hepatocellular carcinoma cells Xin Yin, Su-Su Zheng, Lan Zhang, Xiao-Ying Xie, Yan Wang, Bo-Heng Zhang, Weizhong Wu, Shuangjian Qiu, Zheng-Gang Ren PII: DOI: Reference:

S0378-1119(16)30803-4 doi: 10.1016/j.gene.2016.10.008 GENE 41617

To appear in:

Gene

Received date: Revised date: Accepted date:

21 May 2016 23 September 2016 5 October 2016

Please cite this article as: Yin, Xin, Zheng, Su-Su, Zhang, Lan, Xie, Xiao-Ying, Wang, Yan, Zhang, Bo-Heng, Wu, Weizhong, Qiu, Shuangjian, Ren, Zheng-Gang, Identiﬁcation of long noncoding RNA expression proﬁle in oxaliplatin-resistant hepatocellular carcinoma cells, Gene (2016), doi: 10.1016/j.gene.2016.10.008

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ACCEPTED MANUSCRIPT Identification of long noncoding RNA expression profile in oxaliplatin-resistant

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hepatocellular carcinoma cells

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Xin Yin1, Su-Su Zheng1, Lan Zhang1, Xiao-Ying Xie1, Yan Wang1, Bo-Heng Zhang1, Weizhong Wu1, Shuangjian Qiu1, Zheng-Gang Ren1#

Liver Cancer Institute & Zhongshan Hospital, Fudan University, Shanghai, China.

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# Corresponding author:

Zheng-Gang Ren, Liver Cancer Institute & ZhongShan Hospital, Fudan University,

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136 Yi Xue Yuan Road, Shanghai 200032, China.

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Phone & Fax: +86-21-64037181 Email: [email protected]

Email addresses:

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Xin Yin: [email protected] Su-Su Zheng: [email protected] Lan Zhang: [email protected] Xiao-Ying Xie: [email protected] Yang Wang: [email protected] Bo-Heng Zhang: [email protected] Weizhong Wu: [email protected] Shuangjian Qiu: [email protected]

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ACCEPTED MANUSCRIPT Abstract Hepatocellular carcinoma (HCC) is the most prevalent and malignant type of liver cancer. Besides

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the high incidence, the resistance to chemotherapy is a major problem that leads to the high

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mortality of HCC. Recently, aberrant expression of long noncoding RNAs (lncRNAs) has been considered as a primary feature of many types of cancer. However, the genome-wide expression pattern and associated functional implications of lncRNAs in chemo-resistant HCC cells remain

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unknown. In this study, we identified 120 differentially expressed lncRNAs with 61 up-regulated

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and 59 down-regulated (fold change > 2, P < 0.05) along with 421 differentially expressed mRNAs with 228 up-regulated and 193 down-regulated (fold change > 2, P < 0.05) in

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oxaliplatin-resistant (MHCC97H-OXA) HCC cells, compared to parental oxaliplatin-sensitive

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(MHCC97H) by microarray. The underlying pathways were related to cell death, proliferation,

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cellular response to stimulus, including p53 pathway, ErbB pathway and MAPK pathway. Further, 16 lncRNAs were selected for validation of microarray results with quantitative PCR, and a strong

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correlation was identified between the qPCR results and microarray data. We demonstrated for the first time that ENST00000438347, NR_073453 and ENST00000502804 were up-regulated in MHCC97H-OXA cells as well as chemo-resistant HCC cancerous tissues. Moreover, the expression of ENST00000518376 was significantly associated with the tumor size and differentiation. Overall survival analysis showed that high expression of ENST00000438347 and ENST00000518376 was associated with poor prognosis in HCC patients. Taken together, our results reveal that the expression profile in oxaliplatin-resistant HCC is significantly altered including lncRNAs. And a series of de novo lncRNAs play important functions in HCC oxaliplatin resistance and HCC progression. 2

ACCEPTED MANUSCRIPT Abbreviations HCC: Hepatocellular Carcinoma

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lnc-RNA: Long non-coding RNA:

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FDR: False Discovery Rate GO: Gene Ontology

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OXA: Oxaliplatin

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Key words: Hepatocellular carcinoma, oxaliplatin-resistant, lncRNA, microarray, prognosis 1. Introduction

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Hepatocellular carcinoma (HCC) ranks the fifth among the most common types of cancer and

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is the third leading cause of cancer-related death around the world. HCC alone accounts for

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approximately one million deaths every year [1,2,3]. Surgical resection and liver transplantation are considered as potentially curative treatment. Unfortunately, only 10-23% of patients are

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candidates for surgical resection, most of HCC patients have to receive systemic chemotherapy due to their advanced-stage at diagnosis or disease relapse/refractory [4]. Despite these aggressive treatments, the overall response rate remains low. Most patients will eventually face treatment failure because of HCC relapse or metastasis. Therefore, it is crucial to understand the mechanisms of drug resistance to prevent or reverchemo-resistance. Oxaliplatin is a diaminocyclohexane carrier ligand based platinum compound with a wide range of anti-tumor activity in multiple types of metastatic cancer [5]. It is widely used in the chemotherapeutic regimes for metastatic HCC [3]. Oxaliplatin covalently binds to DNA, forming platinum-DNA complex that inducing cell growth inhibition and cell apoptosis [6]. However, like 3

ACCEPTED MANUSCRIPT most chemotherapeutic agents, the efficacy of oxaliplatin is limited due to the development of cellular resistance [7]. Although several pathways have been identified in the oxaliplatin resistance,

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the precise mechanisms remain elusive.

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Long noncoding RNAs (lncRNAs) are tentatively defined as a class of non-coding RNA molecules longer than 200 nucleotides [8]. Recently, lncRNAs have emerged to exert critical functions in many biological processes including development, tumorigenesis, genetic imprinting,

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immune response, and metabolism [9,10,11,12]. Thus, lncRNAs aberrance has been found in a

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variety of human diseases, for example cancer [13], Huntington’s disease and Alzheimer’s disease [14]. Many lncRNAs have been demonstrated to be associated with HCC progression, such as

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MVIH [15], H19 [16], HEIH [17], HULC [18], TUC338 [18] and MEG3 [19]. Moreover, high

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expression of lncRNA-HEIH promotes HCC growth through Enhancer of Zeste Homolog 2

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(EZH2) [17]. The up-regulated lncRNA-MALAT1 has been verified as a biomarker in HCC tumor recurrence after liver transplantation [20]. Considering these exciting findings, the expression

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pattern and underlying functions of lncRNAs in HCC diagnosis and treatment remain to be clarified, especially in chemo-resistance.

2. Results 2.1 Expression profile of lncRNAs and mRNAs in Oxaliplatin resistant HCC cells To reveal the expression profile of lncRNA and mRNA in oxaliplatin resistant HCC, we performed microarray analysis to identify lncRNAs and mRNAs that were expressed abnormally in parental oxaliplatin-sensitive (MHCC97H) and oxaliplatin-resistant (MHCC97H-OXA) HCC cells. Fold-change (oxaliplatin resistant vs oxaliplatin sensitive) and P value were calculated from 4

ACCEPTED MANUSCRIPT the normalized expression. 120 significantly differentially expressed lncRNAs and 431 significantly differentially expressed mRNAs were identified in MHCC97H-OXA sample

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compared with its parental sensitive MHCC97H cells (fold change > 2, p < 0.05) (Figure 1, Table

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1 and 2). Altogether, our results showed that 61 lncRNAs and 193 mRNAs were upregulated in MHCC97H-OXA cells, while 59 lncRNAs and 228 mRNAs were downregulated (Figure 1, Table 1 and 2). Integrative analysis of lncRNAs and mRNAs was performed as shown in Table 3.

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To validate the results from microarray analysis, we selected 16 lncRNAs with most

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demonstrated

that

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divergences and designed the primers for quantitative polymerase chain reaction (qPCR). qPCR lncRNAENST00000438347,

NR_073453, ENST00000460497,

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NR_033928, NEST00000480069, ENST00000421965, AK055628 and TCONS_00014652 were

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up-regulated in MHCC97H-OXA cells in consistent with microarray results (Figure 2).

2.2 Gene Ontology (GO) and pathway analysis of differentially changed lncRNAs and mRNAs.

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We first applied gene ontology analysis against the differentially expressed genes and discovered that cell death related genes were mostly changed as long as cellular response to stimulus, indicating that genes involved in cell death or apoptosis might confers oxaliplatin resistance in HCC (Figure 3).

Next, we categorized the differentially changed genes into critical pathways involved in oxaliplatin resistance. As expected, most differentially changed genes fell into pathways of cancer related pathways, for example RAS pathway, MAPK pathway and p53 signaling pathway (Figure 4). To our surprise, genes related to proteoglycans in cancer were highly up-regulated

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ACCEPTED MANUSCRIPT (Figure 4). Together with the GO analysis, our results showed that the change in chemo-resistance might be resulted from expression difference of cell death and cancerous related

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genes.

2.3 lncRNA differential expression correlates with oxaliplatin resistance in patients with HCC. In order to explore the relation between lncRNAs expressions and oxaliplatin resistance, we

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collected a cohort of advanced HCC patients (BCLC C stage) treated with oxaliplatin-based

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chemotherapy. After 4-6 cycles of chemotherapy, these patients were divided into oxaliplatin-sensitive (n=8) and oxaliplatin-resistant group (n=10), according to post-chemotherapy

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tumor response (evaluated by the modified Response Evaluation Criteria in Solid Tumors). And

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the expressions of these lncRNAs were analyzed between two groups. The RT-PCR results

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showed that the expressions of lncRNA ENST00000518376, ENST00000502804 and NR_073453 were significantly higher in oxaliplatin-resistant group while lncRNA ENST00000438347 showed

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the opposite pattern (Figure 5A). 2.4 The role of lncRNAs expression on HCC prognosis To further explore the involvement of lncRNAs in HCC, four LncRNAs were selected by expression levels and evaluated in tumor tissues collected from 57 HCC patients through qPCR analysis. The results showed that the expression levels of lncRNA ENST00000438347, ENST00000518376, ENST00000502804, and NR_073453 were significantly higher in HCC specimens than those in corresponding adjacent non-tumorous tissues (Figure 5B). Linear regression function weighted least squares method was adopted to establish linear regression and the result showed that elevated expression of lncRNA ENST00000518376 was associated with 6

ACCEPTED MANUSCRIPT tumor size and tumor differentiation significantly (Table 4). The overall survival rates for the HCC patients were 76.9% at 1 year, 42.4% at 3 years and

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24.2% at 5 years, respectively. Upon univariate analysis, lncRNA ENST00000438347 and

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ENST00000518376 expression levels were found to be unfavorable prognostic predictor for overall survival (P = 0.001 and P = 0.02, Table 5 and Figure 6). ENST00000438347 is located on chromosome 10: 30,403,197-30,403,776 reverse strand, with a length of 580 bp. Moreover,

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multivariate analysis (Table 5) showed that lncRNA ENST00000438347 expression was

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independently associated with overall survival (Hazard Ratio, 3.28; 95% confidence interval, 1.48-7.24, P = 0.003). LncRNA ENST00000518376 expression was also related to poor overall

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survival (Hazard Ratio, 1.69; 95% confidence interval, 1.31-3.69, P = 0.04). Besides, vascular

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invasion was also an independent predictor of overall survival (Hazard Ratio, 2.67; 95%

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3. Discussion

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confidence interval, 1.21-5.88, P = 0.02).

HCC ranks the fifth most malignancy tumors around the world, accounting for approximately 90% of primary liver cancers [1]. Most of HCC patients have to receive transcatheter arterial chemoembolization or systemic chemotherapy due to their advanced-stage at diagnosis or disease relapse/refractory. Over the past decades, oxaliplatin is widely used in the chemotherapeutic regimes for HCC. However, the development of resistance is a great challenge. Increasing evidences indicate that lncRNAs may play important roles in regulating gene expression epigenetically in biology [21]. And abnormal lncRNAs expressions and associated functions are found in many types of cancers, such as HOTAIR promotes breast tumor metastasis [22], and 7

ACCEPTED MANUSCRIPT Gas5 regulates breast cancer cell apoptosis [23]. Dysregulation of lncRNAs, including H19 [24], HEIH [17], MVIH [25], HULC [26] and MEG3 [27], have been demonstrated in HCC. Though

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progresses have been made in the involvement of lncRNAs in HCC progression, the expression

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profile and underlying functions of lncRNAs in oxaliplatin-resistance remain unknown. In this study, we investigated lncRNA and mRNA expression profiles of oxaliplatin-resistant HCC cells by using microarray. We analyzed oxaliplatin sensitive MHCC97H and oxaliplatin

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resistant MHCC97H-OXA and identified 120 lncRNAs and 431 mRNAs abnormally expressed in

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MHCC97H-OXA (fold Change > 2.0, P < 0.05). The microarray we used was human lncRNA microarray version 2.0, whereas the microarray which was used in the above reports was human

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lncRNA microarray version 1.0. Compared with version 1.0, version 2.0 contains more

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comprehensive and reliable array content, more extensive and updated coverage available,

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efficient and robust labeling system and systematic lncRNA classification. According to the absolute expression profile in three pairs of sample, the numbers of significantly differentially

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expressed lncRNAs and mRNAs were 624 and 1050 separately. After statistical analysis (the threshold for deregulated genes was p < 0.05), this number decreased to 120 and 431. These differentially expressed lncRNAs and mRNA might have important functions in HCC chemo-resistance. In

our

study,

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demonstrated

that

ENST00000438347,

ENST00000518376,

ENST00000502804, and NR_073453 was up-regulated in oxaliplatin-resistant HCC cell, oxaliplatin-resistant patients as well as in 57 pairs of HCC samples compared with adjacent normal tissues. Moreover, high expression of ENST00000518376 and ENST00000438347 was associated with HCC poor prognosis. Located on chromosome 10: 30,403,197-30,403,776 reverse 8

ACCEPTED MANUSCRIPT strand, ENST00000438347 is a non-coding RNA with a length of 580 bp. Though many lncRNAs were significantly correlated with multiple protein-coding genes, there is no clear reports on the

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functions of ENST00000438347. These findings would be more useful to further explore the

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functions of these lncRNA in HCC diagnosis and treatment. LncRNAs-linc-VLDLR has been found involved in HCC chemotherapy. Exposure of HCC cells to diverse anticancer agents such as sorafenib, camptothecin, and doxorubicin increased linc-VLDLR expression [30]. Hence, it will

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be of great importance to further explore the role of ENST00000438347 in HCC and potentially in

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other tumors.

Proteoglycans, key effectors of cell surface and pericellular microenvironments, perform

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multiple functions in cancer by virtue of their polyhedric nature and their ability to interact with

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both ligands and receptors that regulate neoplastic growth and neovascularization [31]. Some

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literatures have reported the association of proteoglycans and chemotherapy resistance in colorectal cancer. For example, Syndecan-1, a member of proteoglycans, has been found involved

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in chemotherapy resistance. Patients with high preoperative serum Sdc-1 levels were less responsive to 5-Fluorouracil, Oxaliplatin, Irintecan, Cisplatin or Paclitaxel chemotherapy. Moreover, the disease-free survival of patients with high preoperative Sdc-1 serum levels was significantly poor [32]. In ovarian cancer, hyaluronic acid based nanoparticle system for paclitaxel delivery targeting the CD44 family of cell surface proteoglycans can strongly overcome drug resistance [33]. Our microarray data revealed that the genes related to proteoglycans in cancer were highly up-regulated in oxaliplatin-resistant hepatocellular carcinoma cells, which indicated that proteoglycans might involve in HCC oxaliplatin-resistance.

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ACCEPTED MANUSCRIPT In conclusion, we described the expression profiles of lncRNAs and mRNAs in oxaliplatin resistant HCC cells by microarray and identified 214 lncRNAs and 431 mRNAs abnormally

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expressed (fold Change > 2.0, p < 0.05). More, we demonstrated for the first time that

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ENST00000518376, ENST00000438347, NR_073453 and ENST00000502804 was up-regulated in MHCC97H-OXA cells and in tissues collected from oxaliplatin-resistant HCC patients. The survival analysis showed that high expression of ENST00000438347 and ENST00000518376 was

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associated with poor prognosis. Altogether, our results reveal a new penetrating layer of lncRNAs

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of biological significance in the chemotherapy of HCC, thereby pointing intriguing directions for

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further research.

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ACCEPTED MANUSCRIPT 4. Materials and methods 4.1 Cell lines

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MHCC97H, a high-metastatic human HCC, was established at our institution

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[28]. Oxaliplatin-resistant MHCC97H (MHCC97H-OXA) cell line was constructed as previously described [29]. Briefly, MHCC97H cells were plated in 6cm cell culture dish (5×105 cells per dish) and cultured with DMEM containing 10% FBS and 2 μmol/l oxaliplatin. Change the medium after

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48 hours and drug treatment was terminated. Cells were allowed to recover, and when the

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surviving populations reached 80% confluence, cells were passaged and exposed to 2 μmol/l oxaliplatin again for 48 h. As cells became resistant to oxaliplatin, the above procedure was

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repeated using 5 μmol/l concentration of oxaliplatin. Until 25 μmol/l oxaliplatin were used, the

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cells were becoming stable resistant to oxaliplatin and re-named MHCC97H-OXA cells.

4.2 RNA extraction

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Total RNA was extracted from the cell sample using TRIzol reagent (Sigma, USA) according to the manufacture’s protocol. The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1000 instrument. The OD260/OD280 ratios were inspected as an indication of potential impurity.

4.3 Labeling and Hybridization Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, LncRNAs/mRNAs were purified from total RNA after removal of rRNA (Arraystar rRNA removal kit, Cat#: AS-MB-001, Arraystar). Then, each sample was 11

ACCEPTED MANUSCRIPT amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Cat#: AS-LE-007,

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Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Cat#: 74104, Qiagen). The

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concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally

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25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization

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solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The

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Scanner (part number G2505C).

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hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray

4.4 Data Analysis

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Raw data collection

Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and raw data extraction.

4.5 Expression Profiling Data Quantile normalization of raw data and subsequent data processing were performed using the R limma software package. After quantile normalization of the raw data, low intensity filtering was performed, and the LncRNAs/Coding Genes that at least 2 out of 6 samples have intensity above 32 were retained for further analyses. All the LncRNAs were annotated with the 12

ACCEPTED MANUSCRIPT corresponding target genes and potential regulatory mechanisms. The gene- and transcript-level expression data of the target genes were also provided for unraveling the expressional

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relationships between LncRNAs and their potential target genes.

4.6 Differentially Expressed Data

When comparing two groups of profile differences (such as disease versus control), the “fold

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change” (i.e. the ratio of the group averages) between the groups for each LncRNA or coding gene

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is computed. The statistical significance of the difference may be conveniently estimated by t-test. LncRNAs or coding genes having fold changes 2 and p-values  0.05 are selected as the

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significantly differentially expressed. One can filter the analysis outputs and rank the differentially

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expressed LncRNAs or coding genes according to fold change, p-value and etc using Microsoft

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Excel’s Data/Sort & Filter functionalities (Table 1 and Table 2).

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4.7 Integrative Analysis for LncRNAs and Coding Genes LncPathTM arrays profile LncRNAs and their target genes simultaneously in a pathway-focused or disease-specific manner. By quantifying LncRNAs (at transcript level) and their potential target genes (at both gene and transcript levels) in parallel, LncPathTM Pathway Focus LncRNA Microarrays provide comprehensive insights into the expressional relationship between LncRNAs and their target genes, which will be helpful for establishing rapid connections between the LncRNA regulatory mechanisms and their biological functions (Table 3).

4.8 Quantitative real-time polymerase chain reaction (qRT-PCR) validation 13

ACCEPTED MANUSCRIPT To explore whether the identified lncRNAs were involved in chemo-resistance and clinical outcomes of HCC patients, the expression of lncRNAs ENST00000438347, ENST00000518376,

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ENST00000502804, NR_073453 were examined in 57 pairs of HCC tissues obtained from

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patients who underwent curative liver resection and in 18 HCC tumor tissues obtained from patients who received oxaliplatin-based chemotherapy by using liver biopsy at liver cancer institute , Zhongshan Hospital, Fudan University from January, 2006 to December, 2007. The

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study was performed in accordance with the ethical standards of the Declaration of Helsinki and

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was approved by the Ethics Committee of Zhongshan Hospital, Fudan University. Informed consent was obtained from all patients participating in the present study.

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Total RNA was extracted from HCC cell lines or tumor tissues using Trizol Reagent

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(Invitrogen, Carlsbad, CA). Total RNA was reverse-transcribed using ImProm II Reverse

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Transcriptase (Promega) according to the manufacturer’s protocol. Real-time PCR was done with SYBR Premix Ex Taq (TaKaRa) on MX3000p instrument according to the manufacturer’s

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protocol. Specific primers of each gene are listed in Table S1. The relative fold change was calculated using the 22DDCt method normalized to GAPDH. The differential expression of lncRNAs in HCC samples and adjacent non-tumor liver tissues were determined.

4.9 Statistical analysis Quantitative data between groups were compared using the t test. Categorical data were analyzed by the chi-square test or Fisher exact test as appropriate. Survival probability was determined by Kaplan-Meier method, and the differences were assessed by the log-rank test. Univariate and multivariate analyses were performed using the Cox proportional hazards 14

ACCEPTED MANUSCRIPT regression model. Statistical significance was set at P<0.05 (two sided). All analyses were

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performed using the SPSS 13.0 for Windows (SPSS, Inc., Chicago, IL).

Conflict of interest

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The authors declare no conflicts of interest in association with this manuscript.

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Acknowledgments

This work was supported by two grants of the Natural Science Foundation of China (No.

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81201901 and No.81272565).

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Figure and figure legend

Figure 1. Identification of differentially expressed lncRNAs and mRNAs in oxaliplatin resistant

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HCC cells.

(A) Flowchart of the experiment. Firstly, RNA were extracted and initially assessed by ND1000 and agarose gel. Secondly, RNA were labelled with fluorescent and hybridized onto LncPath Arrays. The data were than collected with GenePix 4000B scanner. And lastly, data were analyzed and validated. (B) Heat map of altered genes (>2 fold) shared among the six profiles of MHCC97H-1A, MHCC97H-1B, MHCC97H-1C, MHCC97H-OXA-1, MHCC97H-OXA-2, and MHCC97H-OXA-3. Log2-based scale. Three replicates of MHCC97H and MHCC97H-OXA were analyzed. (C) Number of altered (>2 fold) mRNAs (up) and lncRNAs (down) in oxaliplatin resistant HCC cells. 15

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Figure 2. qRT-PCR verification of selected lncRNAs.

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LncRNAs expressions were validated with qRT-PCR. Expression in MHCC97H-OXA group were

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normalized to MHCC97H group. At least three biological replicates were performed and each experiment was performed with triplicate or quadruplicate PCR reactions. Data are expressed

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using the comparative cycle threshold method.

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Figure 3. Gene Ontology analysis of differentially expressed genes. (A) Gene ontology enrichment analysis of up-regulated genes. (B) Gene ontology enrichment

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analysis of down-regulated genes.

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Figure 4. Pathway enrichment of differentially changed genes. (A) Signaling pathway enrichment of analysis of up-regulated genes. (B) Signaling pathway

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enrichment analysis of down-regulated genes.

Figure 5. qRT-PCR analysis of lncRNAs in HCC tissues with oxaliplatin treatment.. LncRNAs expressions in oxaliplatin-resistant or oxaliplatin-sensitive HCC tissues were analyzed with qRT-PCR. (B) LncRNAs expressions in HCC tissues were analyzed with qRT-PCR. Cancer (Ca) group were indicated in dotted bars while para-cancer normal (P) group were indicated in blank bars. At least three biological replicates were performed and each experiment was performed with triplicate or quadruplicate PCR reactions. Data are expressed using the comparative cycle threshold method. 16

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Figure 6. K-M analysis of lncRNAs. Survival curve of ENST00000438347 low group (blue line)

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and ENST00000438347 high group (red line).

References

[1] A. Jemal, E. Ward, Y. Hao, M. Thun, Trends in the leading causes of death in the United States, 1970-2002, JAMA 294 (2005) 1255-1259.

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[2] B. Njei, Y. Rotman, I. Ditah, J.K. Lim, Emerging trends in hepatocellular carcinoma incidence and mortality, Hepatology 61 (2015) 191-199.

[3] S.F. Altekruse, K.A. McGlynn, M.E. Reichman, Hepatocellular carcinoma incidence, mortality, and

MA

survival trends in the United States from 1975 to 2005, J Clin Oncol 27 (2009) 1485-1491. [4] M. Kudo, Early detection and curative treatment of early-stage hepatocellular carcinoma, Clin Gastroenterol Hepatol 3 (2005) S144-148.

[5] S. Kiyonari, M. Iimori, K. Matsuoka, S. Watanabe, T. Morikawa-Ichinose, D. Miura, S. Niimi, H. Saeki,

D

E. Tokunaga, E. Oki, M. Morita,

K. Kadomatsu,

Y.

Maehara,

H.

Kitao,

The

TE

1,2-Diaminocyclohexane Carrier Ligand in Oxaliplatin Induces p53-Dependent Transcriptional Repression of Factors Involved in Thymidylate Biosynthesis, Mol Cancer Ther 14 (2015) 2332-2342.

CE P

[6] Q. Hou, H. Zhao, W. Gong, Z. Zhu, Y. Han, D. Chen, H. Guo, Phosphorylation status of ASPP2 modulates p53 apoptotic function in oxaliplatin-induced apoptosis of colorectal cancer HCT116 cells, Zhonghua Zhong Liu Za Zhi 36 (2014) 418-423. [7] E. Martinez-Balibrea, A. Martinez-Cardus, A. Gines, V. Ruiz de Porras, C. Moutinho, L. Layos, J.L.

AC

Manzano, C. Buges, S. Bystrup, M. Esteller, A. Abad, Tumor-Related Molecular Mechanisms of Oxaliplatin Resistance, Mol Cancer Ther 14 (2015) 1767-1776.

[8] M. Furuno, K.C. Pang, N. Ninomiya, S. Fukuda, M.C. Frith, C. Bult, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, J.S. Mattick, H. Suzuki, Clusters of internally primed transcripts reveal novel long noncoding RNAs, PLoS Genet 2 (2006) e37. [9] P.G. Gallagher, Long noncoding RNAs in erythropoiesis, Blood 123 (2014) 465-466. [10] J.R. Alvarez-Dominguez, W. Hu, A.A. Gromatzky, H.F. Lodish, Long noncoding RNAs during normal and malignant hematopoiesis, Int J Hematol 99 (2014) 531-541. [11] M. Ballarino, V. Cazzella, D. D'Andrea, L. Grassi, L. Bisceglie, A. Cipriano, T. Santini, C. Pinnaro, M. Morlando, A. Tramontano, I. Bozzoni, Novel long noncoding RNAs (lncRNAs) in myogenesis: a miR-31 overlapping lncRNA transcript controls myoblast differentiation, Mol Cell Biol 35 (2015) 728-736. [12] M.B. Clark, J.S. Mattick, Long noncoding RNAs in cell biology, Semin Cell Dev Biol 22 (2011) 366-376. [13] M. Sun, S.S. Gadad, D.S. Kim, W.L. Kraus, Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells, Mol Cell 59 (2015) 698-711. 17

ACCEPTED MANUSCRIPT [14] X. Luo, J. Zhu, Z. Cheng, F. Zhang, G. Zhang, J. Yuan, C. Jin, Lack of association of a genetic variant in the long intergenic noncoding RNA (linc01080) with Alzheimer's disease and amnestic mild cognitive impairment in Han Chinese, Int J Neurosci 125 (2015) 419-423. [15] F.Q. Nie, Q. Zhu, T.P. Xu, Y.F. Zou, M. Xie, M. Sun, R. Xia, K.H. Lu, Long non-coding RNA MVIH

T

indicates a poor prognosis for non-small cell lung cancer and promotes cell proliferation and invasion, Tumour Biol 35 (2014) 7587-7594.

IP

[16] E. Zhang, W. Li, D. Yin, W. De, S. Sun, L. Han, c-Myc-regulated long non-coding RNA H19 indicates a poor prognosis and affects cell proliferation in non-small-cell lung cancer, Tumour Biol (2015).

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[17] F. Yang, L. Zhang, X.S. Huo, J.H. Yuan, D. Xu, S.X. Yuan, N. Zhu, W.P. Zhou, G.S. Yang, Y.Z. Wang, J.L. Shang, C.F. Gao, F.R. Zhang, F. Wang, S.H. Sun, Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans, Hepatology 54 (2011) 1679-1689.

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[18] X. Gui, H. Li, T. Li, H. Pu, D. Lu, Long Noncoding RNA CUDR Regulates HULC and beta-Catenin to Govern Human Liver Stem Cell Malignant Differentiation, Mol Ther (2015). [19] T. Mondal, S. Subhash, R. Vaid, S. Enroth, S. Uday, B. Reinius, S. Mitra, A. Mohammed, A.R. James,

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E. Hoberg, A. Moustakas, U. Gyllensten, S.J. Jones, C.M. Gustafsson, A.H. Sims, F. Westerlund, E. Gorab, C. Kanduri, MEG3 long noncoding RNA regulates the TGF-beta pathway genes through formation of RNA-DNA triplex structures, Nat Commun 6 (2015) 7743. [20] L.H. Schmidt, D. Gorlich, T. Spieker, C. Rohde, M. Schuler, M. Mohr, J. Humberg, T. Sauer, N.H.

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Thoenissen, A. Huge, R. Voss, A. Marra, A. Faldum, C. Muller-Tidow, W.E. Berdel, R. Wiewrodt,

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Prognostic impact of Bcl-2 depends on tumor histology and expression of MALAT-1 lncRNA in non-small-cell lung cancer, J Thorac Oncol 9 (2014) 1294-1304. [21] M.J. Milligan, L. Lipovich, Pseudogene-derived lncRNAs: emerging regulators of gene expression,

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Front Genet 5 (2014) 476.

[22] M. Martinez-Fernandez, A. Feber, M. Duenas, C. Segovia, C. Rubio, M. Fernandez, F. Villacampa, J. Duarte, F.F. Lopez-Calderon, M.J. Gomez-Rodriguez, D. Castellano, J.L. Rodriguez-Peralto, F. de la Rosa, S. Beck, J.M. Paramio, Analysis of the Polycomb-related lncRNAs HOTAIR and ANRIL in

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bladder cancer, Clin Epigenetics 7 (2015) 109. [23] M.R. Pickard, M. Mourtada-Maarabouni, G.T. Williams, Long non-coding RNA GAS5 regulates apoptosis in prostate cancer cell lines, Biochim Biophys Acta 1832 (2013) 1613-1623.

[24] L. Zhang, F. Yang, J.H. Yuan, S.X. Yuan, W.P. Zhou, X.S. Huo, D. Xu, H.S. Bi, F. Wang, S.H. Sun, Epigenetic activation of the MiR-200 family contributes to H19-mediated metastasis suppression in hepatocellular carcinoma, Carcinogenesis 34 (2013) 577-586. [25] Y. Shi, Q. Song, S. Yu, D. Hu, X. Zhuang, Microvascular invasion in hepatocellular carcinoma overexpression promotes cell proliferation and inhibits cell apoptosis of hepatocellular carcinoma via inhibiting miR-199a expression, Onco Targets Ther 8 (2015) 2303-2310. [26] J. Li, X. Wang, J. Tang, R. Jiang, W. Zhang, J. Ji, B. Sun, HULC and Linc00152 Act as Novel Biomarkers in Predicting Diagnosis of Hepatocellular Carcinoma, Cell Physiol Biochem 37 (2015) 687-696. [27] M. Zamani, M. Sadeghizadeh, M. Behmanesh, F. Najafi, Dendrosomal curcumin increases expression of the long non-coding RNA gene MEG3 via up-regulation of epi-miRs in hepatocellular cancer, Phytomedicine 22 (2015) 961-967. [28] Y. Li, B. Tian, J. Yang, L. Zhao, X. Wu, S.L. Ye, Y.K. Liu, Z.Y. Tang, Stepwise metastatic human hepatocellular carcinoma cell model system with multiple metastatic potentials established 18

ACCEPTED MANUSCRIPT through consecutive in vivo selection and studies on metastatic characteristics, J Cancer Res Clin Oncol 130 (2004) 460-468. [29] Y. Bu, Q.A. Jia, Z.G. Ren, J.B. Zhang, X.M. Jiang, L. Liang, T.C. Xue, Q.B. Zhang, Y.H. Wang, L. Zhang, X.Y. Xie, Z.Y. Tang, Maintenance of stemness in oxaliplatin-resistant hepatocellular carcinoma

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is associated with increased autocrine of IGF1, PLoS One 9 (2014) e89686. [30] Takahashi K, Yan IK, Wood J, Haga H, Patel T, Involvement of extracellular vesicle long noncoding

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RNA (linc-VLDLR) in tumor cell responses to chemotherapy. Mol Cancer Res 12 (2014):1377-87.

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[31] Iozzo R V, Sanderson R D. Proteoglycans in cancer biology, tumour microenvironment and angiogenesis[J]. Journal of Cellular & Molecular Medicine, (2011): 15(5):1013-31. [32] Wang X, Zuo D, Chen Y, Li W, Liu R, He Y, Ren L, Zhou L, Deng T, Wang X, Ying G, Ba Y, Shed cancer.Br J Cancer 111(2014):1965-76.

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Syndecan-1 is involved in chemotherapy resistance via the EGFR pathway in colorectal [33] Wang L, Jia E. Ovarian cancer targeted hyaluronic acid-based nanoparticle system for paclitaxel

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delivery to overcome drug resistance. Drug Deliv. (2016):23(5):1810-7.

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Figure 1

20

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IP

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ACCEPTED MANUSCRIPT

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Figure 2

21

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IP

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ACCEPTED MANUSCRIPT

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Figure 3

22

SC R

IP

T

ACCEPTED MANUSCRIPT

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D

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Figure 4

23

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IP

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ACCEPTED MANUSCRIPT

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Figure 5

24

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IP

T

ACCEPTED MANUSCRIPT

AC

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TE

D

MA

Figure 6

25

ACCEPTED MANUSCRIPT

FC (abs)

ASPWP0008509

0.017569074

10.0932102

up

noncoding

NR_003605

ASPWP0005576

0.03359029

2.0582219

up

noncoding

ENST00000584934

ASPWP0001803

0.012890215

2.462982

up

noncoding

NR_000029

ASPWP0166920

0.002145012

3.2721609

up

noncoding

ASPWP0187669

0.0010484

2.7976341

up

noncoding

ASPWP0000808

0.012357544

2.1797827

up

noncoding

ENST00000461972

ASPWP0139392

0.049543751

2.6126889

up

noncoding

ASPWP0173416

0.000304973

2.790198

up

noncoding

NR_026761

ASPWP0008694

0.002103469

2.0918571

up

noncoding

NR_036659

ASPWP0180952

0.016412526

2.5154731

up

noncoding

ENST00000422137

ASPWP0003933

0.003003268

5.1775613

up

SC R

ENST00000444980

ENST00000416146

ASPWP0155199

0.006974168

2.274916

up

noncoding

ENST00000502774

ASPWP0006064

0.001218475

4.884602

up

noncoding

uc003xcr.3

ASPWP0103337

0.028446067

2.2921643

NU

noncoding

up

noncoding

ENST00000551588

ASPWP0004263

0.039867169

6.8638643

up

noncoding

ENST00000453523

ASPWP0178525

3.40347E-05

7.6291786

up

noncoding

ENST00000435092

ASPWP0152351

0.001137799

3.6277505

up

noncoding

ENST00000480069

ASPWP0004475

0.044045078

2.3405639

up

noncoding

ENST00000442212

ASPWP0003502

0.036929553

2.5761681

up

noncoding

ENST00000413077

ASPWP0205427

0.017647702

3.2473011

up

noncoding

ENST00000313760

ASPWP0004953

0.015386796

2.0292348

up

noncoding

ENST00000515464

ASPWP0008487

0.002960737

3.1420465

up

noncoding

NR_002578

ASPWP0180632

0.046594874

2.5608525

up

noncoding

ENST00000443688

ASPWP0002154

0.021634735

3.3927149

up

noncoding

ENST00000433407

ASPWP0125317

0.008825541

4.8644417

up

noncoding

ENST00000467018

ASPWP0000710

0.005120724

2.44949

up

noncoding

ENST00000446355

TE

CE P

AC

type

Seq name

ENST00000458247 ENST00000422205

IP

Regulation

T

P-value

MA

Probe ID

D

Table 1. Differentially Expressed lncRNAs.

ASPWP0186648

0.009114881

2.213542

up

noncoding

ENST00000392269

ASPWP0003636

0.026512852

2.1789894

up

noncoding

ENST00000576784

ASPWP0003443

7.05019E-05

7.0095649

up

noncoding

uc002jdy.1

ASPWP0103441

0.010294521

2.3341082

up

noncoding

ENST00000554535

ASPWP0002144

0.002076881

2.2756033

up

noncoding

ENST00000442889

ASPWP0006078

0.020561317

2.9593608

up

noncoding

ENST00000519475

ASPWP0002959

0.043574129

4.2365618

up

noncoding

ENST00000475062

ASPWP0006022

0.036639768

2.0617421

up

noncoding

ENST00000448365

ASPWP0001821

0.033354298

2.6326662

up

noncoding

NR_024530

ASPWP0110676

0.000184538

19.8306381

up

noncoding

ENST00000561649

ASPWP0005872

0.007344462

4.3098611

up

noncoding

uc003vhn.1

ASPWP0008491

0.029632626

2.3131171

up

noncoding

NR_003038

ASPWP0002108

0.032599782

2.2053286

up

noncoding

ENST00000550947

ASPWP0007492

0.027966984

2.6149074

up

noncoding

ENST00000504145

ASPWP0008510

0.012106547

3.9362995

up

noncoding

NR_003606

ASPWP0151921

0.027050431

5.8332645

up

noncoding

ENST00000475925

26

0.00612764

4.41603

up

noncoding

ENST00000460497

ASPWP0186701

0.04425961

3.0006467

up

noncoding

NR_027401

ASPWP0132161

0.045039241

9.2589832

up

noncoding

ENST00000448842

ASPWP0110910

0.019819704

2.1014726

up

noncoding

TCONS_00014652

ASPWP0006737

0.012456285

2.1403314

up

noncoding

ENST00000557989

ASPWP0003037

0.001851437

2.0227017

up

noncoding

ASPWP0005875

0.024813219

2.6136766

up

noncoding

ASPWP0007268

0.045511595

6.5527091

up

noncoding

NR_015377

ASPWP0166376

0.022525342

2.1240977

up

noncoding

ENST00000422817

ASPWP0001940

0.001377405

2.7680029

up

noncoding

ENST00000533528

ASPWP0002267

0.043505276

3.7856338

up

noncoding

ENST00000538113

ASPWP0119169

0.000878695

2.1641678

up

noncoding

ENST00000461109

ASPWP0007515

0.044517061

2.3094919

up

noncoding

ENST00000540066

ASPWP0007521

0.046405804

2.6776789

up

noncoding

NR_003581

ASPWP0003327

0.016814171

3.5930809

up

noncoding

ENST00000425698

ASPWP0004349

0.026418625

2.2608968

up

noncoding

ENST00000432727

ASPWP0196485

0.000521336

3.1499245

up

noncoding

TCONS_00026294

ASPWP0141834

0.027267601

5.633394

up

noncoding

ENST00000436709

ASPWP0132347

0.011408895

5.8889592

up

noncoding

ENST00000433233

ASPWP0008536

0.001235744

2.0684475

down

noncoding

NR_045121

ASPWP0093664

0.002200779

2.9947479

down

noncoding

TCONS_00028472

ASPWP0000096

0.037823947

2.1432439

down

noncoding

ENST00000318333

ASPWP0003993

0.008105178

2.1180716

down

noncoding

ENST00000416673

ASPWP0000564

0.042157419

2.147752

down

noncoding

ENST00000423223

ASPWP0002864

0.006330737

3.1304479

down

noncoding

ENST00000563660

ASPWP0097179

0.023895432

2.480308

down

noncoding

ENST00000552169

ASPWP0161660

0.00299461

2.7818114

down

noncoding

ENST00000404856

ASPWP0193622

0.041103156

2.0703649

down

noncoding

ENST00000542064

NR_033928 ENST00000421965

IP

NU

MA

D

TE

CE P

AC

T

ASPWP0173596

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ACCEPTED MANUSCRIPT

ASPWP0132162

0.002036945

2.157421

down

noncoding

ENST00000415349

ASPWP0006743

0.02343792

2.2504601

down

noncoding

ENST00000427492

ASPWP0002997

0.040688248

3.562257

down

noncoding

AK091357

ASPWP0127559

0.00383112

3.4279063

down

noncoding

ENST00000436229

ASPWP0183247

0.005212404

2.2119967

down

noncoding

ENST00000446295

ASPWP0003834

0.020434649

3.5382318

down

noncoding

ENST00000320232

ASPWP0002479

0.031143954

3.150714

down

noncoding

NR_002612

ASPWP0113233

0.005623835

2.2369848

down

noncoding

ENST00000565374

ASPWP0004368

0.005571721

2.2644136

down

noncoding

ENST00000441270

ASPWP0171081

0.009543864

3.4299535

down

noncoding

ENST00000407916

ASPWP0003067

0.003867476

5.2465002

down

noncoding

TCONS_00014883

ASPWP0003616

0.043483197

6.4972518

down

noncoding

NR_046273

ASPWP0007146

0.034180362

2.3449832

down

noncoding

TCONS_00027767

ASPWP0007914

0.023321074

2.0170271

down

noncoding

uc010czc.3

ASPWP0120131

0.001138742

5.2185751

down

noncoding

ENST00000492507

ASPWP0003687

0.002548532

2.3586131

down

noncoding

ENST00000579595

27

0.01210042

2.3342498

down

noncoding

ENST00000509173

ASPWP0002430

0.02627259

3.8009224

down

noncoding

uc021rgk.1

ASPWP0106538

0.015748942

2.7598516

down

noncoding

ENST00000558620

ASPWP0094390

0.005806045

2.2677675

down

noncoding

TCONS_00028253

ASPWP0001137

0.015748666

3.1881735

down

noncoding

ENST00000504656

ASPWP0134952

0.002674196

2.8863754

down

noncoding

ASPWP0189974

0.009900995

3.0352849

down

noncoding

ASPWP0189117

0.00985981

3.6687397

down

noncoding

NR_073453

ASPWP0227307

0.008966946

2.4518237

down

noncoding

TCONS_00004466

ASPWP0118218

0.005818703

2.0002463

down

noncoding

ENST00000491601

ASPWP0003640

0.027558213

2.64026

down

noncoding

uc021ufh.1

ASPWP0149589

0.004124621

2.2392276

down

noncoding

ENST00000463581

ASPWP0008593

0.017922465

3.2765198

down

noncoding

AK055628

ASPWP0164411

0.015857788

2.2652659

down

noncoding

ENST00000404566

ASPWP0002768

0.003268419

3.822689

down

noncoding

uc001ygz.2

ASPWP0001872

0.048315516

4.3370808

down

noncoding

NR_046375

ASPWP0174269

0.003587598

2.9331345

down

noncoding

ENST00000435260

ASPWP0106782

0.049497845

2.0080898

down

noncoding

ENST00000503999

ASPWP0007611

0.04249903

5.3252278

down

noncoding

ENST00000532714

ASPWP0174926

0.010874977

2.8464166

down

noncoding

ENST00000492365

ASPWP0115060

0.00355071

2.1397097

down

noncoding

ENST00000571486

ASPWP0008557

0.000509232

4.8614195

down

noncoding

NR_004436

ASPWP0100376

0.013396839

2.2407679

down

noncoding

ENST00000455730

ASPWP0002640

0.015829187

4.651898

down

noncoding

ENST00000557078

ASPWP0004214

0.029942709

2.3455125

down

noncoding

ENST00000418335

ASPWP0007001

0.000858181

2.5606116

down

noncoding

ENST00000529841

ASPWP0003301

0.000266089

6.769575

down

noncoding

NR_024399

ASPWP0185143

0.005633713

2.4837777

down

noncoding

ENST00000438347

ENST00000272567 ENST00000562082

IP

NU

MA

D

TE

CE P

AC

T

ASPWP0005303

SC R

ACCEPTED MANUSCRIPT

ASPWP0002413

0.005376907

2.6038434

down

noncoding

ENST00000535200

ASPWP0094316

0.001936114

3.3874115

down

noncoding

NR_028415

ASPWP0003641

0.000378985

3.1626266

down

noncoding

NR_015454

ASPWP0007342

0.047042746

2.133456

down

noncoding

ENST00000433871

ASPWP0196130

0.024699311

2.0496468

down

noncoding

ENST00000325243

ASPWP0151380

0.031304011

2.6202896

down

noncoding

ENST00000484463

28

ACCEPTED MANUSCRIPT

FC (abs)

ASPWP0006923

0.011653467

2.2003486

down

coding_gene_probe

NM_015399

ASPWP0001429

0.011394014

3.671729

down

coding_gene_probe

NM_004236

ASPWP0001307

0.038229139

2.0253052

down

coding_gene_probe

NM_030667

ASPWP0010871

0.01550152

3.188714

down

coding_transcript_probe

NM_001627

ASPWP0000880

0.016321354

4.4988516

down

coding_gene_probe

NM_003071

ASPWP0003801

0.009888781

3.1031815

down

coding_gene_probe

NM_001048201

ASPWP0009361

0.023905572

2.1740468

down

coding_transcript_probe

NM_001218

ASPWP0000463

0.019659646

2.1702962

down

coding_gene_probe

NM_006024

ASPWP0002367

0.023186503

3.2153229

down

coding_gene_probe

NM_181861

ASPWP0009538

0.005249306

2.7069585

down

NM_004557

ASPWP0004365

0.003737303

30.7393222

down

coding_gene_probe

NM_000782

ASPWP0011196

0.00142517

2.2532327

down

coding_transcript_probe

NM_003941

ASPWP0010045

0.029781986

2.4139741

NU

coding_transcript_probe

down

coding_transcript_probe

NM_000059

ASPWP0001547

0.017366536

2.5481601

down

coding_gene_probe

NM_000442

ASPWP0001368

0.000740486

4.3116063

down

coding_gene_probe

NM_002178

ASPWP0010505

0.00775254

2.0950746

down

coding_transcript_probe

NM_013398

ASPWP0009744

0.029001803

2.0513216

down

coding_transcript_probe

NM_021111

ASPWP0010039

0.023303201

2.0013968

down

coding_transcript_probe

NM_017817

ASPWP0004818

0.030740546

2.6486906

down

coding_gene_probe

NM_173084

ASPWP0010996

0.007285942

3.4931955

down

coding_transcript_probe

NM_001962

ASPWP0010269

0.008172063

3.1558973

down

coding_transcript_probe

NM_000572

ASPWP0006561

0.009962002

8.3236029

down

coding_gene_probe

NM_001171092

ASPWP0001758

0.011303089

2.275589

down

coding_gene_probe

NM_016370

ASPWP0006830

0.002267419

3.1541203

down

coding_gene_probe

NM_002528

ASPWP0011540

0.031608948

3.2172729

down

coding_transcript_probe

NM_002426

TE

CE P

AC

Regulation

type

SC R

IP

T

P-value

MA

probeID

D

Table 2. Differentially Expressed mRNAs. seqname

ASPWP0005478

0.00854915

2.1597946

down

coding_gene_probe

NM_002084

ASPWP0003073

0.010835489

2.248732

down

coding_gene_probe

NM_005802

ASPWP0003416

0.034506899

2.0445984

down

coding_gene_probe

NM_030753

ASPWP0010968

0.012518357

2.1507331

down

coding_transcript_probe

NM_199320

ASPWP0005431

0.0015098

3.5422733

down

coding_gene_probe

NM_000906

ASPWP0000362

0.007373958

3.1883865

down

coding_gene_probe

NM_002759

ASPWP0010671

0.01074578

2.6680741

down

coding_transcript_probe

NM_005225

ASPWP0002295

0.024142532

3.1200971

down

coding_gene_probe

NM_005556

ASPWP0006661

9.08527E-05

2.950597

down

coding_gene_probe

NM_000462

ASPWP0001124

0.001448226

2.4896214

down

coding_gene_probe

NM_003472

ASPWP0012608

0.009457865

2.2229404

down

coding_transcript_probe

NM_004330

ASPWP0010371

0.009596359

2.6389482

down

coding_transcript_probe

NM_005406

ASPWP0006486

0.0001938

3.8254067

down

coding_gene_probe

NM_000425

ASPWP0002759

0.034539851

2.0137441

down

coding_gene_probe

NM_005113

ASPWP0011325

0.001808989

2.0745563

down

coding_transcript_probe

NM_006378

ASPWP0000298

0.044751801

2.7601115

down

coding_gene_probe

NM_006705

29

ACCEPTED MANUSCRIPT 0.007873799

2.2040414

down

coding_gene_probe

NM_014002

ASPWP0000827

0.004053569

2.9449793

down

coding_gene_probe

NM_078468

ASPWP0001201

0.013712374

2.3861962

down

coding_gene_probe

NM_020771

ASPWP0000205

0.000392754

2.1477757

down

coding_gene_probe

NM_016578

ASPWP0006764

0.017501162

4.0604449

down

coding_gene_probe

NM_000314

ASPWP0002568

0.03234835

2.1503044

down

coding_gene_probe

NM_005537

ASPWP0011756

0.001212087

4.2264578

down

coding_transcript_probe

NM_173842

ASPWP0011080

0.040866511

2.2633283

down

coding_transcript_probe

NM_014452

ASPWP0001023

0.001298008

3.8539631

down

coding_gene_probe

NM_002412

ASPWP0008851

0.017603304

3.7727807

down

coding_transcript_probe

NM_014739

ASPWP0007183

0.000445637

2.3489877

down

coding_gene_probe

NM_002634

ASPWP0012032

0.046349932

2.0711095

down

coding_transcript_probe

NM_005732

ASPWP0006553

0.046735017

2.3158336

down

coding_gene_probe

NM_001198777

ASPWP0000443

0.015562142

4.8452663

down

coding_gene_probe

NM_000251

ASPWP0005893

0.002953083

2.1163944

down

coding_gene_probe

NM_001628

ASPWP0000311

0.036595425

2.0425595

down

coding_gene_probe

NM_001105562

ASPWP0004838

0.001750914

2.4374654

down

coding_gene_probe

NM_007034

ASPWP0004427

0.013576228

2.8784606

down

coding_gene_probe

NM_005985

ASPWP0000601

0.022415883

4.1916758

down

coding_gene_probe

NM_006306

ASPWP0004012

0.007719864

3.1324836

down

coding_gene_probe

NM_004688

ASPWP0010575

0.002606117

2.412779

down

coding_transcript_probe

NM_005235

ASPWP0012432

0.020833839

2.0875512

down

coding_transcript_probe

NM_004075

ASPWP0007142

0.018746937

2.077384

down

coding_gene_probe

NM_153253

ASPWP0010011

0.033130593

2.3502276

down

coding_transcript_probe

NM_014708

ASPWP0010151

0.007812521

2.1825875

down

coding_transcript_probe

NM_016530

ASPWP0008743

0.009335901

2.9119169

down

coding_transcript_probe

NM_000930

ASPWP0003030

1.3525E-05

2.7710947

down

coding_gene_probe

NM_002513

ASPWP0003783

0.013292565

2.0919851

down

coding_gene_probe

NM_001136201

IP

SC R

NU

MA

D

TE

CE P

AC

T

ASPWP0005986

ASPWP0011823

0.000236731

6.4326257

down

coding_transcript_probe

NM_006806

ASPWP0006404

0.016633524

2.0980048

down

coding_gene_probe

NM_013355

ASPWP0003629

0.04547025

2.8940382

down

coding_gene_probe

NM_001113491

ASPWP0010541

0.00529153

2.571834

down

coding_transcript_probe

NM_022173

ASPWP0004831

0.016004658

2.2970434

down

coding_gene_probe

NM_000460

ASPWP0006726

0.00727356

2.8086216

down

coding_gene_probe

NM_012242

ASPWP0002674

0.041371788

2.5528645

down

coding_gene_probe

NM_005348

ASPWP0000345

0.048420183

2.6723867

down

coding_gene_probe

NM_005657

ASPWP0009314

0.006797886

2.0501234

down

coding_transcript_probe

NM_001955

ASPWP0003620

0.000143333

2.4501173

down

coding_gene_probe

NM_212472

ASPWP0011347

0.026122351

2.4756063

down

coding_transcript_probe

NM_178448

ASPWP0001712

0.001282509

2.7167289

down

coding_gene_probe

NM_005234

ASPWP0000653

0.023886296

2.1245581

down

coding_gene_probe

NM_014708

ASPWP0000342

0.003636047

3.0414744

down

coding_gene_probe

NM_006826

ASPWP0004021

0.001125726

2.6839091

down

coding_gene_probe

NM_016836

ASPWP0003158

0.006174954

2.2891523

down

coding_gene_probe

NM_002434

30

ACCEPTED MANUSCRIPT 0.000117397

6.6659442

down

coding_transcript_probe

NM_003474

ASPWP0001151

0.04452149

3.2201634

down

coding_gene_probe

NM_004415

ASPWP0003868

0.001565595

2.0585705

down

coding_gene_probe

NM_138761

ASPWP0010517

0.027857475

2.1989578

down

coding_transcript_probe

NM_199294

ASPWP0009337

0.023856993

2.3200931

down

coding_transcript_probe

NM_001356

ASPWP0009893

0.025636676

3.3709824

down

coding_transcript_probe

NM_015313

ASPWP0011198

0.032833375

3.5743742

down

coding_transcript_probe

NM_016478

ASPWP0000390

0.000404498

2.9344985

down

coding_gene_probe

NM_004322

ASPWP0000481

0.00218154

3.4639948

down

coding_gene_probe

ENST00000413366

ASPWP0010227

0.043162555

2.3564709

down

coding_transcript_probe

NM_022162

ASPWP0007228

0.000293964

19.5559658

down

coding_gene_probe

NM_004364

ASPWP0010790

0.021455323

2.5862962

down

coding_transcript_probe

NM_004628

ASPWP0011057

0.014113158

3.3928299

down

coding_transcript_probe

NM_004060

ASPWP0010679

0.006034811

12.5172767

down

coding_transcript_probe

NM_000782

ASPWP0009996

0.003354532

2.1389168

down

coding_transcript_probe

NM_003211

ASPWP0003716

0.005561451

2.4007776

down

coding_gene_probe

NM_006785

ASPWP0006027

0.030459467

2.8567313

down

coding_gene_probe

NM_003461

ASPWP0002507

0.005761768

3.0607429

down

coding_gene_probe

NM_002312

ASPWP0012326

0.010967949

2.0420639

down

coding_transcript_probe

NM_005851

ASPWP0009644

0.020256322

3.0440221

down

coding_transcript_probe

NM_012239

ASPWP0001786

0.00933664

2.4436007

down

coding_gene_probe

NM_052850

ASPWP0003520

0.005266297

2.4548241

down

coding_gene_probe

ENST00000316843

ASPWP0001120

0.036282044

3.023817

down

coding_gene_probe

NM_018046

ASPWP0003433

0.000280535

3.3453586

down

coding_gene_probe

NM_005749

ASPWP0011053

0.021870207

2.5863257

down

coding_transcript_probe

NM_005754

ASPWP0005674

0.001089417

3.3230291

down

coding_gene_probe

NM_005346

ASPWP0011143

0.00275131

2.0412449

down

coding_transcript_probe

NM_000165

ASPWP0010786

0.004297864

2.0340145

down

coding_transcript_probe

NM_020165

IP

SC R

NU

MA

D

TE

CE P

AC

T

ASPWP0011461

ASPWP0001396

0.021260795

2.6957305

down

coding_gene_probe

NM_002687

ASPWP0005949

0.008358395

2.2903209

down

coding_gene_probe

NM_004760

ASPWP0011222

0.030391631

2.6261759

down

coding_transcript_probe

NM_014002

ASPWP0003076

0.0232111

2.4728234

down

coding_gene_probe

NM_013258

ASPWP0011502

0.000152288

4.9733157

down

coding_transcript_probe

NM_002412

ASPWP0010203

0.011426238

3.3674354

down

coding_transcript_probe

NM_002434

ASPWP0010176

0.000297423

3.2568186

down

coding_transcript_probe

NM_013258

ASPWP0000100

0.021925585

6.3927918

down

coding_gene_probe

ENST00000320476

ASPWP0006772

0.003320929

2.3400293

down

coding_gene_probe

NM_025235

ASPWP0006312

0.016046567

2.0103675

down

coding_gene_probe

NM_001134398

ASPWP0001251

0.002085732

5.8335179

down

coding_gene_probe

NM_012153

ASPWP0006032

0.010671013

2.2978479

down

coding_gene_probe

NM_003592

ASPWP0004250

5.96872E-05

11.6000922

down

coding_gene_probe

ENST00000304636

ASPWP0012462

0.006929371

2.0784841

down

coding_transcript_probe

NM_002128

ASPWP0012042

1.60464E-05

3.274553

down

coding_transcript_probe

NM_002084

ASPWP0001275

0.028067895

2.1109055

down

coding_gene_probe

NM_001620

31

ACCEPTED MANUSCRIPT 0.005916259

2.6427225

down

coding_transcript_probe

NM_001530

ASPWP0000391

0.003773189

2.6352329

down

coding_gene_probe

NM_005633

ASPWP0011035

0.025111249

2.7531995

down

coding_transcript_probe

NM_018046

ASPWP0005706

0.002728615

2.4455348

down

coding_gene_probe

NM_001253

ASPWP0011088

0.010724377

2.7449585

down

coding_transcript_probe

NM_005190

ASPWP0010097

0.038453496

2.4692171

down

coding_transcript_probe

NM_004094

ASPWP0011098

0.001435949

2.0607178

down

coding_transcript_probe

NM_004690

ASPWP0009288

0.001635008

3.1408245

down

coding_transcript_probe

NM_001136201

ASPWP0012104

0.048859493

2.4669805

down

coding_transcript_probe

ENST00000392142

ASPWP0009673

0.002634375

4.017782

down

coding_transcript_probe

NM_014750

ASPWP0006165

0.002719123

2.915358

down

coding_gene_probe

NM_020247

ASPWP0010305

0.033812094

2.7310465

down

coding_transcript_probe

NM_134268

ASPWP0005117

0.027915154

2.1175954

down

coding_gene_probe

NM_005245

ASPWP0010342

0.014566735

2.8299192

down

coding_transcript_probe

NM_001254

ASPWP0002055

0.042253665

2.4345084

down

coding_gene_probe

NM_004447

ASPWP0011034

0.001628485

3.3193633

down

coding_transcript_probe

NM_001992

ASPWP0012144

0.037529635

7.7872629

down

coding_transcript_probe

NM_001913

ASPWP0011941

0.00438362

2.002372

down

coding_transcript_probe

NM_172027

ASPWP0001413

0.00935985

2.473546

down

coding_gene_probe

NM_001530

ASPWP0006026

0.012888416

2.4278156

down

coding_gene_probe

NM_032982

ASPWP0011453

0.002293257

7.1960164

down

coding_transcript_probe

NM_003015

ASPWP0003394

0.01161455

2.3299322

down

coding_gene_probe

NM_003079

ASPWP0006159

0.034159408

3.4586659

down

coding_gene_probe

NM_006207

ASPWP0000951

0.025373012

2.7112723

down

coding_gene_probe

NM_016207

ASPWP0009434

0.036744889

2.5452821

down

coding_transcript_probe

NM_002165

ASPWP0008902

0.018974959

2.0604616

down

coding_transcript_probe

NM_022777

ASPWP0008952

0.002209501

4.427294

down

coding_transcript_probe

NM_000534

ASPWP0003613

0.000266673

4.0096556

down

coding_gene_probe

NM_005994

IP

SC R

NU

MA

D

TE

CE P

AC

T

ASPWP0009363

ASPWP0011519

0.016211798

2.1133584

down

coding_transcript_probe

NM_001620

ASPWP0011199

0.003580058

3.6233876

down

coding_transcript_probe

NM_022740

ASPWP0004113

0.000615777

10.8973381

down

coding_gene_probe

NM_005378

ASPWP0006852

0.02788044

3.0959097

down

coding_gene_probe

NM_145040

ASPWP0009466

0.000855721

10.2484462

down

coding_transcript_probe

NM_002923

ASPWP0001671

0.016461579

2.2660427

down

coding_gene_probe

NM_002647

ASPWP0010914

0.000864546

6.5021296

down

coding_transcript_probe

NM_002994

ASPWP0000350

0.002972031

2.1536725

down

coding_gene_probe

NM_001184

ASPWP0010084

0.002376739

2.3140301

down

coding_transcript_probe

NM_000396

ASPWP0008880

0.003480726

2.3812699

down

coding_transcript_probe

NM_002485

ASPWP0011391

0.034099619

2.6848787

down

coding_transcript_probe

NM_000489

ASPWP0002308

0.002051121

3.3603282

down

coding_gene_probe

NM_134323

ASPWP0007484

0.020697358

2.159611

down

coding_gene_probe

NM_001001924

ASPWP0000181

0.039695075

2.1204106

down

coding_gene_probe

NM_032415

ASPWP0010426

0.010425415

2.6267681

down

coding_transcript_probe

NM_005234

ASPWP0010482

0.000141922

2.1958046

down

coding_transcript_probe

NM_052876

32

ACCEPTED MANUSCRIPT 0.010408061

2.567952

down

coding_gene_probe

NM_001218

ASPWP0011762

0.020325195

2.0750975

down

coding_transcript_probe

NM_001254738

ASPWP0010576

0.001455501

3.7685926

down

coding_transcript_probe

ENST00000359671

ASPWP0005987

0.00148744

5.3569439

down

coding_gene_probe

NM_182663

ASPWP0009499

0.003193012

2.0572231

down

coding_transcript_probe

NM_003590

ASPWP0005562

0.000715508

2.2640388

down

coding_gene_probe

NM_001760

ASPWP0009357

7.37549E-05

2.1674066

down

coding_transcript_probe

NM_016009

ASPWP0000152

0.001144402

2.4311366

down

coding_gene_probe

ENST00000359671

ASPWP0006810

0.000561312

2.2111479

down

coding_gene_probe

NM_002775

ASPWP0003155

0.010004632

2.2773487

down

coding_gene_probe

NM_000101

ASPWP0006302

0.000275249

4.1191344

down

coding_gene_probe

NM_004878

ASPWP0006416

0.000787664

2.9223413

down

coding_gene_probe

NM_004496

ASPWP0006677

0.005315893

2.8888388

down

coding_gene_probe

NM_002417

ASPWP0011078

0.000590056

2.3188968

down

coding_transcript_probe

NM_001760

ASPWP0010016

0.047800687

2.0323252

down

coding_transcript_probe

NM_006325

ASPWP0005603

0.048142295

2.8770202

down

coding_gene_probe

NM_000416

ASPWP0001560

0.008145535

2.4007151

down

coding_gene_probe

NM_000660

ASPWP0010825

0.00155717

2.2788862

down

coding_transcript_probe

NM_016577

ASPWP0001350

0.002663876

5.5761128

down

coding_gene_probe

NM_006838

ASPWP0009258

0.016002559

2.2644802

down

coding_transcript_probe

NM_001096

ASPWP0010669

0.007165143

2.6805288

down

coding_transcript_probe

NM_016037

ASPWP0004665

0.002461355

3.2080969

down

coding_gene_probe

NM_022094

ASPWP0001276

0.008792034

2.0649301

down

coding_gene_probe

NM_003977

ASPWP0009822

0.001116649

4.8365948

down

coding_transcript_probe

NM_145040

ASPWP0010294

0.000533985

3.9537008

down

coding_transcript_probe

NM_002634

ASPWP0010262

0.000511943

4.4545175

down

coding_transcript_probe

NM_001973

ASPWP0005013

0.0160928

2.533074

down

coding_gene_probe

NM_015560

ASPWP0007133

0.006053539

2.2745155

down

coding_gene_probe

NM_003377

IP

SC R

NU

MA

D

TE

CE P

AC

T

ASPWP0001426

ASPWP0010278

0.000588525

2.4962445

down

coding_transcript_probe

NM_002276

ASPWP0010787

0.000312751

3.4597799

down

coding_transcript_probe

NM_003256

ASPWP0011256

0.007751818

3.7783857

down

coding_transcript_probe

NM_003840

ASPWP0012068

0.003303374

6.0188666

down

coding_transcript_probe

NM_005346

ASPWP0011304

0.03694974

3.0742213

down

coding_transcript_probe

NM_017489

ASPWP0012136

0.025731375

2.0635485

down

coding_transcript_probe

NM_002835

ASPWP0009070

0.00174151

2.0346251

down

coding_transcript_probe

NM_015399

ASPWP0012261

0.005647806

2.0731135

down

coding_transcript_probe

NM_001654

ASPWP0000254

0.005229293

2.27261

down

coding_gene_probe

ENST00000371485

ASPWP0009020

0.005729014

2.1407359

down

coding_transcript_probe

NM_001177701

ASPWP0010524

0.004983697

2.4077102

down

coding_transcript_probe

NM_006826

ASPWP0003849

0.002177832

2.5819604

down

coding_gene_probe

NM_001014831

ASPWP0010437

0.000277075

2.7727381

down

coding_transcript_probe

NM_000660

ASPWP0011484

0.043092834

3.311776

down

coding_transcript_probe

NM_000314

ASPWP0004897

3.70557E-05

2.9214994

down

coding_gene_probe

NM_016381

ASPWP0010824

0.024784407

2.4810627

down

coding_transcript_probe

NM_007027

33

ACCEPTED MANUSCRIPT 0.021235542

2.0259439

down

coding_gene_probe

NM_021873

ASPWP0007170

0.000124716

7.3331073

down

coding_gene_probe

NM_031934

ASPWP0003405

0.007902023

3.2552582

down

coding_gene_probe

NM_003474

ASPWP0009006

0.004321311

2.0563339

down

coding_transcript_probe

NM_058216

ASPWP0004374

8.58074E-05

2.9283534

down

coding_gene_probe

NM_005560

ASPWP0010427

0.001959342

6.2751184

down

coding_transcript_probe

NM_002866

ASPWP0001666

0.009607521

2.7065581

down

coding_gene_probe

NM_002423

ASPWP0009163

0.020113449

4.3235755

down

coding_transcript_probe

NM_000251

ASPWP0005838

0.001036382

3.8065733

down

coding_gene_probe

NM_002923

ASPWP0011351

0.000153872

2.6173409

down

coding_transcript_probe

NM_002451

ASPWP0003548

0.011371601

4.0046909

down

coding_gene_probe

NM_015355

AC

CE P

TE

D

MA

NU

SC R

IP

T

ASPWP0000889

34

ACCEPTED MANUSCRIPT Table 3．Intergrative analysis of lncRNAs and mRNAs. LncRNA information

Relationship

Potential target gene information Genomic

TCONS_00026294

ENST00000529841

ENST00000529841

ENST00000461109

ENST00000480069

ENST00000480069

ENST00000492507

uc003xcr.3

NR_045121

ENST00000533528

ENST00000533528

NR_033928

NR_033928

NR_028415

ENST00000442889

ce

symbol

up

enhancer

upstream

10460

UBE2I

19.8306

38

381

0.0005213

3.14992

36

45

0.0005213

3.14992

36

45

0.0008581

2.56061

81

16

0.0008581

2.56061

81

16

0.0008786

2.16416

95

78

0.0011377

3.62775

99

05

0.0011377

3.62775

99

05

up

up

up

enhancer

enhancer

enhancer

5.21857

42

51

0.0012184

4.88460

75

2

0.0012184

4.88460

75

2

0.0012357

2.06844

44

75

0.0013774

2.76800

05

29

0.0013774

2.76800

05

29

0.0018514

2.02270

37

17

0.0018514

2.02270

37

17

0.0019361

3.38741

14

15

0.0020768

2.27560

81

33

upstream

10460

79475

upstream

79475

UBE2I

RBBP8

RBBP8

down

enhancer

down

Neighboring

m

NM_194259

NM_002894

NM_002894

enhancer

up

up

enhancer

enhancer

upstream

upstream

upstream

2222

PPP2R1B

NM_002716

2222

PPP2R1B

NM_002716

10726

10590

10590

enhancer

m

5648

up

Neighboring

upstream

799

up

enhancer

Neighboring

upstream

upstream

799

34046

261

up

Neighboring

upstream

261

up

Neighboring

upstream

53

PECAM1

FGF2

FGF2

XAF1

10B

10B

PRODH

RAB30

RAB30

10A

upstream

53

10A

up

0.833542

1.037815

555

5

up

0.135168

1.718815

dow

423

4

n

0.344725

1.488316

dow

864

9

n

91

dow 1.774753

n dow

2.548160

dow

536

1

n

2.33685E

4.722031

-05

2

0.724931

1.066944

576

3

0.106826

1.791473

715

3

0.000326

3.338442

186

1

0.055396

1.646470

NM_003842

078

1

NM_001195

0.091740

2.203021

226

193

5

up

0.239208

1.975850

dow

52

7

n

0.662734

1.259968

329

4

up

945

2.11807

up

0.018342

2.046663

73

3

up

016

1.668695

up

0.026977

1.561550

177

7

NM_000442

NM_002006

NM_002006

NM_017523

NM_003842

NM_014488

NM_014488

up

up

up

up

up

0.006900 NM_003844

TNFRSF Neighboring

3

0.017366

TNFRSF

up

2.230281

n

TNFRSF

down

0.056517

1.774753

TNFRSF

upstream

on

91

downstrea

Neighboring

change

0.148406

down

up

P-value

0.148406

downstrea m

ulati

NM_194259 921

downstrea

up

0.0011387

upstream

n

Fold

T

hip

19.83063 81

0.0001845

AC

uc003xcr.3

Mechanism

TE

TCONS_00026294

n

CE P

ENST00000561649

Accessio

IP

38

Distan

SC R

0.0001845

561649

Relations

NU

ENST00000

Fold change

Potential

MA

P-value

Regulatio

D

Seq name

Reg

NM_003844

0.457369 down

up

enhancer

Neighboring

upstream

upstream

35

4557

480

ERC1

CAMTA1

NM_178040

NM_015215

up

ACCEPTED MANUSCRIPT

ENST00000579595

ENST00000272567

ENST00000404856

ENST00000404856

ENST00000416146

uc001ygz.2

0.0023757

1.69283

54

12

0.0023757

1.69283

54

12

0.0025485

2.35861

32

31

0.0025485

2.35861

32

31

0.0026741

2.88637

96

54

0.0029946

2.78181

1

14

0.0029946

2.78181

1

14

0.0030032

5.17756

68

13

0.0032684

3.82268

19

9

0.0032684

3.82268

19

9

uc001ygz.2

upstream

7720

EEF1A2

NM_001958

down

enhancer

upstream

16375

WEE1

NM_003390

ENST00000571486

ENST00000571486

ENST00000435260

ENST00000435260

ENST00000436229

ENST00000436229

TCONS_00014883

TCONS_00014883

Neighboring

Neighboring

down

enhancer

down

enhancer

3.82268

19

9

0.0035507

2.13970

1

97

0.0035507

2.13970

1

97

0.0035875

2.93313

98

45

0.0035875

2.93313

98

45

0.0038311

3.42790

2

63

0.0038311

3.42790

2

63

0.0038674

5.24650

76

02

0.0038674

5.24650

76

02

ng

ng

16375

upstream

WEE1

NM_003390

0

0

YES1

YES1

NM_005433

NM_005433

14509

RABL2A

NM_013412

98848

DEK

NM_003472

downstrea m

downstrea

enhancer

m

98848

DEK

NM_003472

overlappi

up

0.0032684

upstream

overlappi

down

9

AC

uc001ygz.2

enhancer

overlappi

down

3.82268

NM_001958

enhancer

down

19

EEF1A2

down

down

0.0032684

7720

Neighboring

down

down

down

down

Neighboring

ng

upstream

0

1944

PRKCE

YY1

NM_005400

NM_003403

enhancer

upstream

1377

YY1

NM_003403

Neighboring

upstream

1944

YY1

NM_003403

enhancer

upstream

1377

YY1

NM_003403

enhancer

m

5287

FUS

NM_004960

enhancer

m

5287

FUS

NM_004960

downstrea down

enhancer

down

enhancer

m

37590

LYN

NM_002350

37590

LYN

NM_002350

downstrea m downstrea down

enhancer

m

29627

ENO1

NM_001428

downstrea down

enhancer

m

29627

ENO1

NM_001428

overlappi down

Neighboring

ng

0

MAFA

NM_201589

overlappi down

dow

495

9

n

0.698387

1.193249

939

3

0.001239

4.638571

up

423

4

up

0.036432

1.611211

994

9

up

0.027397

1.908683

dow

801

5

n

0.862207

1.056627

23

8

up

0.123840

1.328539

dow

695

1

n

0.001448

2.489621

dow

226

4

n

0.166930

1.717881

302

1

0.198648

1.168872

691

6

up

0.035249

1.259212

dow

525

9

n

0.035249

1.259212

dow

525

9

n

1.513715

up

702

1.513715

up

0.037645

2.468630

597

5

up

0.849144

1.039972

dow

699

6

n

0.001250

1.846699

dow

992

3

n

0.142321

1.404576

dow

672

7

n

0.140035

1.354805

854

9

0.999563

1.000065

744

5

up

0.130002

1.640361

dow

14

7

n

0.234789

2.105270

dow

879

7

n

up

702 0.339136

downstrea down

1.301996

0.339136

downstrea down

0.198714

T

79

upstream

IP

79

CE P

uc001ygz.2

2.99474

enhancer

SC R

ENST00000579595

0.0022007

down

NU

ENST00000475608

79

MA

ENST00000475608

79

D

TCONS_00028472

2.99474

TE

TCONS_00028472

0.0022007

Neighboring

ng

36

0

MAFA

NM_201589

up

ACCEPTED MANUSCRIPT downstrea

21

76

0.0041246

2.23922

21

76

down

enhancer

2.44949

up

Neighboring

down

enhancer

24

13682

RNF7

m

13682

RNF7

NM_014245

0

TES

NM_015641

overlappi ng

0.0051207 24

2.44949

up

Neighboring

0.0051207 ENST00000446355

24

upstream overlappi

2.44949

up

Neighboring

ng

0.0051207

ENST00000441270

ENST00000565374

ENST00000438347

ENST00000438347

67

0.0052124

2.21199

04

67

0.0055717

2.26441

21

36

0.0055717

2.26441

21

36

0.0056238

2.23698

35

48

0.0056337

2.48377

13

77

ENST00000478318

ENST00000491601

ENST00000491601

ENST00000491601

down

enhancer

down

enhancer

down

down

down

down

0.0056337

2.48377

13

77

0.0056858

1.65699

36

6

0.0056858

1.65699

36

6

0.0058187

2.00024

03

63

0.0058187

2.00024

03

63

0.0058187

2.00024

03

63

down

up

upstream

Neighboring

Neighboring

enhancer

0

135

NU

04

AC

ENST00000478318

2.21199

Neighboring

CAV2

NM_001233

TES

CAV2

NM_015641

NM_001233

upstream

47616

ARAF

NM_001654

upstream

47616

ARAF

NM_001654

MA

ENST00000441270

0.0052124

up

D

ENST00000446295

2.44949

TE

ENST00000446295

24

CE P

ENST00000446355

135

SC R

ENST00000446355

NM_014245

downstrea

0.0051207 ENST00000446355

m

upstream

upstream

upstream

2544

2544

51583

GNAS

GNAS

CDH13

NM_000516

NM_000516

NM_001257

enhancer

upstream

30244

MAP3K8

NM_005204

enhancer

upstream

30244

MAP3K8

NM_005204

overlappi Neighboring

ng

0

STEAP1

NM_012449

overlappi up

Neighboring

ng

0

STEAP1

NM_012449

downstrea down

enhancer

m

21516

TOP2A

NM_001067

downstrea down

enhancer

m

21516

TOP2A

NM_001067

down

enhancer

upstream

3506

IGFBP4

NM_001552

0.0061276 ENST00000460497

4

4.41603

up

enhancer

upstream

5438

ZDHHC2

NM_016353

0.0061276 ENST00000460497

ENST00000563660

ENST00000502774

1.9749E-

2.396596

05

6

0.027625

1.529908

753

9

0.000370

4.183967

T

ENST00000463581

2.23922

IP

ENST00000463581

0.0041246

up

up

68

3

up

0.009110

1.400622

976

2

0.084418

2.354450

488

1

up

368

1.147247

up

0.005647

2.073113

dow

806

5

n

0.085253

1.737908

639

1

0.543239

1.137375

471

3

up

0.945428

1.012160

dow

769

9

n

0.200570

1.444105

311

5

0.002977

3.005260

529

7

0.022792

2.101547

037

5

0.595312

1.102351

559

5

0.635474

1.193695

295

4

up

0.134734

2.188041

dow

699

2

n

0.192250

2.033302

dow

432

9

n

0.193570

1.653247

dow

075

8

n

0.008749

1.945717

012

6

up

1.983138

up

up

0.150695

up

up

up

up

up

0.018512

4

4.41603

0.0063307

3.13044

37

79

0.0069741

2.27491

68

6

up

enhancer

upstream

5438

ZDHHC2

NM_016353

overlappi down

Neighboring

ng

0.119448 0

NEIL1

NM_024608

downstrea up

enhancer

m

37

901

24635

TLR2

NM_003264

dow

784

1.836527

0.012140

4.733994

635

1

n

up

ACCEPTED MANUSCRIPT

ENST00000407916

NR_073453

NR_073453

ENST00000554535

ENST00000554535

ENST00000492365

ENST00000492365

4.30986

62

11

0.0081051

2.11807

78

16

0.0082423

1.99224

85

49

0.0095438

3.42995

64

35

0.0095438

3.42995

64

35

0.0098598

3.66873

1

97

0.0098598

3.66873

1

97

0.0102945

2.33410

21

82

0.0102945

2.33410

21

82

0.0108749

2.84641

77

66

ENST00000524619

ENST00000524619

ENST00000524619

ENST00000509173

ENST00000461972

ENST00000557989

NR_000029

uc010hbj.3

up

Neighboring

up

Neighboring

Neighboring

5.88895

95

92

0.0118869

1.51611

2

97

0.0118869

1.51611

2

97

0.0118869

1.51611

2

97

0.0121004

2.33424

2

98

0.0123575

2.17978

44

27

0.0124562

2.14033

85

14

0.0128902

2.46298

15

2

0.0130528

1.84070

76

53

upstream

Neighboring

ng

enhancer

m downstrea

down

enhancer

down

enhancer

A

077

346

5

n

0.000370

4.183967

68

3

0.084418

2.354450

0

TES

NM_015641

0

TES

NM_015641

199

m

RABL2A

0

80847

RAD51B

EGFR

m

1

up

0.123840

1.328539

dow

695

1

n

813

2.076731

up

8.77632E

2.022504

-05

9

0.092458

2.011233

954

5

up

0.000117

6.665944

dow

397

2

n

0.007902

3.255258

dow

023

2

n

0.010748

1.913919

804

4

up

0.678193

1.208360

dow

308

5

n

0.128603

1.706885

dow

898

8

n

006

1.053145

up

0.064548

1.884122

dow

41

9

n

0.029153

1.583117

54

2

0.091330

2.165875

634

7

0.742569

1.121800

32

3

0.744662

1.277230

549

5

up

0.077933

1.910998

dow

463

1

n

0.091755

1.536860

393

9

up

0.123840

1.328539

dow

NM_013412

695

1

n

NM_001130

0.865573

1.065539

922

015

3

NM_013412

NM_133509

NM_005228

80847

EGFR

NM_005228

25310

ADAM12

NM_003474

downstrea

enhancer

enhancer

up

down

down

up

enhancer

m

upstream

upstream

25310

25505

25505

ADAM12

NFKBIA

NFKBIA

NM_003474

NM_020529

NM_020529

enhancer

upstream

19099

MTDH

NM_178812

enhancer

upstream

19099

MTDH

NM_178812

down

downstrea enhancer

Neighboring

Neighboring

down

Neighboring

down

Neighboring

m

90224

IGFBP5

NM_000599

ng

upstream

upstream

0

203

PPFIA1

CTTN

NM_003626

NM_005231

203

CTTN

NM_005231

0

FER

NM_005246

overlappi ng overlappi up

up

up

up

0.155711

up

0.787547

overlappi down

up

488

downstrea

up

0.0114088

ng

downstrea

down

66

ng

overlappi

down

2.84641

dow

overlappi

down

77

1.256831

overlappi

down

0.0108749

0.553977

T

0.0073444

7510

NM_001185

IP

11

AC

ENST00000433233

62

m

ARHGDI

SC R

ENST00000407916

4.30986

enhancer

NU

ENST00000473054

0.0073444

down

MA

ENST00000416673

2

D

uc003vhn.1

49

downstrea

TE

uc003vhn.1

1.72321

CE P

ENST00000582866

0.0070690

Neighboring

Neighboring

Neighboring

Neighboring

ng

upstream

upstream

upstream

38

0

127

101

137

TP53I3

TJP1

RABL2A

RABL2B

NM_004881

NM_003257

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000443818

ENST00000443818

ENST00000515464

ENST00000515464

ENST00000504656

ENST00000504656

ENST00000558620

1.79557

08

51

0.0143162

1.74668

13

68

0.0146613

1.93274

79

98

0.0146613

1.93274

79

98

0.0146613

1.93274

79

98

0.0146613

1.93274

79

98

0.0153867

2.02923

96

48

0.0153867

2.02923

96

48

0.0157486

3.18817

66

35

0.0157486

3.18817

66

35

ENST00000557078

ENST00000404566

ENST00000422137

ENST00000422137

ENST00000425698

ENST00000425698

ENST00000523470

AK055628

overlappi down

Neighboring

down

Neighboring

enhancer

enhancer

Neighboring

down

Neighboring

down

enhancer

2.75985

42

16

0.0158291

4.65189

87

8

0.0158577

2.26526

88

59

0.0164125

2.51547

26

31

0.0164125

2.51547

26

31

0.0168141

3.59308

71

09

0.0168141

3.59308

71

09

0.0169492

1.24175

72

14

0.0179224

3.27651

65

98

0

YAP1

644

SCRIB

m

12058

m

dow

145

311

8

n

NM_001130

0.601049

1.043769

145

952

5

up

ENST00000

0.021925

6.392791

dow

320476

585

8

n

NM_001130

0.865573

1.065539

RABL2B

922

015

3

0.469058

1.171725

2808

2808

RAB10

31

1

0.469058

1.171725

RAB10

31

1

0.651121

1.122227

001

7

0.651121

1.122227

001

7

up

0.060060

1.617436

dow

814

8

n

0.373756

1.128589

023

7

up

0.036720

1.438300

dow

209

7

n

0.130863

1.320059

182

3

up

0.009457

2.222940

dow

865

4

n

0.236704

1.247943

dow

355

4

n

2.076731

up

547

1.521922

up

0.029001

2.051321

dow

803

6

n

0.160629

1.880980

dow

445

3

n

0.030569

3.416195

33

5

0.158242

1.504651

453

6

up

0.000280

3.345358

dow

535

6

n

0.000117

6.665944

dow

397

2

n

NM_016131

NM_016131

2808

RAB10

NM_016131

2808

RAB10

NM_016131

downstrea m

overlappi

Neighboring

ng

0

MYLK

NM_053025

overlappi

up

0.0157489

m

downstrea

up

16

upstream

downstrea down

2.75985

m

downstrea down

42

ng downstrea

down

0.0157489

YAP1

1.137394

T

0.0139401

0

0.404355

IP

27

AC

ENST00000558620

04

ng

NM_001130

SC R

ENST00000443818

1.96753

Neighboring

NU

ENST00000443818

0.0130932

down

MA

ENST00000514936

27

Neighboring

D

ENST00000532625

04

overlappi

TE

ENST00000526310

1.96753

down

down

CE P

ENST00000526310

0.0130932

down

down

Neighboring

Neighboring

ng

0

MYLK

NM_053025

overlappi ng

0

PDCD6

NM_013232

overlappi ng

0

PDCD6

NM_013232

182065

BNIP2

NM_004330

downstrea enhancer

m downstrea

enhancer

m

182065

BNIP2

NM_004330

overlappi down

Neighboring

ng

up

up

up

up

0.155711 0

RAD51B

NM_133509

813 0.001586

down

enhancer

upstream

3509

SOX4

NM_003107

downstrea up

enhancer

up

enhancer

m

14799

RECK

NM_021111

14799

RECK

NM_021111

downstrea

up

up

up

Neighboring

Neighboring

Neighboring

m

upstream

upstream

upstream

987

987

404

BTG2

BTG2

TOB1

NM_006763

NM_006763

NM_005749

overlappi down

Neighboring

ng

39

0

ADAM12

NM_003474

up

ACCEPTED MANUSCRIPT

ENST00000366466

ENST00000320232

ENST00000519475

ENST00000433407

ENST00000422817

ENST00000422817

ENST00000414042

1.72573

16

04

0.0198197

2.10147

04

26

0.0198197

2.10147

04

26

0.0199884

1.45146

47

48

0.0199884

1.45146

47

48

0.0204346

3.53823

49

18

0.0205613

2.95936

17

08

0.0216347

3.39271

35

49

0.0225253

2.12409

42

77

0.0225253

2.12409

42

77

ENST00000584794

ENST00000584794

uc010czc.3

ENST00000427492

ENST00000427492

ENST00000444359

ENST00000552169

ENST00000552169

up

Neighboring

up

Neighboring

enhancer

enhancer

Neighboring

up

Neighboring

down

Neighboring

1.63995

9

92

0.0226538

1.49534

26

59

0.0226538

1.49534

26

59

0.0233210

2.01702

74

71

0.0234379

2.25046

2

01

0.0234379

2.25046

2

01

0.0235521

1.51825

02

25

0.0238954

2.48030

32

8

0.0238954

2.48030

32

8

NM_053025

ng

0

MYLK

NM_053025

upstream

4259

10A

NM_003844

upstream

upstream

4259

560

10A

TOPORS

NM_003844

NM_005802

upstream

560

TOPORS

NM_005802

upstream

545

CEBPA

NM_004364

overlappi

Neighboring

ng

0

WRN

NM_000553

overlappi

up

0.0225671

MYLK

TNFRSF

up

92

0

TNFRSF

up

1.63995

ng overlappi

up

9

NM_003474

overlappi

up

0.0225671

ADAM12

Neighboring

up

up

down

down

down

down

enhancer

ng

upstream

0

37572

CAMTA1

CREG1

NM_015215

NM_003851

enhancer

upstream

37572

CREG1

NM_003851

Neighboring

upstream

2739

LAMA5

NM_005560

Neighboring

enhancer

enhancer

down

Neighboring

down

Neighboring

upstream

upstream

upstream

upstream

2739

19911

19911

LAMA5

YES1

YES1

NM_005560

NM_005433

NM_005433

90

NBR1

NM_031858

0

ANXA7

NM_004034

overlappi ng overlappi down

Neighboring

ng

0

ANXA7

0.007902

3.255258

dow

023

2

n

0.060060

1.617436

dow

814

8

n

0.373756

1.128589

T

0.0188527

0

IP

04

AC

ENST00000414042

16

ng

SC R

ENST00000366466

1.72573

Neighboring

NU

TCONS_00014652

0.0188527

down

MA

TCONS_00014652

98

D

NR_038266

65

overlappi

TE

NR_038266

3.27651

CE P

AK055628

0.0179224

NM_004034

023

7

up

945

2.11807

up

0.018342

2.046663

73

3

0.006900

0.010835 489

up dow

2.248732

n

301

1.120601

up

0.000293

19.55596

dow

964

58

n

0.894081

1.028302

dow

038

4

n

0.026977

1.561550

177

7

0.849591

1.074674

653

9

up

0.984924

1.011806

dow

767

7

n

8.58074E

2.928353

dow

-05

4

n

0.185805

1.626521

dow

161

5

n

0.027397

1.908683

dow

801

5

n

0.862207

1.056627

23

8

up

0.452979

1.217732

dow

98

1

n

0.031595

1.646898

843

4

0.446143

1.284990

086

7

up

986

1.340324

up

0.020833

2.087551

dow

839

2

n

0.322926

up

up

0.649157 up

down

Neighboring

enhancer

upstream

upstream

79

177535

CHUK

CRY1

NM_001278

NM_004075

0.707810 down

enhancer

upstream

40

177535

CRY1

NM_004075

879

dow 1.143362

n

ACCEPTED MANUSCRIPT

ENST00000421965

ENST00000421965

ENST00000421965

ENST00000421965

ENST00000421965

ENST00000566108

ENST00000445874

uc021rgk.1

1.43724

96

47

0.0247487

1.43724

96

47

0.0247487

1.43724

96

47

0.0248132

2.61367

19

66

0.0248132

2.61367

19

66

0.0248132

2.61367

19

66

0.0248132

2.61367

19

66

0.0248132

2.61367

19

66

0.0248132

2.61367

19

66

0.0252934

1.92414

1

16

ENST00000432727

ENST00000576784

ENST00000576784

ENST00000529735

ENST00000504145

ENST00000504145

ENST00000502804

down

enhancer

down

enhancer

up

enhancer

enhancer

enhancer

up

enhancer

up

Neighboring

0.0262725

3.80092

9

24

0.0262725

3.80092

9

24

0.0264186

2.26089

25

68

0.0265128

2.17898

52

94

0.0265128

2.17898

52

94

0.0279171

1.43887

76

85

0.0279669

2.61490

84

74

0.0279669

2.61490

84

74

0.0292937

1.84927

7

37

upstream

upstream

upstream

m

m

enhancer

upstream

up

down

down

down

down

Neighboring

enhancer

m

upstream

Neighboring

Neighboring

ng

upstream

upstream

Neighboring

ng

Neighboring

up

Neighboring

ng

up

up

up

enhancer

Neighboring

Neighboring

enhancer

m

upstream

upstream

upstream

41

0.210432

1.213820 6

NM_001001

0.792408

1.019802

419

6

9

NM_001001

0.818688

1.054148

419

731

6

0.004961

2.081756

401

9

up

1.238425

up

1.238425

up

52249

52249

101170

SMAD5

SMAD5

MET

NM_000245

2408

CAV1

NM_001753

2408

CAV1

NM_001753

101170

2408

2408

MET

NM_000245

CAV1

NM_001753

CAV1

NM_001753

RBBP6

NM_006910

0

TNKS2

NM_025235

128

BRI3BP

BRI3BP

NM_080626

NM_080626

L3MBTL 0

1

NM_032107

0

P4HB

NM_000918

0

P4HB

NM_000918

ARHGEF 129997

35

35

36525

up

up

up

986 0.384985

37403

128

up

0.384985

986 0.502060

downstrea up

6

864

overlappi ng

057

NM_000358

overlappi up

1.728721

TGFBI

overlappi up

0.001208

up

16679

overlappi Neighboring

1

NM_000358

downstrea m

74

TGFBI

downstrea

enhancer

1.175744

16679

downstrea

up

85

m

downstrea

up

1.89391

m downstrea

down

74

NM_170735

downstrea

down

0.0254615

BDNF

0.782380

T

0.0247487

146793

IP

47

AC

uc021rgk.1

96

upstream

SC R

ENST00000421965

1.43724

enhancer

NU

NR_030583

0.0247487

down

MA

NR_030583

68

D

NR_030583

11

TE

NR_030583

2.04964

CE P

ENST00000325243

0.0246993

12

RIPK2

RIPK2

PF4

NM_015313

NM_003821

NM_003821

NM_002619

dow

741

1.086228

n

0.771815

1.018521

dow

166

3

n

0.771815

1.018521

dow

166

3

n

0.341350

1.913474

41

8

up

0.003320

2.340029

dow

929

3

n

0.195321

1.392810

dow

545

9

n

0.220451

3.308575

814

9

up

0.889034

1.020496

dow

989

9

n

0.047153

1.295498

dow

28

7

n

0.733186

1.087969

981

3

up

0.025636

3.370982

dow

676

4

n

0.030772

2.145666

682

1

up

0.157585

1.468559

dow

792

1

n

0.002706

6.339024

248

1

up

ACCEPTED MANUSCRIPT

NR_002612

NR_002612

ENST00000484463

ENST00000427342

ENST00000427342

ENST00000416050

ENST00000423595

1.59006

26

82

0.0299427

2.34551

09

25

0.0299427

2.34551

09

25

0.0311439

3.15071

54

4

0.0311439

3.15071

54

4

0.0311439

3.15071

54

4

0.0313040

2.62028

11

96

0.0314939

1.91510

86

69

0.0314939

1.91510

86

69

0.0315055

1.60110

4

42

ENST00000466133

ENST00000466133

ENST00000550947

ENST00000550947

NR_024530

ENST00000584934

ENST00000584934

TCONS_00027767

enhancer

down

enhancer

Neighboring

Neighboring

1.79853

77

62

0.0320875

1.65283

71

56

0.0320875

1.65283

71

56

0.0325997

2.20532

82

86

0.0325997

2.20532

82

86

0.0333542

2.63266

98

62

0.0335902

2.05822

9

19

0.0335902

2.05822

9

19

0.0341803

2.34498

62

32

ng

Neighboring

ng overlappi

down

Neighboring

down

Neighboring

1

n

NM_001110

0.266569

1.445308

788

5

up

0.026784

FLNA

556

30686

GSC

NM_173849

0

ng

DPP4

1.570800

dow

623

2

n

0.127734

1.359031

675

6

0.985446

1.004849

279

2

0.075964

3.705717

852

7

0.485580

1.484587

862

7

0.986998

1.003394

069

4

0.526975

1.748480

274

5

up

568

2.199184

up

0.052517

1.858319

NM_015646

824

8

up

NM_001083

0.150459

1.240133

dow

866

8

n

NM_001935

0

0

DPP4

TRIM13

NM_001935

NM_213590

0

TRIM13

NM_213590

0

KCNRG

NM_173605

overlappi ng

downstrea

enhancer

m

235443

KIT

NM_000222

overlappi

down

0.0318685

ng

overlappi

down

62

m

overlappi

down

1.79853

86

13512

overlappi

down

77

NM_001511

downstrea

down

0.0318685

upstream

CXCL1

dow

T

0.0294362

up

72708

1.515832

IP

38

AC

ENST00000423595

61

m

0.379050

SC R

NR_002612

1.97541

enhancer

NU

ENST00000418335

0.0293053

up

MA

ENST00000418335

37

Neighboring

D

ENST00000490252

7

downstrea

TE

ENST00000433825

1.84927

down

up

CE P

ENST00000502804

0.0292937

down

down

Neighboring

enhancer

ng

0

RAP1B

0

RAP1B

downstrea m

NM_015646

191302

GPD2

112

39624

PMS1

NM_000534

downstrea enhancer

m

0.002209

downstrea enhancer

m

up

up

up

up

0.034490

overlappi ng

up

39624

PMS1

NM_000534

dow

501

4.427294

n

0.202165

1.445311

563

1

up

118

4.34639

up

0.452865

1.248691

717

5

0.001448 down

down

enhancer

enhancer

upstream

upstream

104830

104830

IL12A

IL12A

NM_000882

NM_000882

overlappi up

Neighboring

up

Neighboring

ng

0.246032 0

ZC3H10

NM_032786

0

ZC3H10

NM_032786

overlappi

up

Neighboring

ng

upstream

101

RABL2A

NM_013412

overlappi up

Neighboring

ng

0

PTP4A1

NM_003463

overlappi up

down

Neighboring

Neighboring

ng

upstream

42

0

1071

PTP4A1

BCL3

NM_003463

NM_005178

up dow

219

1.4094

n

0.351538

1.641292

dow

668

4

n

0.123840

1.328539

dow

695

1

n

0.139441

2.406715

99

6

0.624322

1.216346

656

7

0.401360

1.333358

745

8

up

up

up

ACCEPTED MANUSCRIPT

ENST00000318333

ENST00000458001

uc002zti.1

ENST00000453523

ENST00000453523

ENST00000510160

AK091357

1.82985

74

57

0.0359008

1.82985

74

57

0.0366397

2.06174

68

21

0.0378239

2.14324

47

39

0.0386097

1.70168

21

23

0.0395492

1.89343

43

42

0.0398671

6.86386

69

43

0.0398671

6.86386

69

43

0.0401878

1.83910

97

23

0.0406882

3.56225

48

7

down

Neighboring

down

enhancer

AK091357

AK091357

ENST00000542064

ENST00000542064

ENST00000451056

ENST00000451056

ENST00000423223

enhancer

Neighboring

3.56225

48

7

0.0406882

3.56225

48

7

0.0406882

3.56225

48

7

0.0406882

3.56225

48

7

0.0411031

2.07036

56

49

0.0411031

2.07036

56

49

0.0412323

1.89318

46

32

0.0412323

1.89318

46

32

0.0421574

2.14775

19

2

ng

Neighboring

ng overlappi

up

Neighboring

down

Neighboring

319

5

0.401360

1.333358

745

8

0.281880

1.568565

2769

BCL3

NM_005178

18090

CD40

NM_001250

18090

ng

CD40

NM_001250

0

0

PTN

TNKS2

NM_002825

NM_025235

0

GAS6

NM_000820

540

AIFM3

NM_144704

downstrea m

overlappi

Neighboring

ng

0

SUMO1

NM_003352

overlappi

up

0.0406882

m

overlappi

up

7

m

overlappi

down

3.56225

m

downstrea

up

48

421745

downstrea

down

0.0406882

BIRC6

T

0.0359008

0

1.481564

IP

37

AC

AK091357

AK091357

87

ng

0.531006

downstrea

down

down

CE P

AK091357

1.55572

Neighboring

ENST00000

SC R

ENST00000448365

0.0354400

down

NU

ENST00000440687

18

MA

ENST00000440687

17

overlappi

Neighboring

D

TCONS_00027578

1.74288

TE

ENST00000455572

0.0344106

down

down

Neighboring

Neighboring

ng

0

SUMO1

NM_003352

overlappi ng

0

PRLR

NM_000949

downstrea m

2234

ZDHHC2

NM_016353

2234

ZDHHC2

NM_016353

downstrea enhancer

m downstrea

Neighboring

m

down

enhancer

Neighboring

m

upstream

2234

ZDHHC2

NM_016353

2234

1953

ZDHHC2

CNOT7

NM_016353

NM_013354

enhancer

upstream

1953

CNOT7

NM_013354

down

enhancer

upstream

161164

CCND1

NM_053056

enhancer

upstream

161164

CCND1

NM_053056

overlappi up

Neighboring

ng

Neighboring

ng

0

RPA1

NM_002945

0

RPA1

NM_002945

overlappi down

Neighboring

ng

43

dow

539

1.972842

n

0.302328

1.563560

dow

829

6

n

0.003320

2.340029

dow

929

3

n

0.170289

dow

839

2.542615

0.112494

1.291536

229

6

up

0.147245

1.107817

dow

212

1

n

0.297350

1.041809

044

9

up

0.822306

1.216662

dow

477

7

n

0.008749

1.945717

012

6

0.008749

1.945717

012

6

up

1.983138

up

901

1.983138

up

0.188359

1.336355

dow

317

4

n

0.188359

1.336355

dow

317

4

n

0.021473

1.623567

403

7

0.513256

1.143922

75

7

901

0.044771

overlappi up

0.318383

up

n

up

0.018512

down

down

9

up

0.018512

downstrea down

112

up

0

SVIL

NM_021738

up

up dow

973

1.809502

0.869131

1.051210

09

4

0.132982

1.765005

659

9

n

up

up

ACCEPTED MANUSCRIPT

ENST00000475062

ENST00000475062

ENST00000442212

ENST00000442212

NR_027401

ENST00000540066

0.0424990

5.32522

3

78

0.0428347

1.40619

07

44

0.0435052

3.78563

76

38

0.0435741

4.23656

29

18

0.0435741

4.23656

29

18

0.0440450

2.34056

78

39

0.0440450

2.34056

78

39

0.0442596

3.00064

1

67

0.0445170

2.30949

61

19

0.0445170

2.30949

61

19

NR_015377

down

Neighboring

down

Neighboring

6.55270

95

91

ENST00000504573

ENST00000504573

ENST00000504573

ENST00000504573

uc011asd.2

ENST00000443688

ENST00000443688

ENST00000433871

0.0455762

1.36461

83

68

0.0455762

1.36461

83

68

0.0455762

1.36461

83

68

0.0455762

1.36461

83

68

0.0456231

1.86693

72

27

0.0465948

2.56085

74

25

0.0465948

2.56085

74

25

0.0470427

2.13345

46

6

ng

Neighboring

ng

Neighboring

ng overlappi

up

Neighboring

up

Neighboring

0

EI24

NM_004879

0

EI24

NM_004879

0

ng

PRKRA

0

0

PTHLH

ANXA2

0

ANXA2

0

ERG

overlappi ng

overlappi

up

0.0455115

AC

NR_015377

Neighboring

overlappi

up

91

ng

overlappi

up

6.55270

ng

overlappi

up

95

NM_021738

overlappi

down

0.0455115

SVIL

Neighboring

enhancer

up

up

up

up

up

up

Neighboring

Neighboring

ng

upstream

0

6217

ng

Neighboring

enhancer

ng

upstream

upstream

3

n

0.165545

1.226711

dow

645

8

n

0.233072

1.551651

0.030974

1.552535

dow

603

3

n

0.140373

2.101017

dow

NM_198965

002

3

n

NM_001136

0.042010

1.616466

dow

015

019

6

n

NM_001136

0.981640

1.003338

015

27

3

NM_001243

0.039709

1.381228

428

964

6

up

NM_001243

0.516659

1.247078

dow

428

705

2

n

NM_001099

0.636444

1.391896

dow

857

701

4

n

NM_003690

ERG

IKBKG

0.010835 0

TOPORS

NM_005802

489

up

dow 2.248732

n

1.120601

up

0.322926 0

TOPORS

NM_005802

0

PAX8

NM_003466

301 0.326797

overlappi Neighboring

174

up

overlappi Neighboring

dow

2

overlappi ng

1.183261

733

overlappi ng

0.617486

T

78

0

IP

3

ng overlappi

CE P

ENST00000540066

5.32522

Neighboring

SC R

ENST00000538113

0.0424990

down

NU

ENST00000453026

2

MA

ENST00000532714

19

overlappi

D

ENST00000532714

2.14775

TE

ENST00000423223

0.0421574

0

1173

1173

PAX8

MAPK9

MAPK9

NM_003466

NM_002752

NM_002752

dow

65

1.188004

n

0.688520

1.109148

215

8

0.370937

1.476251

353

7

0.370937

1.476251

353

7

up

0.376471

1.607054

dow

87

1

n

up

up

up

enhancer

upstream

1173

MAPK9

NM_002752

0.376471

1.607054

dow

up

Neighboring

upstream

1173

MAPK9

NM_002752

87

1

n

NM_001130

0.865573

1.065539

922

015

3

0.004794

3.118403

178

6

0.313305

1.298101

033

4

overlappi down

Neighboring

ng

0

RABL2B

downstrea up

enhancer

m

38270

KDM4C

NM_015061

downstrea up

enhancer

m

38270

KDM4C

NM_015061

0.013485 down

Neighboring

upstream

44

2681

FANCD2

NM_033084

543

up

up

up dow

1.866954

n

ACCEPTED MANUSCRIPT

ENST00000414898

ENST00000414898

ENST00000467381

ENST00000503999

ENST00000503999

TCONS_00023428

TCONS_00023428

1.41307

07

29

0.0474043

1.41307

07

29

0.0483155

4.33708

16

08

0.0483155

4.33708

16

08

0.0483454

1.34142

34

44

0.0483454

1.34142

34

44

0.0484299

1.96152

79

4

0.0494978

2.00808

45

98

0.0494978

2.00808

45

98

0.0505683

2.26154

46

01

ENST00000564977

ENST00000419668

ENST00000547326

ENST00000547326

TCONS_00013950

ENST00000550263

ENST00000550263

ENST00000451920

Neighboring

down

Neighboring

Neighboring

Neighboring

Neighboring

1.51250

32

66

0.0509581

1.51250

32

66

0.0510126

4.69609

12

96

0.0517577

3.00984

82

76

0.0517577

3.00984

82

76

0.0519117

1.96680

4

46

0.0523641

1.87485

73

1

0.0523641

1.87485

73

1

0.0529040

1.91801

09

28

ng downstrea

up

enhancer

up

enhancer

m

NM_014488

RAB30

NM_014488

TNFRSF 0

8

8

0

0

MRVI1

MRVI1

m

enhancer

down

up

up

down

enhancer

enhancer

m

upstream

upstream downstrea m

49562

ANXA2

49562

ANXA2

downstrea enhancer

m downstrea

enhancer

m downstrea

down

up

enhancer

enhancer

m

upstream

1

18281

1

CDK6

ENST00000

0.255327

1.340035

dow

436272

793

1

n

ENST00000

0.434203

1.172122

436272

255

1

Neighboring

down

Neighboring

ng

n

0.916079

1.033205

dow

406

6

n

0.789105

1.033150

dow

814

1

n

0.001283

1.974532

dow

071

1

n

0.708918

1.090412

NM_004663

335

2

up

NM_001136

0.042010

1.616466

dow

015

019

6

n

NM_001136

0.981640

1.003338

015

27

3

0.017000

2.152237

654

3

0.907843

1.038100

NM_000602

637

5

NM_001145

0.141225

1.316373

306

557

4

9.70913E

16.84170

-05

52

0.000489

8.425751

107

9

up

0.767862

1.150987

dow

578

7

n

0.077157

1.774913

dow

075

1

n

0.570715

1.136097

NM_002624

37

9

up

NM_001198

0.046735

2.315833

dow

777

017

6

n

NM_014567

NM_004663

NM_000602

0

GLIPR1

NM_006851

0

GLIPR1

NM_006851

downstrea down

enhancer

m

23888

LEP

NM_000230

overlappi down

Neighboring

ng

0

PFDN5

NM_002624

overlappi down

Neighboring

ng

0

PFDN5

downstrea down

enhancer

m

45

42291

CUL2

dow 1.281779

overlappi ng

0.724784

up

092

overlappi down

0.499915

up

SERPINE 29121

up

9

SERPINE 29121

4

012

NM_130398

RAB11A

329

NM_001243

EXO1

51977

1.259968

1.205025

15403

RAB11A

0.662734

0.830390

NM_130398

51977

n

n

EXO1

BCAR1

7

dow

15403

834

52

4

downstrea

Neighboring

dow

1.115677

TNFRSF 0

1.975850

368

NM_001243

downstrea

down

0.0509581

ng overlappi

down

01

ng overlappi

down

2.26154

ng overlappi

down

46

275

overlappi

down

0.0505683

upstream

RAB30

0.239208

T

0.0474043

up

275

IP

58

AC

ENST00000564977

2

upstream

SC R

NR_046375

1.76007

Neighboring

NU

NR_046375

0.0471117

up

MA

ENST00000439324

58

D

ENST00000439324

2

TE

ENST00000533708

1.76007

CE P

ENST00000533708

0.0471117

up

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000518376

0.0551438

2.08472

04

24

0.0555094

2.29916

88

31

0.0555094

2.29916

88

31

down

enhancer

m

2694

CCNF

NM_001761

up

Neighboring

upstream

2101

MYC

NM_002467

Neighboring

TCONS_00016355

TCONS_00016355

NR_038351

NR_038351

8

0.0579713

1.41210

92

8

0.0581061

2.27267

84

52

0.0581061

2.27267

84

52

0.0591947

1.75481

47

4

0.0591947

1.75481

47

4

0.0598861

1.91304

36

48

ENST00000425094

ENST00000439070

ENST00000439070

ENST00000439070

ENST00000439070

ENST00000429006

uc003opt.2

ENST00000514984

down

enhancer

down

enhancer

down

Neighboring

1.91304 48

0.0599758

1.50603

91

51

0.0599758

1.50603

91

51

0.0609268

1.37963

65

37

0.0609268

1.37963

65

37

0.0609268

1.37963

65

37

0.0609268

1.37963

65

37

0.0616704

2.33362

59

88

0.0620749

2.61895

24

26

0.0627708

1.77080

23

05

upstream

upstream

MYC

17917

60545

E2F2

TFRC

60545

TFRC

ng

0

NRP1

overlappi

Neighboring

ng

0

NRP1

enhancer

up

up

up

up

enhancer

Neighboring

m

11817

m

11817

ng

ng

Neighboring

ng

enhancer

up

enhancer

up

enhancer

m

upstream

2

0.004613

2.301847

ANXA1

up

9

0.420993

2.662551

71

4

up

0.044474

1.967337

dow

108

6

n

0.208995

1.308827

dow

NM_003234

544

1

n

ENST00000

0.025859

1.923299

374867

424

7

up

ENST00000

0.854714

1.081138

dow

374867

661

4

n

0.140817

1.346798

647

4

up

0.445174

1.133974

dow

653

2

n

0.140035

1.354805

854

9

NM_004091

NM_003234

NM_000700

NM_000700

up

up

ENO1

NM_001428

0.999563

1.000065

0

ENO1

NM_001428

744

5

up

ARHGEF

NM_001113

0.219410

7

511

043

1.947096

up

ARHGEF

NM_001113

0.684713

1.098458

dow

7

511

114

9

n

0.000370

4.183967

68

3

0.009110

1.400622

976

2

0.084418

2.354450

488

1

up

368

1.147247

up

0.051316

2.235152

624

9

0

0

157333

TES

NM_015641

34324

CAV2

NM_001233

157333

TES

NM_015641

downstrea m

274

685

NM_002467

downstrea up

1.853335

0

overlappi Neighboring

0.347664

n

2.558130

overlappi Neighboring

1.630923

0.065265

overlappi ng

295

4

downstrea

overlappi up

ANXA1

dow

673

downstrea

up

36

m

2101

overlappi

down

0.0598861

AC

ENST00000425094

92

enhancer

MA

ENST00000451530

up

D

ENST00000451530

1.41210

upstream downstrea

TE

NR_034088

0.0579713

NM_006293

Neighboring

CE P

NR_034088

96

TYRO3

up

up

0.0557031

30127

downstrea

2.20952 ENST00000451217

m

T

39

0.329729

IP

ENST00000518376

81

downstrea

SC R

NR_003574

4.05114

NU

ENST00000565259

0.0549537

up

up

up

0.150695 up

enhancer

upstream

34324

CAV2

NM_001233

overlappi down

Neighboring

ng

0

EDA

NM_001399

0.683921 down

down

enhancer

Neighboring

upstream

upstream

46

6541

989

NFYA

CTBP1

NM_002505

NM_001328

up dow

344

1.395271

n

0.019939

1.587189

dow

826

8

n

ACCEPTED MANUSCRIPT

NR_028059

NR_028059

TCONS_00025721

NR_033850

ENST00000446011

ENST00000446011

ENST00000565575

1.50458

85

28

0.0636184

1.50458

85

28

0.0650315

4.06693

97

26

0.0650315

4.06693

97

26

0.0655691

1.56793

05

7

0.0655691

1.56793

05

7

0.0659401

1.66204

62

3

0.0662762

1.56415

48

47

0.0666997

1.32173

27

04

0.0666997

1.32173

27

04

ENST00000488229

TCONS_00020502

TCONS_00020502

NR_024529

ENST00000415651

ENST00000415651

ENST00000463969

ENST00000463969

enhancer

upstream

13741

HPGD

NM_000860

down

Neighboring

upstream

64

GTSE1

NM_016426

Neighboring

Neighboring

Neighboring

up

enhancer

up

enhancer

1.68503

06

31

0.0670669

3.66053

49

52

0.0678677

2.85523

53

14

0.0678677

2.85523

53

14

0.0691169

2.81521

4

47

0.0691527

11.5034

42

12

0.0691527

11.5034

42

12

0.0727842

1.78672

05

61

0.0727842

1.78672

05

61

ng

Neighboring

64

GTSE1

NM_016426

0

0

CBY1

CBY1

NM_015373

NM_015373

upstream

5165

HIP1

NM_005338

upstream

5165

HIP1

NM_005338

upstream

1840

TBX2

NM_005994

overlappi

up

0.0669157

ng overlappi

up

31

upstream overlappi

down

1.68503

1.054176

dow

061

3

n

0.799989

1.070383

08

4

0.132972

down

06

NM_000860

down

down

0.0669157

HPGD

0.798586

T

0.0636184

13741

IP

61

AC

ENST00000565575

48

upstream

SC R

ENST00000422408

1.60672

enhancer

NU

ENST00000422408

0.0628367

down

MA

uc011ara.2

61

Neighboring

D

uc011ara.2

48

TE

ENST00000507483

1.60672

up

up

CE P

ENST00000507483

0.0628367

up

up

enhancer

ng

0

WDR11

NM_018117

5207

TIA1

NM_022173

downstrea m

5207

Neighboring

upstream

107

TIA1

NM_022173

SH3GLB 1

NM_016009

SH3GLB upstream

107

1

NM_016009

downstrea up

enhancer

m

41047

GSC

NM_173849

downstrea down

enhancer

m

73485

KITLG

NM_000899

downstrea down

enhancer

m

73485

KITLG

NM_000899

up

Neighboring

upstream

101

RABL2A

NM_013412

downstrea up

enhancer

m

38778

RAB10

NM_016131

downstrea up

enhancer

m

38778

RAB10

NM_016131

downstrea down

enhancer

m

21643

BIRC3

NM_001165

downstrea down

enhancer

m

47

1.62841

n

0.247847

1.374430

dow

822

8

n

0.073457

2.311943

481

8

0.233010

1.450730

923

6

up

265

2.059761

up

0.735130

1.163290

442

5

up

0.000266

4.009655

dow

673

6

n

1.367327

up

up

0.011655

577 0.005291

enhancer

Neighboring

dow

812

0.472329

downstrea m

up

21643

BIRC3

NM_001165

dow

53

2.571834

n

0.564604

1.148166

dow

43

9

n

7.37549E

2.167406

dow

-05

6

n

0.004620

1.763440

dow

613

8

n

0.026784

1.570800

dow

623

2

n

0.439755

1.242000

dow

537

2

n

0.702026

1.157251

dow

128

1

n

0.123840

1.328539

dow

695

1

n

0.469058

1.171725

31

1

0.651121

1.122227

001

7

0.084294

2.340736

699

5

0.270516

1.517405

482

7

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000553944

ENST00000553944

ENST00000530270

ENST00000530270

TCONS_00021922

TCONS_00021922

ENST00000407291

1.78963

26

92

0.0744833

1.54025

48

85

0.0744833

1.54025

48

85

0.0746256

1.47966

69

21

0.0752072

1.51888

58

64

0.0752072

1.51888

58

64

0.0757286

8.80967

45

83

0.0757286

8.80967

45

83

0.0760634

1.66006

71

84

0.0760634

1.66006

71

84

ENST00000585002

NR_026887

ENST00000436855

ENST00000435997

ENST00000435997

ENST00000435879

ENST00000435879

ENST00000573935

enhancer

down

Neighboring

down

Neighboring

Neighboring

Neighboring

up

Neighboring

up

Neighboring

up

up

5.11283 07

0.0771135

5.03183

63

93

0.0771135

5.03183

63

93

0.0777255

1.90777

97

48

0.0779479

2.41409

79

52

0.0782874

1.58083

38

42

0.0782874

1.58083

38

42

0.0792151

1.32046

55

75

0.0792151

1.32046

55

75

0.0796503

1.97243

29

24

ng

upstream

upstream overlappi

down

56

dow

145

311

8

n

NM_001130

0.601049

1.043769

952

5

up

0.001808

2.074556

dow

3

n

61636

YAP1

145

0

SEMA4D

NM_006378

overlappi

down

0.0768757

upstream

YAP1

1.137394

down

down

up

up

up

down

ng

Neighboring

Neighboring

enhancer

enhancer

64

GTSE1

T

0.0738303

down

61636

0.404355

IP

61

AC

ENST00000585002

05

upstream

NM_001130

NM_016426

64

0

GTSE1

CDK6

0.247847

1.374430

dow

NM_016426

822

8

n

NM_001145

0.141225

1.316373

306

557

4

0.167669

1.499588

662

8

0.672502

1.079628

266

4

up

0.239208

1.975850

dow

52

7

n

0.662734

1.259968

NM_014488

329

4

NM_001078

0.458590

1.371997

645

75

8

up

NM_001078

0.511559

1.148942

dow

45

8

n

0.002751

2.041244

dow

31

9

n

0.026408

1.287219

21

2

up

0.274838

1.244492

dow

679

8

n

0.000293

19.55596

dow

964

58

n

0.518889

1.234817

dow

836

4

n

0.021074

1.355585

291

7

0.232082

1.234095

722

9

up

568

2.199184

up

0.052517

1.858319

824

8

up

0.187270

2.120531

dow

596

8

n

ACTN1

NM_001102

upstream

674

ACTN1

NM_001102

upstream

512

RAB30

RAB30

downstrea m

55798

CDC16

downstrea m

NM_014488

55798

CDC16

645

53738

GJA1

NM_000165

downstrea enhancer

enhancer

enhancer

Neighboring

m

upstream

upstream

upstream

24154

24154

332

MAP2K3

MAP2K3

CEBPA

NM_145109

NM_145109

NM_004364

up

enhancer

upstream

18586

TLR4

NM_138554

up

enhancer

upstream

40916

S100A11

NM_005620

up

enhancer

upstream

40916

S100A11

dow n

674

512

0.132972 1.62841

upstream

upstream

989

812

SC R

ENST00000452050

1.78672

enhancer

NU

uc003bho.4

0.0727842

down

MA

uc003bho.4

61

D

ENST00000438325

05

TE

ENST00000463969

1.78672

CE P

ENST00000463969

0.0727842

NM_005620

up

up

up

up

0.034490 up

up

enhancer

enhancer

upstream

upstream

56956

56956

RAP1B

RAP1B

NM_015646

NM_015646

overlappi down

Neighboring

ng

48

0

CARD14

NM_024110

ACCEPTED MANUSCRIPT

TCONS_00004186

ENST00000475089

ENST00000475089

ENST00000393177

ENST00000393177

ENST00000393177

ENST00000393177

2.29303

23

12

0.0809330

2.68766

15

11

0.0811054

1.77033

04

67

0.0816730

1.54454

4

1

0.0816730

1.54454

4

1

0.0822921

1.58468

62

02

0.0822921

1.58468

62

02

0.0834284

1.65088

12

23

0.0834284

1.65088

12

23

0.0834284

1.65088

12

23

ENST00000420409

ENST00000420409

ENST00000420409

NR_026766

NR_026766

ENST00000411586

ENST00000411586

ENST00000551107

down

Neighboring

ng

0

TOM1L1

NM_005486

up

Neighboring

upstream

1230

FBXW7

NM_033632

Neighboring

Neighboring

enhancer

up

enhancer

down

Neighboring

1.51263

59

7

0.0834805

1.51263

59

7

0.0834805

1.51263

59

7

0.0834805

1.51263

59

7

0.0851814

1.78094

59

52

0.0851814

1.78094

59

52

0.0858373

3.45649

12

72

0.0858373

3.45649

12

72

0.0859896

1.84902

35

09

101

0

m

ng

39992

ng

NM_013412

DACH1

NM_004392

AP

NM_018158

SLC4A1

39992

0

overlappi

Neighboring

RABL2A

SLC4A1

overlappi

AP

NM_018158

ARHGEF 5

NM_005435

ARHGEF 0

5

NM_005435

downstrea

down

0.0834805

m downstrea

down

23

ng downstrea

up

1.65088

upstream overlappi

down

12

NM_005486

overlappi

up

0.0834284

TOM1L1

enhancer

down

down

down

up

enhancer

m

upstream

21432

74701

ACTR2

RAB1A

NM_005722

NM_004161

downstrea

enhancer

m

21432

ACTR2

NM_005722

enhancer

upstream

74701

RAB1A

NM_004161

downstrea Neighboring

m

1421

SNRPE

NM_003094

downstrea up

enhancer

m

1421

SNRPE

NM_003094

downstrea up

enhancer

m

1421

SNRPE

NM_003094

downstrea up

Neighboring

up

Neighboring

m

1421

SNRPE

NM_003094

0

MYCN

NM_005378

overlappi ng overlappi up

up

up

Neighboring

enhancer

enhancer

ng

upstream

upstream

0

30463

30463

MYCN

PARP1

PARP1

NM_005378

NM_001618

NM_001618

overlappi down

Neighboring

ng

49

0

CRADD

0.239072

1.294000

dow

098

1

n

0.995922

1.000740

dow

331

5

n

0.004284

2.809073

T

0.0803022

0

IP

44

AC

ENST00000420409

41

ng

SC R

TCONS_00004186

1.25959

Neighboring

NU

ENST00000440551

0.0801074

down

MA

NR_024531

44

D

NR_033797

41

overlappi

TE

ENST00000572088

1.25959

CE P

ENST00000572088

0.0801074

NM_003805

747

9

up

0.123840

1.328539

dow

695

1

n

0.802622

1.344726

677

4

up

0.022546

1.870973

dow

389

6

n

0.687861

1.062139

606

7

0.004146

1.690112

292

4

0.009466

2.320339

704

5

0.005825

2.490778

327

6

0.049976

1.532530

431

2

0.235855

1.716864

573

3

up

0.265477

1.062623

dow

82

6

n

0.424243

1.784367

dow

132

2

n

0.424243

1.784367

dow

132

2

n

0.666444

1.051922

141

3

0.666444

1.051922

141

3

up

0.000615

10.89733

dow

777

81

n

0.540193

1.261414

dow

935

6

n

0.242680

1.418953

dow

341

8

n

0.399226

1.245985

dow

522

5

n

0.004524

1.686237

233

4

up

up

up

up

up

up

up

ACCEPTED MANUSCRIPT

AY927582

AY927582

AY927582

ENST00000433132

ENST00000433132

TCONS_00027385

uc003bnr.1

1.50534

25

1

0.0862127

1.50534

25

1

0.0872647

1.52384

84

2

0.0876425

1.75971

47

14

0.0876425

1.75971

47

14

0.0876425

1.75971

47

14

0.0876425

1.75971

47

14

0.0879156

2.09621

13

32

0.0879156

2.09621

13

32

0.0879188

3.73813

84

62

ENST00000441872

TCONS_00011636

ENST00000437232

NR_038458

ENST00000411449

ENST00000411449

ENST00000436455

ENST00000436455

up

Neighboring

ng

0

PELP1

NM_014389

up

Neighboring

upstream

119

RAB7L1

NM_003929

Neighboring

down

Neighboring

enhancer

down

enhancer

down

enhancer

0.0888282

2.53427

5

8

0.0888282

2.53427

5

8

0.0896632

2.15936

39

08

0.0901809

1.48451

77

98

0.0911367

1.71878

61

55

0.0929943

1.88841

09

3

0.0929943

1.88841

09

3

0.0939770

3.06756

09

14

0.0939770

3.06756

09

14

upstream

119

RAB7L1

0

41396

CDK6

MET

enhancer

enhancer

up

up

up

up

enhancer

9

NM_001145

0.141225

1.316373

306

557

4

0.004961

2.081756

401

9

up

1.238425

up

NM_000245

CAV1

FGR

IFI6

downstrea m

6354

BBC3

Neighboring

upstream

137

RABL2B

enhancer

m

5156

BAG3

enhancer

m

3375

FOXC1

0.771815

1.018521

dow

NM_001753

166

3

n

NM_001042

0.473422

1.322662

747

175

9

up

0.676924

1.039291

dow

NM_002038

183

9

n

NM_001127

0.082149

1.694875

240

206

6

NM_001130

0.865573

1.065539

922

015

3

up

0.272492

1.168618

dow

087

8

n

0.562349

1.260813

935

8

up

0.386484

1.180765

dow

534

8

n

0.119585

1.370159

912

2

up

0.000280

3.345358

dow

535

6

n

0.032348

2.150304

dow

35

4

n

0.806903

1.046200

dow

396

6

n

0.240450

2.100515

774

8

up

0.967820

1.011965

dow

472

8

n

NM_004281

NM_004281

NM_001453

down

Neighboring

upstream

1360

VIM

NM_003380

down

Neighboring

upstream

324

TOB1

NM_005749

downstrea up

enhancer

m

41599

ING1

NM_005537

downstrea up

enhancer

m

41599

ING1

NM_005537

downstrea up

enhancer

m

18717

ETV1

NM_004956

downstrea up

enhancer

m

50

18717

ETV1

dow n

downstrea down

986

1.086228

downstrea up

up

741

downstrea BAG3

up

0.384985

0.502060

downstrea

5156

0.174822

116

NM_000245

m

up

NM_003929

MET

enhancer

enhancer

3

1.227505

41396

16450

039

0.474687

upstream

m

1.078252

n

NM_001753

23178

0.832031

up

dow

CAV1

upstream

8

8

68942

68942

83

1.265564

m

m

1.365797

995

downstrea

up

48

ng

downstrea

down

1.68689

upstream overlappi

up

77

NM_003805

overlappi

up

0.0879550

CRADD

0.008475

T

0.0862127

0

IP

03

AC

ENST00000441872

53

ng

SC R

AY927582

1.44228

Neighboring

NU

ENST00000435695

0.0861021

down

MA

TCONS_00001250

09

D

TCONS_00001250

35

overlappi

TE

ENST00000497885

1.84902

CE P

ENST00000551107

0.0859896

NM_004956

up

ACCEPTED MANUSCRIPT

TCONS_00018594

TCONS_00016098

79

0.0953753

2.36472

96

72

0.0953753

2.36472

96

72

0.0954152

2.55683

03

53

0.0964155

1.85129

7

9

up

Neighboring

0.096777

up

Neighboring

up

Neighboring

down

ng

Neighboring

enhancer

ng

upstream

upstream downstrea

down

enhancer

m

0.096777

63

ENST00000573301

0.096777

63

0.0989944

1.97577

54

09

0.0989944

1.97577

54

09

0.0990051

1.68120

5

09

0.0994211

2.14657

91

27

down

enhancer

down

enhancer

ENST00000566532

ENST00000424933

NR_003930

1.60398

31

22

0.1002650

1.60398

31

22

NR_003930

ENST00000444330

ENST00000444330

ENST00000497954

TCONS_00004377

TCONS_00004377

ENST00000521552

0.1013356

1.38546

74

06

0.1013356

1.38546

74

06

0.1021487

1.75071

8

93

0.1021487

1.75071

8

93

0.1031669

1.88652

22

73

0.1033732

2.41010

77

82

0.1033732

2.41010

77

82

0.1047525

1.76262

07

14

up

0.003859

1.965775

dow

514

3

n

0.341518

2.244439

NM_020341

0

PAK7

NM_020341

700

SLK

225

9

up

0.364348

1.194190

dow

956

1

n

0.742372

1.052010

317

2

up

0.000280

3.345358

dow

NM_005749

535

6

n

NM_001130

0.075070

1.612737

528

018

8

NM_001130

0.431253

1.340764

528

846

6

8.77632E

2.022504

-05

9

0.092458

2.011233

954

5

0.832031

1.078252

039

3

0.038386

1.643122

52

8

up

0.799983

1.136320

dow

489

2

n

0.942516

1.029395

dow

859

9

n

0.132982

1.765005

659

9

up

0.617486

1.183261

dow

174

3

n

0.061521

1.241273

dow

512

7

n

1.05542

up

NM_014720

19554

43282

NR4A3

TOB1

51941

SPAG9

upstream

51941

SPAG9

NM_006981

Neighboring

ng

0

EGFR

NM_005228

overlappi

Neighboring

D

down

0.1002650

AC

ENST00000424933

down

TE

ENST00000466297

3

overlappi

up

up

CE P

NR_047551

015

PAK7

upstream

MA

1.86238

NR_047551

922

0

NU

1.86238 ENST00000573301

RABL2B

1.065539

overlappi

up

63

0

0.865573

overlappi

1.86238 ENST00000573301

ng

NM_001130

T

ENST00000428769

8

overlappi

IP

ENST00000428769

4.92070

SC R

ENST00000467796

0.0950644

down

down

Neighboring

ng

0

EGFR

NM_005228

downstrea m

478

PELP1

NM_014389

downstrea

enhancer

m

5092

TOP3A

NM_004618

enhancer

upstream

27938

CRYAA

NM_000394

enhancer

upstream

27938

CRYAA

NM_000394

downstrea up

enhancer

m

34977

SVIL

NM_021738

downstrea up

enhancer

m

34977

SVIL

NM_021738

downstrea down

enhancer

down

enhancer

m

64228

FH

NM_000143

64228

FH

NM_000143

downstrea m

Neighboring

ng

enhancer

m

0

BRCA1

NM_007294

79170

EDAR

NM_022336

downstrea up

enhancer

m

79170

EDAR

NM_022336

downstrea down

enhancer

m

51

021 0.075283

downstrea up

up

up

up

up

0.821458

overlappi up

up

61448

BNIP1

NM_001205

dow

263

3.046271

n

0.025372

2.214844

111

6

up

0.180643

1.680603

dow

712

7

n

0.127873

1.353498

567

9

up

ACCEPTED MANUSCRIPT

NR_046648

ENST00000452014

NR_034151

NR_034151

ENST00000440142

ENST00000440142

ENST00000442409

1.63567

16

47

0.1054438

1.90494

34

96

0.1057621

3.71515

49

97

0.1057621

3.71515

49

97

0.1060704

3.90113

6

94

0.1072506

1.68215

83

5

0.1078701

1.78508

1

17

0.1078701

1.78508

1

17

0.1130274

3.08957

67

75

0.1130274

3.08957

67

75

ENST00000493479

ENST00000514414

ENST00000514414

ENST00000514414

ENST00000514414

ENST00000473094

ENST00000473094

ENST00000534518

up

enhancer

upstream

8191

SS18

up

enhancer

upstream

8191

SS18

enhancer

enhancer

Neighboring

down

Neighboring

up

enhancer

1.18401

31

33

0.1142239

1.62383

44

43

0.1144173

1.27631

22

44

0.1144173

1.27631

22

44

0.1144173

1.27631

22

44

0.1144173

1.27631

22

44

0.1148052

1.78499

79

46

0.1148052

1.78499

79

46

0.1152903

16.8298

73

79

891

8

NM_001007

0.026442

1.828679

559

911

4

up

NM_001007

0.294842

559

64288

ng

8

NM_015444

1586

1586

TYRO3

TYRO3

NM_006293

NM_006293

0

HLTF

NM_003071

110581

POU4F1

NM_006237

downstrea

up

0.1131142

m overlappi

up

33

m downstrea

up

1.18401

upstream downstrea

up

31

NM_001205

TMEM15 up

0.1131142

BNIP1

up

up

down

down

m

Neighboring

Neighboring

enhancer

enhancer

upstream

upstream

210

210

BTG2

BTG2

NM_006763

NM_006763

downstrea m

6819

KISS1

NM_002256

downstrea m

6819

KISS1

NM_002256

61115

SFPQ

NM_005066

downstrea enhancer

m downstrea

enhancer

m

61115

SFPQ

NM_005066

downstrea up

down

enhancer

enhancer

down

enhancer

down

enhancer

m

upstream

upstream

16243

10364

FBXW7

CXCL2

NM_033632

NM_002089

10364

CXCL2

NM_002089

47221

CXCL3

NM_002090

downstrea m downstrea down

enhancer

m

47221

CXCL3

NM_002090

downstrea down

enhancer

m

138054

PMAIP1

NM_021127

downstrea down

enhancer

m

138054

PMAIP1

NM_021127

downstrea up

enhancer

m

52

up

1.336477

dow

112

4

n

0.268195

1.544453

172

6

T

0.1047821

61448

1.810151

IP

47

AC

ENST00000442409

16

m

0.165741

SC R

ENST00000566760

1.63567

enhancer

NU

ENST00000566760

0.1047821

down

MA

ENST00000431490

14

D

ENST00000468051

07

downstrea

TE

ENST00000468051

1.76262

CE P

ENST00000521552

0.1047525

0.329729 295

up dow

1.630923

0.329729

n dow

295

1.630923

n

0.016321

4.498851

dow

354

6

n

0.446366

1.109011

dow

3

9

n

0.030569

3.416195

33

5

0.158242

1.504651

453

6

up

0.109121

2.434699

dow

736

5

n

0.648211

1.234034

dow

001

6

n

0.043928

1.439463

dow

495

7

n

0.177732

1.207910

088

9

0.004284

2.809073

747

9

0.000317

4.896629

548

5

0.054757

3.209357

574

7

0.114833

1.312362

875

1

up

0.538480

1.162757

dow

714

2

n

0.002638

2.554357

487

4

0.008034

1.764963

348

4

up

2.508115

up

up

up

up

up

up

up

0.002420 7982

PAK1

NM_002576

366

ACCEPTED MANUSCRIPT

ENST00000473109

TCONS_00011805

TCONS_00011805

ENST00000434255

73

79

0.1155634

1.58985

23

09

0.1158944

1.75170

59

81

0.1158944

1.75170

59

81

0.1161156

2.94876

77

2

0.1161156

2.94876

77

2

0.1164062

3.58021

7

84

down

enhancer

61

2.55415

up

Neighboring

0.1167351

1.33238

28

21

0.1167351

1.33238

28

21

0.1167351

1.33238

28

21

0.1167351

1.33238

28

21

up

enhancer

TCONS_00029913

TCONS_00029913

ENST00000486628

79

77

AC

ENST00000486628

1.45575

ENST00000415794

ENST00000563192

ENST00000563192

ENST00000563192

ENST00000441399

ENST00000441399

ENST00000424509

ENST00000424509

0.1177695

1.38423

3

26

0.1178067

1.85769

53

82

0.1178067

1.85769

53

82

0.1178067

1.85769

53

82

0.1183374

1.70823

09

89

0.1183374

1.70823

09

89

0.1201455

1.74538

29

11

0.1201455

1.74538

29

11

0.226162

1.591247

dow

935

6

n

1.395663

up

193

1.043051

up

0.312202

1.162176

dow

424

7

n

0.725168

1.061011

405

8

up

0.275011

2.166717

dow

322

4

n

0.404299

1.210801

269

3

0.148121

1.295808

499

8

0.148121

1.295808

499

8

up

0.609892

1.139701

dow

493

1

n

0.609892

1.139701

dow

493

1

n

211

1.065241

up

0.985024

1.003946

dow

NM_024835

222

4

n

NM_001130

0.827046

1.054677

992

673

7

up

0.022341

1.730917

dow

146

7

n

0.769107

1.101316

171

3

0.916637

1.028306

439

9

0.487015

1.402799

128

3

up

0.844148

1.038380

dow

429

7

n

0.078142

2.031346

dow

825

7

n

0.078142

2.031346

dow

825

7

n

up

enhancer

upstream

23399

DDB2

NM_000107

enhancer

upstream downstrea

enhancer

m downstrea

enhancer

m

23399

DDB2

T

0.250158

NM_000107

17407

17407

GLO1

GLO1

NM_006708

NM_006708

40823

MYB

NM_005375

upstream

944

EPAS1

NM_001430

MA

upstream

downstrea

enhancer

m

2492

XRCC6

NM_001469

downstrea

Neighboring

D

down

0.1170341

NM_001042 492

down

77

up

NF1

down

1.45575

9

1799

down

79

853

m

up

0.1170341

NM_002576

Neighboring

TE

TCONS_00029913

PAK1

4.202081

down

down

down

CE P

TCONS_00029913

7982

downstrea

0.1166338 TCONS_00004241

m

0.004924

IP

ENST00000473109

downstrea

SC R

ENST00000580053

16.8298

NU

ENST00000534518

0.1152903

down

down

enhancer

Neighboring

m

2492

XRCC6

downstrea m

2492

XRCC6

down

NM_001469

downstrea m

2492

XRCC6

NM_001469

0

GGNBP2

NM_024835

overlappi Neighboring

ng overlappi

Neighboring

ng

enhancer

Neighboring

m

upstream

0

GGNBP2

31467

439

RBP1

TRAF7

NM_032271

downstrea down

Neighboring

m

656

RAB26

NM_014353

down

Neighboring

upstream

439

TRAF7

NM_032271

up

up

down

down

Neighboring

Neighboring

enhancer

Neighboring

upstream

upstream

upstream

upstream

53

0.855353

up

up

0.725144

downstrea up

NM_001469

286

345

345

2659

2659

RAP2C

RAP2C

NEIL2

NEIL2

NM_021183

NM_021183

NM_145043

NM_145043

up

up

ACCEPTED MANUSCRIPT

NR_002330

NR_002330

ENST00000424191

uc001lwe.3

uc001lwe.3

TCONS_00002568

ENST00000420788

3.08536

22

62

0.1210060

3.08536

22

62

0.1210060

3.08536

22

62

0.1210060

3.08536

22

62

0.1220853

3.34741

65

81

0.1220853

3.34741

65

81

0.1221009

1.21528

17

71

0.1234068

1.50453

47

77

0.1234068

1.50453

47

77

0.1242975

2.76766

3

54

ENST00000443579

ENST00000534499

ENST00000534499

NR_038269

NR_038269

NR_026932

NR_026932

TCONS_00028455

enhancer

down

Neighboring

enhancer

enhancer

4.32670

77

38

0.1255997

2.23608

2

43

0.1257853

1.58718

54

9

0.1257853

1.58718

54

9

0.1271829

1.70630

52

38

0.1271829

1.70630

52

38

0.1284225

1.73466

37

02

0.1284225

1.73466

37

02

0.1307961

2.42566

04

03

m

Neighboring

m overlappi

up

Neighboring

up

Neighboring

NEIL2

NM_145043

2818

S100P

NM_005980

2818

ng

S100P

NM_005980

2818

2818

S100P

S100P

NM_005980

NM_005980

0

ST7

NM_021908

0

ST7

NM_021908

overlappi ng

Neighboring

upstream

239

ZEB1

NM_030751

overlappi

up

0.1252534

m

downstrea

down

38

m

downstrea

down

4.32670

2659

downstrea

down

77

NM_145043

downstrea

down

0.1252534

upstream

NEIL2

Neighboring

up

down

up

up

up

up

Neighboring

ng

0

CD81

NM_004356

overlappi ng

0

CD81

NM_004356

enhancer

upstream

5903

IL24

NM_006850

enhancer

upstream

51046

MSH6

NM_000179

enhancer

enhancer

Neighboring

upstream

upstream

upstream

51046

35637

279

up

Neighboring

upstream

279

up

enhancer

upstream

5497

MSH6

WASF2

RAB30

RAB30

NM_000179

NM_006990

NM_014488

NM_014488

XRCC6B P1

NM_033276

XRCC6B up

up

up

up

enhancer

Neighboring

Neighboring

enhancer

upstream

upstream

upstream

upstream

54

5497

890

890

137594

0.894301

1.052392

765

4

0.894301

1.052392

765

4

0.031984

1.370795

T

0.1210060

down

2659

IP

11

AC

ENST00000420788

29

upstream

SC R

TCONS_00007971

1.74538

Neighboring

NU

TCONS_00007971

0.1201455

down

MA

TCONS_00007971

11

D

TCONS_00007971

29

TE

ENST00000424509

1.74538

CE P

ENST00000424509

0.1201455

P1

PDCD4

PDCD4

RAB22A

NM_033276

NM_014456

NM_014456

NM_020673

up

up

083

7

up

0.031984

1.370795

083

7

0.076893

3.317500

826

7

0.076893

3.317500

826

7

0.077837

2.687264

951

8

0.979963

1.009919

347

5

0.275786

2.274973

883

3

up

0.031376

1.714055

dow

045

4

n

0.218691

1.292565

dow

045

1

n

0.270241

1.221267

dow

94

1

n

0.113533

2.347306

dow

287

1

n

0.505597

1.300861

dow

797

3

n

0.356864

1.227667

593

8

up

0.239208

1.975850

dow

52

7

n

0.662734

1.259968

329

4

up

0.133044

1.416093

dow

571

9

n

0.165314

1.368836

dow

639

9

n

0.131988

2.644989

105

4

0.848332

1.056179

765

9

up

0.150769

1.582905

dow

307

3

n

up

up

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000415194

ENST00000415194

ENST00000423783

ENST00000423783

ENST00000440726

ENST00000450669

ENST00000450669

1.71840

53

83

0.1333893

1.77111

65

94

0.1350828

2.13333

81

53

0.1350828

2.13333

81

53

0.1358470

1.73764

07

91

0.1358470

1.73764

07

91

0.1358773

9.19850

82

98

0.1358773

9.19850

82

98

0.1362209

1.56376

8

41

0.1363224

1.45147

4

52

ENST00000469484

ENST00000524963

ENST00000524963

TCONS_00027580

TCONS_00027580

ENST00000509498

ENST00000509498

ENST00000581080

Neighboring

upstream

81

RASSF4

NM_032023

down

Neighboring

upstream

81

RASSF4

NM_032023

overlappi Neighboring

enhancer

enhancer

down

Neighboring

down

Neighboring

2.89109

96

25

0.1377318

1.46813

98

61

0.1378207

1.79463

88

79

0.1378207

1.79463

88

79

0.1390236

1.73308

3

84

0.1390236

1.73308

3

84

0.1399397

2.07604

22

63

0.1399397

2.07604

22

63

0.1411996

1.32097

6

62

0

ng

UVRAG

44209

44209

CRADD

CRADD

up

down

down

up

up

up

ng

enhancer

enhancer

enhancer

upstream

upstream

233

4

0.008475

1.365797

83

8

up

824

1.331219

up

0.367610

1.110857

dow

98

5

n

0.036544

1.441360

595

8

up

0.922260

1.025355

dow

337

8

n

0.180794

1.976398

dow

656

4

n

0.009356

2.443296

327

2

0.378139

1.372709

836

9

up

0.014500

1.818404

dow

133

8

n

0.472266

1.258015

dow

868

1

n

0.060634

1.808970

dow

611

7

n

0.469522

1.158655

dow

413

5

n

0.401360

1.333358

745

8

0.401360

1.333358

745

8

0.134408

1.969617

366

2

0.428522

1.351177

NM_005130

174

7

NM_001145

0.670882

1.203022

301

964

9

NM_003805

NM_003805

NM_144997

NM_144997

NM_001048

BTRC

NM_033637

enhancer

upstream

31026

BTRC

NM_033637

overlappi

Neighboring

enhancer

up

enhancer

down

Neighboring

upstream

upstream

upstream

56

74950

RBL1

WNT5A

PTPRJ

NM_002895

NM_003392

NM_002843

74950

PTPRJ

NM_002843

1071

BCL3

NM_005178

downstrea m downstrea down

down

down

enhancer

enhancer

enhancer

m

upstream

upstream

1071

69629

69629

BCL3

FGFBP1

FGFBP1

overlappi up

Neighboring

ng

55

0

RARA

0.322469

1.686237

31026

0

n

0.004524

upstream

ng

7

7

enhancer

Neighboring

312

236

NM_003369

NM_016217

SST

dow

1.242833

HECA

219455

1.617640

0.528658

downstrea m

0.143413

n

0

FLCN

up

dow

NM_016217

4821

8

3

HECA

FLCN

621

1.180449

0

4821

1.028891

545

overlappi

up

0.1363781

m overlappi

up

52

m downstrea

down

1.45147

ng downstrea

down

4

NM_020673

down

up

0.1363224

RAB22A

0.880000

T

0.1321378

137594

IP

83

AC

ENST00000453803

53

upstream

SC R

ENST00000550687

1.71840

enhancer

NU

ENST00000550687

0.1321378

up

MA

ENST00000529719

03

D

ENST00000450287

04

TE

ENST00000450287

2.42566

CE P

TCONS_00028455

0.1307961

NM_005178

NM_005130

up

up

0.024995

up

up

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000462305

ENST00000420452

ENST00000420452

ENST00000567108

ENST00000567108

ENST00000456356

ENST00000433761

uc003yrb.3

2.06929

17

24

0.1436476

1.49055

75

03

0.1445608

2.27067

42

45

0.1452243

1.44262

79

19

0.1452243

1.44262

79

19

0.1452941

1.95514

88

04

0.1452941

1.95514

88

04

0.1464698

1.44631

61

67

0.1464698

1.44631

61

67

0.1465040

1.75955

21

84

NR_033341

NR_033886

NR_033886

ENST00000469948

NR_038873

NR_038873

ENST00000400056

down

Neighboring

down

Neighboring

enhancer

1.97711

27

26

0.1477896

1.97711

27

26

0.1478396

1.43015

58

02

0.1495339

1.49874

38

3

0.1495339

1.49874

38

3

0.1510700

2.24774

13

13

0.1527727

1.67678

81

74

0.1527727

1.67678

81

74

0.1571273

1.44417

88

64

upstream

Neighboring

ng

Neighboring

ng overlappi

down

Neighboring

up

Neighboring

036

2

n

0.269249

2.138634

365

5

0.355992

1.507999

0

CCND2

NM_001759

0

CCND2

NM_001759

304

1

up

NM_001122

0.452464

1.177579

dow

821

664

4

n

0.277805

1.829750

373

4

0.004146

1.690112

292

4

0.009466

2.320339

704

5

up

0.000615

10.89733

dow

777

81

n

0.540193

1.261414

dow

935

6

n

0.244032

1.271861

dow

335

7

n

0.952662

1.027694

79

8

up

0.026122

2.475606

dow

351

3

n

0.034247

4.293003

475

7

up

0.396740

1.148727

dow

741

1

n

0.544210

1.158095

dow

165

8

n

0.007752

2.095074

dow

54

6

n

0.029016

1.613154

dow

815

1

n

0.213683

1.226131

dow

863

8

n

0.002916

6.898194

07

5

0.000326

3.338442

186

1

0.055396

1.646470

078

1

20076

ng

SET

0

NR4A1

NM_002135

ARHGEF

0

5

NM_005435

ARHGEF

0

5

NM_005435

0

MYCN

NM_005378

overlappi ng

overlappi

Neighboring

ng

0

MYCN

NM_005378

overlappi

down

0.1477896

ng

overlappi

up

22

ng

overlappi

down

2.62439

301

overlappi

down

14

dow

overlappi

up

0.1473624

RARA

1.000360

T

0.1418975

0

0.998934

IP

24

AC

uc003yrb.3

17

ng

NM_001145

SC R

ENST00000462305

2.06929

Neighboring

NU

ENST00000564531

0.1418975

up

MA

ENST00000428643

62

Neighboring

D

ENST00000537370

6

overlappi

TE

ENST00000537370

1.32097

down

up

CE P

ENST00000581080

0.1411996

up

down

down

Neighboring

Neighboring

ng

0

KDM8

NM_024773

overlappi ng

0

KDM8

NM_024773

overlappi ng

0

SAPCD2

NM_178448

20062

RIPK1

NM_003804

downstrea enhancer

Neighboring

Neighboring

m

upstream

upstream

203

203

RNF139

RNF139

NM_007218

NM_007218

overlappi down

Neighboring

ng

0

ZNF224

NM_013398

overlappi down

Neighboring

down

Neighboring

ng

0

RAD21

NM_006265

0

RAD21

NM_006265

overlappi

up

enhancer

ng

upstream

4428

overlappi up

Neighboring

ng

Neighboring

ng

NM_001964

TNFRSF 0

overlappi up

EGR1

10B

NM_003842

TNFRSF 0

10B

NM_003842

0.457271 down

Neighboring

upstream

56

1557

XPA

NM_000380

569

up

up

up

up

up

up dow

1.05824

n

ACCEPTED MANUSCRIPT

ENST00000512850

NR_027103

ENST00000418672

ENST00000418672

ENST00000567829

ENST00000567829

ENST00000534168

1.51490

97

34

0.1604803

1.32718

1

35

0.1631817

2.00331

49

55

0.1640836

1.32664

96

97

0.1640836

1.32664

96

97

0.1650151

1.99810

79

83

0.1678379

1.62994

87

22

0.1678379

1.62994

87

22

0.1681377

1.56361

37

04

0.1681377

1.56361

37

04

ENST00000514593

ENST00000395664

ENST00000395664

uc010tfr.2

uc010tfr.2

TCONS_00001037

ENST00000416241

ENST00000416241

enhancer

upstream

43271

FXYD5

NM_144779

down

enhancer

upstream

43271

FXYD5

NM_144779

enhancer

enhancer

enhancer

down

enhancer

up

enhancer

1.79195

68

31

0.1699722

1.79195

68

31

0.1702742

1.78048

35

85

0.1702742

1.78048

35

85

0.1707223

1.40926

66

4

0.1707223

1.40926

66

4

0.1714866

2.85372

92

72

0.1727400

1.31713

36

29

0.1727400

1.31713

36

29

9593

m

MAP2K4

NM_003010

16966

181556

FGFR2

EFNA5

NM_000141

NM_001962

181556

EFNA5

NM_001962

71949

WNT7A

NM_004625

downstrea m

downstrea

enhancer

m

80517

ETV1

NM_004956

downstrea

up

0.1699722

m downstrea

up

61

m downstrea

down

1.67657

upstream downstrea

down

84

NM_000380

down

down

0.1698035

XPA

enhancer

up

up

down

down

Neighboring

Neighboring

m

80517

ETV1

NM_004956

overlappi ng

0

UBE2I

NM_194259

overlappi ng

0

UBE2I

NM_194259

0

GAB2

NM_080491

overlappi Neighboring

ng downstrea

enhancer

m

20870

DEFB1

NM_005218

downstrea down

up

enhancer

enhancer

m

upstream

20870

10286

DEFB1

DDX3X

NM_005218

NM_001356

up

enhancer

upstream

10286

DDX3X

NM_001356

down

Neighboring

upstream

182

TPT1

NM_003295

down

up

down

down

Neighboring

Neighboring

enhancer

enhancer

upstream

upstream

upstream

upstream

57

182

194

107548

107548

TPT1

F3

GNAS

GNAS

NM_003295

NM_001993

NM_000516

NM_000516

dow

569

1.05824

n

0.377344

1.105988

dow

781

2

n

0.958756

1.013481

T

0.1599149

1557

IP

34

AC

ENST00000514593

97

upstream

SC R

ENST00000512850

1.51490

enhancer

NU

ENST00000434988

0.1599149

down

MA

ENST00000460347

64

D

TCONS_00027004

88

0.457271

TE

TCONS_00027004

1.44417

CE P

ENST00000400056

0.1571273

516

8

up

0.246949

1.527790

dow

901

9

n

0.981361

1.007540

957

7

up

0.007285

3.493195

dow

942

5

n

0.671920

1.439986

073

5

up

0.890980

1.025130

dow

185

9

n

0.240450

2.100515

774

8

up

0.967820

1.011965

dow

472

8

n

0.056517

2.230281

921

3

0.833542

1.037815

555

5

0.000911

2.201538

773

8

0.006759

13.45544

581

72

0.022072

3.993339

147

4

up

0.023856

2.320093

dow

993

1

n

0.660393

1.170304

dow

661

9

n

0.035951

1.803423

503

9

0.088486

1.397619

28

8

0.167732

1.629966

273

2

0.543239

1.137375

471

3

up

0.945428

1.012160

dow

769

9

n

up

up

up

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000493920

ENST00000493920

ENST00000493920

ENST00000393668

uc002jtz.3

ENST00000566875

uc003fdu.3

1.34015

17

4

0.1737642

1.34015

17

4

0.1764965

3.49673

5

63

0.1765827

3.89705

09

19

0.1765827

3.89705

09

19

0.1765827

3.89705

09

19

0.1765827

3.89705

09

19

0.1778419

1.64756

26

91

0.1779662

1.64418

72

54

0.1790996

3.86216

11

47

ENST00000553961

ENST00000553832

overlappi down

Neighboring

up

Neighboring

1.75724

24

49

0.1800881

1.75724

24

49

Neighboring

Neighboring

up

enhancer

up

enhancer

NR_033868

NR_033868

ENST00000559821

ENST00000559821

ENST00000406301

0.1813096

69

0.1823337

1.56629

57

17

0.1823337

1.56629

57

17

0.1831358

2.79563

82

51

0.1831358

2.79563

82

51

0.1841743

1.48519

58

66

NM_001014

0.092416

1.947294

71

7

0.019800

1.468896

ILK

795

0

MAP2K1

NM_002755

ng

m

0

m

MAP2K1

NM_002755

0

1413

TP63

RINT1

NM_003722

NM_021930

1413

RINT1

NM_021930

m

1413

RINT1

NM_021930

downstrea

Neighboring

enhancer

up

up

down

up

up

enhancer

m

upstream

upstream

1413

RINT1

NM_021930

35974

27528

PHOX2A

SEPT9

0.012551

1.450987

dow

499

9

n

0.027570 654

dow 1.883396

0.027570

dow

654

1.883396

0.790821

1.072945

939

5

0.790821

1.072945

939

5

315

315

ACTN1

ACTN1

0

MNAT1

Neighboring

ng

0

MNAT1

down

enhancer

upstream

42585

API5

dow

175

1.218611

up

0.740696

1.152833

296

1

0.167669

1.499588

662

8

0.672502

1.079628

266

4

0.142740

2.721659

554

9

0.547130

1.170222

NM_002431

152

1

up

NM_001142

0.369788

1.236647

dow

930

481

9

n

NM_001142

0.647933

1.124326

dow

930

478

3

n

NM_001102

NM_001102

NM_002431

42585

API5

0.010408

down

enhancer

upstream

8353

8353

CA12

CA12

NM_001218

NM_001218

downstrea down

enhancer

m

58

up

n

NM_139245

upstream

up

2

PPM1L

enhancer

n

0.298289

down

down

n

25

3623

upstream

n

491

upstream

enhancer

9

dow

overlappi

down

619

2.894038

enhancer

ng

dow

0.045470

NM_015322

Neighboring

1.126218

NM_001113

overlappi down

0.510111

n

FEM1B

upstream

up

1.592249

22902

Neighboring

5

801

downstrea

upstream

up

NM_005169

m

Neighboring

up

603

0.547196

enhancer

2.39747 ENST00000553832

7

downstrea

2.39747 69

ng

downstrea

up

0.1800881

0.1813096

Neighboring

downstrea

up

35

ng

overlappi

up

1.75712

514

0

overlappi

up

56

ng

NM_014572

overlappi

up

0.1792314

LATS2

T

0.1737642

10841

1.365930

IP

06

AC

ENST00000553961

98

m

0.047032

SC R

ENST00000493920

1.70325

enhancer

NU

ENST00000427601

0.1732255

up

MA

ENST00000469688

87

D

ENST00000469688

67

downstrea

TE

ENST00000527398

4.72847

CE P

ENST00000454001

0.1729693

1927

RBM3

NM_006743

up

up

up

up

dow

061

2.567952

n

0.023905

2.174046

dow

572

8

n

0.002192

2.741097

595

7

up

ACCEPTED MANUSCRIPT

ENST00000429630

ENST00000434779

ENST00000568106

ENST00000568106

ENST00000472730

ENST00000453860

0.1841743

1.48519

58

66

0.1856259

1.27204

06

18

0.1856259

1.27204

06

18

0.1859703

1.29384

86

12

0.1873030

1.95552

85

65

0.1877919

2.35835

48

8

0.1877919

2.35835

48

8

0.1914834

1.86028

03

81

0.1919789

1.51481

77

12

0.1921741

2.19877

08

74

NR_024009

down

Neighboring

down

enhancer

ENST00000506340

ENST00000506340

NR_028370

NR_028370

NR_046374

NR_046374

ENST00000520023

ENST00000503504

Neighboring

Neighboring

down

Neighboring

up

Neighboring

1.81193

76

57

0.1934058

1.34408

73

08

0.1934058

1.34408

73

08

0.1944991

1.31369

67

01

0.1944991

1.31369

67

01

0.1947491

1.29379

25

23

0.1947491

1.29379

25

23

0.1950738

2.36259

15

85

0.1962256

1.15393

6

21

ng

ng

upstream

ng

ng

ng

down

up

down

down

down

down

enhancer

ng

upstream

dow

178

5

n

0.948778

1.012409

dow

178

5

n

NM_001010

0.251449

1.288408

dow

935

236

7

n

NM_001010

0.418310

1.419594

935

479

8

up

0.030459

2.856731

dow

NM_003461

467

3

n

NM_001033

0.048676

1.356781

dow

147

6

n

0.056517

2.230281

921

3

0.833542

1.037815

555

5

0.500420

1.313293

59

5

0.483635

1.152738

909

1

up

0.109926

1.905422

dow

005

8

n

0

RAP1A

0

771

RAP1A

ZYX

0

MTUS2

602

0

UBE2I

NM_194259

0

UBE2I

NM_194259

0

147020

PTPRG

CSF3R

NM_002841

NM_000760

43609

XRCC2

NM_005431

Neighboring

upstream

80

GTSE1

NM_016426

0.132972

Neighboring

Neighboring

Neighboring

down

Neighboring

upstream

upstream

upstream

80

2618

2618

GTSE1

GNB2L1

GNB2L1

NM_016426

NM_006098

NM_006098

ng

ng

ng

Neighboring

Neighboring

ng

upstream

upstream

59

up

dow

812

1.62841

n

0.247847

1.374430

dow

822

8

n

0.451332

1.127489

786

7

up

0.725742

1.060917

dow

271

4

n

0.200620

1.517417

dow

515

6

n

NM_002592

0.393709

1.546439

dow

0

PCNA

NM_002592

596

7

n

ENST00000

0.255327

1.340035

dow

436272

793

1

n

ENST00000

0.434203

1.172122

436272

255

1

up

0.675957

1.275291

dow

874

3

n

0.014113

3.392829

dow

158

9

n

0

MRVI1

overlappi Neighboring

up

PCNA

overlappi Neighboring

up

0

overlappi

down

1.012409

NM_006743

upstream

Neighboring

down

0.948778

RBM3

enhancer

down

down

up

1927

overlappi

down

7

NM_006743

overlappi

Neighboring

595

RBM3

overlappi

Neighboring

2.741097

1927

overlappi

up

0.1922508

AC

NR_024009

Neighboring

overlappi

up

57

m

overlappi

down

1.81193

m

overlappi

down

76

NM_006743

downstrea

down

0.1922508

RBM3

0.002192

T

66

1927

IP

58

m downstrea

CE P

ENST00000451203

1.48519

Neighboring

SC R

ENST00000443599

0.1841743

down

NU

ENST00000443599

66

MA

ENST00000406301

58

downstrea

D

ENST00000406301

1.48519

TE

ENST00000406301

0.1841743

0

171

244

MRVI1

EXTL3

CCNG1

NM_001440

NM_004060

ACCEPTED MANUSCRIPT

NR_034150

ENST00000422415

ENST00000422415

NR_002786

NR_045406

NR_045406

ENST00000477729

1.59526

97

01

0.2013364

1.67618

43

84

0.2013364

1.67618

43

84

0.2015222

2.27296

06

81

0.2015222

2.27296

06

81

0.2018929

1.21005

13

47

0.2018929

1.21005

13

47

0.2019416

1.26889

7

49

0.2030989

1.59318

24

11

0.2030989

1.59318

24

11

ENST00000573346

ENST00000512859

ENST00000486386

ENST00000486386

NR_002733

ENST00000422303

ENST00000422303

ENST00000477514

up

Neighboring

down

Neighboring

Neighboring

Neighboring

Neighboring

down

Neighboring

up

enhancer

1.33987

46

42

0.2056028

1.72264

17

5

0.2059896

2.11328

22

9

0.2066812

4.73037

86

24

0.2066812

4.73037

86

24

0.2072443

1.80078

03

84

0.2085580

1.22892

71

94

0.2085580

1.22892

71

94

0.2087596

1.76003

19

3

ERCC4

NM_005236

0

TNFSF10

NM_003810

ng

ng

upstream

0

upstream

DDB2

NM_000107

0

210

DDB2

BTG2

NM_000107

NM_006763

210

BTG2

NM_006763

50041

MYCN

NM_005378

downstrea m

downstrea

down

0.2051889

ng

overlappi

up

42

0

overlappi

down

1.33987

ng overlappi

up

46

NM_005236

overlappi

up

0.2051889

ERCC4

enhancer

Neighboring

up

up

down

down

Neighboring

m

upstream

50041

MYCN

292

FANCD2

NM_033084

0

HIF1A

NM_001530

overlappi 0

HIF1A

enhancer

upstream

6476

ANXA2

up

Neighboring

enhancer

ng

upstream

enhancer

up

enhancer

m

down

enhancer

upstream

Neighboring

ng

up

Neighboring

Neighboring

ng

upstream

60

1.292456

325

5

0.865254

1.134133

859

6476

ANXA2

0

100347

CARD14

SSBP2

up

6

up

1.395663

up

193

1.043051

up

0.030569

3.416195

33

5

0.158242

1.504651

453

6

up

0.000615

10.89733

dow

777

81

n

0.540193

1.261414

dow

935

6

n

0.250158 286 0.855353

up

dow

543

1.866954

n

0.005916

2.642722

dow

259

5

n dow

NM_001136

0.042010

1.616466

dow

015

019

6

n

NM_001136

0.981640

1.003338

015

27

3

up

0.187270

2.120531

dow

596

8

n

0.922904

1.029675

dow

292

6

n

0.212356

1.607061

57

3

up

NM_024110

NM_012446

13877

BCL2L10

NM_020396

0.619623

1.153773

dow

13877

BCL2L10

NM_020396

857

7

n

NM_001195

0.091740

2.203021

226

193

5

0.000864

3.038371

676

1

up

0.005465

1.846814

dow

508

8

n

0.001125

2.683909

dow

726

1

n

34046

PRODH

0

TSC22D1

NM_183422

overlappi down

0.687064

n

overlappi down

n

2.473546

downstrea m

6

85

downstrea up

571

NM_001530

overlappi down

dow

0.009359

ng

upstream

1.299885

0.013485

Neighboring

enhancer

NM_005378

overlappi ng

0.372673

T

0.1973569

0

IP

61

AC

ENST00000477729

16

ng

SC R

NR_034150

1.97865

Neighboring

NU

ENST00000540410

0.1969379

up

MA

ENST00000540410

61

D

ENST00000429380

16

overlappi

TE

ENST00000463867

1.97865

CE P

ENST00000463867

0.1969379

0

901

TSC22D1

RBMS1

NM_183422

NM_016836

up

ACCEPTED MANUSCRIPT

ENST00000498563

ENST00000479588

ENST00000458417

ENST00000439180

ENST00000439180

ENST00000475212

ENST00000475212

1.57101

69

48

0.2094336

1.57101

69

48

0.2094336

1.57101

69

48

0.2095188

1.20932

33

57

0.2095188

1.20932

33

57

0.2110642

2.28877

47

74

0.2117481

1.98502

29

56

0.2135393

1.44235

33

4

0.2135393

1.44235

33

4

0.2136024

1.39677

4

84

ENST00000414870

ENST00000414870

ENST00000413110

ENST00000541494

ENST00000541494

ENST00000430654

TCONS_00006841

ENST00000576084

up

Neighboring

upstream

2107

BLCAP

up

enhancer

upstream

2107

BLCAP

up

up

down

enhancer

Neighboring

enhancer

down

enhancer

up

Neighboring

1.39677 84

0.2137752

1.30352

76

77

0.2151386

1.80898

38

36

0.2151386

1.80898

38

36

0.2158772

2.35139

28

87

0.2159264

2.61553

99

73

0.2159264

2.61553

99

73

0.2211645

1.58522

24

34

0.2218291

1.92264

15

93

0.2224082

2.04780

49

96

upstream

upstream

2107

upstream

BLCAP

575

2

n

NM_001167

0.198429

820

244

NM_001167

0.198429

2107

41161

BLCAP

PPP2CA

ng

enhancer

upstream

Neighboring

down

up

up

down

up

up

Neighboring

ng

0.249960

1.600060

820

719

6

NM_001167

0.249960

1.600060

820

719

6

up

0.438787

1.269949

dow

949

9

n

0.981729

1.002708

dow

802

8

n

0.500420

1.313293

59

5

up

0.120773

2.031873

dow

916

8

n

0.000615

10.89733

dow

777

81

n

0.540193

1.261414

dow

935

6

n

0.147245

1.107817

dow

212

1

n

0.297350

1.041809

044

9

up

0.030974

1.552535

dow

603

3

n

0.731050

1.225570

dow

05

4

n

0.793348

1.066066

264

5

0.108524

2.567406

044

6

up

0.195321

1.392810

dow

545

9

n

0.220451

3.308575

814

9

0.802622

1.344726

677

4

NM_002715

0

PTPRG

NM_002841

MYCN

NM_033341

NM_005378

overlappi ng

0

MYCN

NM_005378

enhancer

upstream

4293

SUMO1

NM_003352

enhancer

upstream

4293

SUMO1

NM_003352

downstrea enhancer

enhancer

enhancer

m

upstream

upstream

28522

9306

9306

PRKRA

FRAT1

FRAT1

NM_003690

NM_005479

NM_005479

downstrea up

enhancer

up

enhancer

m

33254

MYH9

NM_002473

30555

BRI3BP

NM_080626

downstrea m downstrea up

enhancer

m

30555

BRI3BP

NM_080626

downstrea down

enhancer

m

46547

DACH1

NM_004392

downstrea up

Neighboring

m

0.104907 198

SEMA3B

NM_004636

overlappi down

Neighboring

ng

61

dow

NM_001167

NM_002715

0

0

TOM1L1

n

1.936424

PPP2CA

BIRC8

1.936424

244

41161

23514

dow

820

overlappi

down

4

upstream

NM_016836

overlappi

down

0.2136024

RBMS1

dow

T

0.2094336

901

1.152899

IP

48

AC

ENST00000565104

69

upstream

0.651763

SC R

ENST00000498563

1.57101

Neighboring

NU

ENST00000450588

0.2094336

up

MA

ENST00000450588

3

D

ENST00000450588

19

TE

ENST00000450588

1.76003

CE P

ENST00000477514

0.2087596

NM_005486

n

up

up

up

up dow

242

2.977922

n

0.239072

1.294000

dow

098

1

n

ACCEPTED MANUSCRIPT

ENST00000411645

ENST00000504539

ENST00000399027

ENST00000399027

uc003koo.1

NR_002189

ENST00000507044

1.23902

94

77

0.2237803

1.71545

03

39

0.2237803

1.71545

03

39

0.2238577

2.13370

79

5

0.2238577

2.13370

79

5

0.2242178

1.42092

39

06

0.2261779

3.44024

75

49

0.2261779

3.44024

75

49

0.2267900

1.59948

56

41

0.2285991

4.58839

06

71

ENST00000512717

ENST00000512717

ENST00000512717

uc003akv.1

uc003akv.1

uc003myx.3

TCONS_00004256

TCONS_00004256

overlappi down

Neighboring

down

Neighboring

up

Neighboring

Neighboring

Neighboring

up

Neighboring

down

Neighboring

0.2312918

1.50417

77

18

0.2315017

1.39137

4

88

0.2315017

1.39137

4

88

0.2315017

1.39137

4

88

0.2320760

1.28689

06

72

0.2320760

1.28689

06

72

0.2323005

1.10582

19

42

0.2333099

1.39248

03

26

0.2333099

1.39248

03

26

0

ng

5

NM_005435

ARHGEF 0

368

5

NM_005435

368

0

enhancer

C11orf30

C11orf30

ELK4

ng

0

ELK4

upstream

2954

KDM3B

m

16806

up

up

down

down

down

enhancer

m

16806

15984

HMGA1

HMGA1

FER

5

n

0.004146

1.690112

292

4

0.009466

2.320339

1.539086

065

2

up

579

1.714978

up

0.000511

4.454517

dow

943

5

n

0.003041

2.070807

NM_001973

795

2

up

ENST00000

0.629421

1.137422

dow

314358

74

3

n

0.004605

1.893866

dow

551

3

n

0.512137

1.132213

dow

647

6

n

0.744662

1.277230

549

5

0.451654

1.722487

779

5

up

NM_020193

NM_020193

NM_001973

NM_145901

NM_145901

NM_005246

0.447649

BCAS1

NM_003657

0.019939

1.587189

dow

Neighboring

upstream

179

CTBP1

NM_001328

826

8

n

NM_001008

0.174450

2.663445

493

107

5

up

0.000280

3.345358

dow

NM_005749

535

6

n

NM_001130

0.075070

1.612737

528

018

8

NM_001130

0.431253

1.340764

846

6

downstrea enhancer

enhancer

m

upstream

14376

77759

ENAH

TOB1

enhancer

m

13423

SPAG9

enhancer

m

13423

SPAG9

528

up

Neighboring

upstream

1050

DRG1

NM_004147

0.113694

Neighboring

upstream

1050

DRG1

NM_004147

overlappi Neighboring

ng

0

TFAP2A

NM_003220

downstrea down

enhancer

m

100478

RTN4

NM_020532

downstrea down

up

67830

down

up

up

upstream

downstrea

up

up

enhancer

downstrea down

331

0.223014

downstrea m

dow

5

downstrea

enhancer

1.000740

704

downstrea

up

85

upstream

overlappi

up

1.26407

upstream

overlappi up

99

ng

NM_005486

ARHGEF

overlappi

up

0.2286754

ng

TOM1L1

0.995922

T

0.2237323

0

IP

77

AC

TCONS_00001304

94

ng

SC R

ENST00000411645

1.23902

Neighboring

NU

ENST00000572035

0.2237323

down

MA

ENST00000572035

96

D

ENST00000496968

49

overlappi

TE

ENST00000496968

2.04780

CE P

ENST00000576084

0.2224082

enhancer

m

62

100478

RTN4

NM_020532

up

up dow

275

1.382347

n

0.691262

1.051111

573

8

up

0.534984

1.616829

dow

234

6

n

0.166051

1.577909

dow

804

6

n

0.524882

1.141941

539

2

up

ACCEPTED MANUSCRIPT

ENST00000560419

ENST00000572417

uc021onu.1

uc021onu.1

ENST00000423096

ENST00000423096

ENST00000521252

1.85007

83

12

0.2341497

1.36572

11

14

0.2341497

1.36572

11

14

0.2360791

1.76698

35

2

0.2367637

1.38232

39

39

0.2368475

1.62505

64

94

0.2373373

1.35137

73

8

0.2373373

1.35137

73

8

0.2389530

1.42822

51

23

0.2389530

1.42822

51

23

ENST00000578488

ENST00000422551

ENST00000422551

ENST00000442557

ENST00000446052

ENST00000446052

TCONS_00016398

TCONS_00016398

up

Neighboring

up

Neighboring

up

enhancer

enhancer

enhancer

up

Neighboring

down

Neighboring

0.2404760

1.29342

03

03

0.2413287

1.39739

58

02

0.2436894

1.44609

94

43

0.2436894

1.44609

94

43

0.2449178

1.32926

7

96

0.2497322

1.22262

62

46

0.2497322

1.22262

62

46

0.2505537

2.16940

91

86

0.2505537

2.16940

91

86

MYL9

NM_006097

ng

0

MYL9

NM_006097

upstream

upstream

upstream

12440

12440

13167

upstream

ng

Neighboring

ng

NFKBIA

NFKBIA

HTRA3

615

JDP2

0

KCTD11

0

down

down

up

down

up

enhancer

enhancer

ng

0

17718

ng

enhancer

Neighboring

Neighboring

Neighboring

down

Neighboring

0.280322

1.205845

DHCR24

DHCR24

NLRP12

upstream

dow

308

5

n

0.637141

1.179423

dow

765

7

n

0.513860

1.225722

dow

NM_130469

325

5

n

NM_001002

0.132389

1.286352

914

203

1

up

0.013016

1.821137

dow

579

4

n

0.213061

1.946391

dow

787

6

n

0.111650

1.571402

64

5

up

0.975166

1.023792

dow

604

4

n

0.894081

1.028302

dow

038

4

n

NM_020529

NM_053044

NM_014762

NM_014762

NM_144687

17718

NLRP12

NM_144687

0

WRN

NM_000553

upstream

9596

18

GATA1

LIG3

ng

NM_002049

NM_013975

RAB3B

NM_002867

ng

0

RAB3B

NM_002867

ng

0

MKL1

NM_020831

enhancer

upstream

69575

0

NM_002446

MAP3K1 enhancer

upstream

69575

0

NM_002446

downstrea enhancer

m

120304

SEMA4D

NM_006378

GADD45 enhancer

upstream

63

4245

G

NM_006705

up

dow

614

1.959945

0.264663

1.379448

936

9

0.245631 0

up

1.208360

MAP3K1

down

4

0.678193

overlappi

down

109

0.085675

up

down

1.505376

up

overlappi

down

0.207236

4

overlappi up

n

804

NM_020529

overlappi Neighboring

2

1.913919

downstrea m

017

0.010748

downstrea m

dow

1

overlappi

Neighboring

1.096269

932

overlappi

down

09

0

overlappi

down

2.46422

ng overlappi

down

24

NM_022648

overlappi

down

0.2403700

TNS1

0.498366

T

0.2341185

38497

IP

12

AC

ENST00000419045

83

upstream

SC R

ENST00000503186

1.85007

enhancer

NU

ENST00000459899

0.2341185

down

MA

ENST00000459899

5

D

ENST00000425233

77

TE

ENST00000425233

2.16383

CE P

ENST00000431298

0.2333864

n

up dow

203

1.731149

n

0.822845

1.136353

dow

306

4

n

0.121411

1.292118

dow

169

6

n

0.325039

1.982783

dow

386

6

n

0.966380

1.008776

dow

419

2

n

0.001808

2.074556

dow

989

3

n

0.044751

2.760111

dow

801

5

n

ACCEPTED MANUSCRIPT

ENST00000469148

ENST00000463353

ENST00000443015

ENST00000443015

ENST00000496103

ENST00000283110

ENST00000429227

1.35405

68

8

0.2523631

1.88526

62

92

0.2523631

1.88526

62

92

0.2550557

1.47786

06

95

0.2558741

1.22259

59

7

0.2573130

1.72169

04

23

0.2579321

2.08343

41

22

0.2579321

2.08343

41

22

0.2589186

1.31841

13

19

0.2596981

2.23134

33

98

1.48913

81

05

ENST00000553543

ENST00000435287

ENST00000435287

uc001uzl.3

uc001uzl.3

NR_038237

NR_038237

NR_038237

0.2623294

1.58219

55

61

0.2633613

1.19777

88

72

0.2633613

1.19777

88

72

0.2633682

1.23611

19

91

0.2633682

1.23611

19

91

0.2635357

2.13282

16

21

0.2635357

2.13282

16

21

0.2635357

2.13282

16

21

1.539086

065

2

up

579

1.714978

up

0.196795

1.246897

dow

132

8

n

0.619253

1.488794

151

5

up

0.034099

2.684878

dow

619

7

n

0.500420

1.313293

59

5

up

0.789105

1.033150

dow

814

1

n

0.455981

1.387755

129

8

0.563611

1.230147

691

9

0.517475

1.206141

522

2

up

0.002376

2.314030

dow

739

1

n

0.064244

1.431258

dow

571

3

n

0.885460

1.126193

15

4

0.717582

1.168526

NM_022151

78

2

ENST00000

5.92508E

2.960837

367976

-05

7

ENST00000

0.860613 67

1.147476

0.000864

3.038371

676

1

up

0.005465

1.846814

dow

508

8

n

0.085350

1.823464

dow

912

8

n

0.306899

1.264012

dow

801

8

n

0.606803

1.117302

dow

775

9

n

C11orf30

NM_020193

up

Neighboring

upstream

450

C11orf30

NM_020193

n

0.447649

downstrea enhancer

m downstrea

enhancer

m overlappi

Neighboring

ng overlappi

down

Neighboring

down

Neighboring

13297

ng

NOX1

NM_007052

13297

0

NOX1

ATRX

NM_007052

NM_000489

0

PTPRG

NM_002841

914

BCAR1

NM_014567

downstrea m

overlappi

Neighboring

ng

0

RARB

uc011awl.2

overlappi

up

0.2599093

0.223014 450

up

05

2.950597

upstream

down

1.48913

dow

-05

Neighboring

up

81

NM_000462

up

up

0.2599093

UBE3A

T

0.2509312

125215

IP

8

AC

ENST00000429227

68

m

SC R

ENST00000453566

1.35405

enhancer

9.08527E

NU

ENST00000412087

0.2509312

down

MA

ENST00000412087

41

Neighboring

D

ENST00000530759

86

downstrea

TE

ENST00000530759

1.48149

up

down

CE P

NR_022010

0.2506780

up

up

Neighboring

ng

0

RARB

uc011awl.2

overlappi ng

0

DIAPH1

NM_005219

downstrea

enhancer

m

15563

CTSK

NM_000396

Neighboring

upstream

128

RAB4A

NM_004578

Neighboring

upstream

128

RAB4A

NM_004578

downstrea down

enhancer

m

43698

MOAP1

overlappi down

Neighboring

ng

0

CTGF

overlappi down

Neighboring

ng

0

CTGF

367976

up

enhancer

upstream

26257

TSC22D1

NM_183422

up

enhancer

upstream

26257

downstrea up

Neighboring

m

TSC22D1

NM_183422

ANGPTL 2

4

NM_139314

overlappi up

Neighboring

ng

0

RAB11B

NM_004218

overlappi up

Neighboring

ng

64

0

RAB11B

NM_004218

up

up

up

up

up dow n

ACCEPTED MANUSCRIPT

ENST00000563833

ENST00000563833

ENST00000417957

ENST00000448300

ENST00000576963

ENST00000407121

ENST00000407121

1.38947

39

86

0.2673301

1.38947

39

86

0.2685786

1.60577

27

87

0.2697609

1.66566

44

77

0.2708749

1.52417

39

51

0.2708749

1.52417

39

51

0.2739719

1.75704

66

33

0.2744681

1.50819

54

65

0.2759337

1.35366

57

05

0.2790232

1.29418

12

8

ENST00000474167

ENST00000523806

ENST00000523806

uc003uig.3

ENST00000446663

ENST00000446663

ENST00000455774

ENST00000455774

down

enhancer

m

67301

CXCL1

NM_001511

up

Neighboring

upstream

223

RAB30

NM_014488

Neighboring

Neighboring

enhancer

up

Neighboring

up

Neighboring

1.59844

16

32

0.2799250

1.79014

94

25

0.2830252

1.83097

25

31

0.2830252

1.83097

25

31

0.2832748

2.28814

67

68

0.2860281

1.32883

82

52

0.2860281

1.32883

82

52

0.2878823

1.15634

9

43

0.2878823

1.15634

9

43

RAB30

0

5593

ENG

EPAS1

upstream

9

NFKB1

upstream

9

NFKB1

enhancer

m

enhancer

down

up

up

down

enhancer

m

26599

up

NM_001114

0.046330

1.865591

dow

753

345

4

n

0.404299

1.210801

NM_001430

269

3

up

NM_001165

0.025092

1.555700

dow

412

514

8

n

NM_001165

0.213008

2.009355

412

905

8

MN1

NM_002430

4271

ACSL4

NM_022977

5451

CBX4

NM_003655

upstream

6897

CCNC

NM_005190

overlappi 0

BDNF

NM_170735

0

JMY

NM_152405

TNFRSF 2841

10B

NM_003842

TNFRSF

down

Neighboring

m

2841

10B

NM_003842

up

Neighboring

upstream

274

DMTF1

NM_021145

downstrea enhancer

m

18223

BIK

NM_001197

downstrea down

enhancer

m

18223

BIK

NM_001197

overlappi down

Neighboring

ng

0

SVIL

NM_021738

overlappi down

Neighboring

ng

65

437

0

SVIL

NM_021738

up dow

1.13455

0.362367

downstrea

down

0.239208

4

enhancer

m

n

329

NM_005190

Neighboring

1

0.560175

downstrea down

86

NM_014488

CCNC

ng

dow

1.259968

6897

Neighboring

1.515832

0.662734

overlappi up

0.379050

n

upstream

ng

up

dow

enhancer

Neighboring

1

7

downstrea m

248

1.975850

downstrea

up

0.2797367

m

223

6.339024

52

downstrea

down

8

ng downstrea

up

1.29418

upstream overlappi

down

12

NM_002619

downstrea

up

0.2790232

PF4

0.002706

T

0.2673301

41263

IP

2

AC

NR_033315

17

upstream

SC R

ENST00000418415

1.17519

enhancer

NU

ENST00000425991

0.2648324

down

MA

NR_038903

2

D

NR_038903

17

TE

ENST00000505935

1.17519

CE P

ENST00000505935

0.2648324

n dow

646

1.546909

n

0.367921

1.063183

237

8

up

0.010724

2.744958

dow

377

5

n

0.011692

1.513980

dow

309

8

n

0.782380

1.175744

74

1

0.052601

1.787245

957

6

0.000326

3.338442

186

1

0.055396

1.646470

078

1

up

0.120529

1.593059

dow

803

9

n

0.001152

1.770968

dow

642

3

n

0.656921

1.215008

dow

535

5

n

0.132982

1.765005

659

9

up

0.617486

1.183261

dow

174

3

n

up

up

up

ACCEPTED MANUSCRIPT

TCONS_00025724

ENST00000485162

ENST00000485162

NR_046600

NR_001275

NR_001275

ENST00000429656

1.44583

41

39

0.2905343

1.44583

41

39

0.2913906

1.29043

31

27

0.2913906

1.29043

31

27

0.2920078

1.62691

34

52

0.2929429

1.18688

54

15

0.2929429

1.18688

54

15

0.2932850

1.29325

62

32

0.2991179

1.26753

91

55

0.2991179

1.26753

91

55

ENST00000495884

ENST00000549457

ENST00000549457

ENST00000513338

ENST00000513338

ENST00000571370

ENST00000571370

NR_033711

down

Neighboring

ng

0

CCND2

NM_001759

down

enhancer

upstream

86372

MGMT

NM_002412

enhancer

Neighboring

Neighboring

up

Neighboring

down

Neighboring

1.98117

07

81

0.3012972

1.98117

07

81

0.3018714

1.50103

28

97

0.3018714

1.50103

28

97

0.3020293

1.69855

32

41

0.3020293

1.69855

32

41

0.3061816

2.10514

4

78

0.3061816

2.10514

4

78

0.3063820

1.51189

37

58

upstream

MGMT

0

0

ng

Neighboring

ng

up

up

up

up

enhancer

enhancer

ng

STIM1

STIM1

ng

ng

1

n

0.450093

1.403992

dow

407

1

n

0.678830

1.118678

dow

707

6

n

0.000266

4.009655

dow

673

6

n

0.060060

1.617436

dow

814

8

n

0.373756

1.128589

023

7

0.004786

2.074211

408

9

up

397

1.569417

up

0.721799

1.081764

dow

NM_006266

052

7

n

ENST00000

0.060752

1.737212

396634

016

5

up

0.357412

1.279931

dow

356

4

n

0.745203

1.127397

447

5

0.000217

2.195998

814

2

0.026457

1.949652

309

3

up

2.025653

up

NM_003156

NM_003156

0

MYLK

NM_053025

MYLK

NM_053025

MTOR

NM_004958

Neighboring

ng

10628

RALGDS

NM_006266

10628

RALGDS

0

HLA-A

0

STK3

NM_006281

0

STK3

NM_006281

downstrea up

enhancer

m

32798

PAWR

NM_002583

downstrea up

enhancer

down

enhancer

m

32798

PAWR

NM_002583

65049

UBE2D2

NM_003339

downstrea m

enhancer

m

Neighboring

ng

65049

UBE2D2

NM_003339

0

TP53

NM_000546

overlappi down

Neighboring

ng

0

TP53

NM_000546

overlappi down

Neighboring

ng

66

288 0.036108

overlappi down

up

up

0.010167

downstrea down

up

0.481341

overlappi up

0.000152

008

NM_002412

overlappi Neighboring

up

dow

NM_005994

overlappi Neighboring

1

3.853963

downstrea m

304

0.001298

downstrea m

1.507999

n

TBX2

0

0.355992

up

dow

overlappi

Neighboring

5

7

476

0

365

4.973315

overlappi

up

0.3012972

ng

86372

2.138634

288

overlappi

down

94

ng overlappi

down

1.50194

upstream overlappi

down

69

NM_001759

overlappi

down

0.3007678

CCND2

0.269249

T

0.2905343

0

IP

1

AC

ENST00000495884

92

ng

SC R

ENST00000308739

1.90301

Neighboring

NU

ENST00000308739

0.2902555

down

MA

TCONS_00018642

1

D

TCONS_00018642

92

overlappi

TE

ENST00000539135

1.90301

CE P

ENST00000539135

0.2902555

0

TP73

NM_005427

dow

264

1.392144

n

0.284701

1.402327

dow

687

4

n

0.593868

1.511437

195

7

up

0.071000

1.798254

dow

952

3

n

ACCEPTED MANUSCRIPT

ENST00000398410

ENST00000438202

ENST00000438202

ENST00000436882

ENST00000430449

ENST00000430449

uc021uec.1

1.25016

22

08

0.3120597

1.23098

79

8

0.3120597

1.23098

79

8

0.3135222

1.82021

59

98

0.3151442

1.18778

93

58

0.3160477

1.77992

48

2

0.3160477

1.77992

48

2

0.3163015

1.17245

46

61

0.3164241

1.34737

01

05

0.3164241

1.34737

01

05

ENST00000411871

ENST00000411871

enhancer

upstream

22274

IER3

NM_003897

down

Neighboring

upstream

133

DMTF1

NM_021145

down

up

enhancer

ceRNA

enhancer

down

Neighboring

up

Neighboring

44

0.3205928

1.20212

2

44

0.3213076

1.13028

26

41

0.3213076

1.13028

26

41

77

Neighboring

ENST00000403415

ENST00000403415

ENST00000542805

ENST00000542805

RAP1A

upstream

20180

ng

ng

ng

Neighboring

down

down

down

down

enhancer

enhancer

ng

upstream

upstream

HHEX

ng

ng

SVIL

down

YWHAH

YWHAH

0

BIRC5

enhancer

m

60869

enhancer

m overlappi

1.16319

down

Neighboring

77

1.16319

down

Neighboring

0.3219780

1.57915

74

44

0.3219780

1.57915

74

44

0.3240167

1.54279

55

02

0.3240167

1.54279

55

02

ng

n

NM_001010

0.418310

1.419594

935

479

8

0.082004

1.438761

052

7

up

0.322356

1.340660

dow

424

2

n

0.132982

1.765005

659

9

up

0.617486

1.183261

dow

174

3

n

0.091755

1.536860

393

9

0.012265

2.553007

189

1

0.063433

1.640543

NM_003405

695

2

up

NM_001012

0.003034

1.782198

dow

270

662

8

n

NM_001012

0.942397

1.039677

dow

270

32

6

n

0.239819

2.290166

789

4

up

0.915744

1.055573

dow

463

9

n

0.214149

1.219508

293

1

up

1.28583

up

NM_002729

NM_021738

overlappi ng

BIRC5

NM_003257

NM_003405

S18

NM_199355

S18

NM_199355

CBFA2T 0

3

NM_005187

CBFA2T 0

3

up

up

up

enhancer

enhancer

Neighboring

enhancer

m

upstream

upstream

upstream

67

158 0.210380

92357

111955

1870

1870

PERP

TNFAIP3

PLA2G16

PLA2G16

up

up

up

0.485714 NM_005187

downstrea up

0.120529

5

ADAMT 60869

n

308

ADAMT

downstrea down

TJP1

5753

downstrea

2

NM_002507

NM_021738

0

728

dow

SVIL

overlappi Neighboring

dow

1.402221

0

overlappi Neighboring

1.277982

0.115365

NM_005211

5753

0.237962

n

CSF1R

0

up

dow

0

0

9

9

overlappi

0.3215093 ENST00000562405

NGFR

314

1.593059

overlappi

0.3215093 ENST00000562405

5729

3.796432

803

overlappi

down

1.20212

upstream

overlappi

up

2

NM_003897

down

down

0.3205928

IER3

0.002665

T

0.3102722

22274

IP

56

AC

uc021uec.1

57

upstream

SC R

ENST00000428356

1.71060

enhancer

NU

TCONS_00025234

0.3083164

down

MA

TCONS_00025234

56

D

ENST00000446309

57

TE

ENST00000439406

1.71060

CE P

ENST00000439406

0.3083164

dow

NM_022121

659

1.117821

n

NM_001270

0.278889

1.425385

dow

508

136

7

n

0.061214

1.276646

467

3

0.061214

1.276646

467

3

NM_007069

NM_007069

up

up

ACCEPTED MANUSCRIPT

NR_046326

NR_046326

NR_046326

NR_046326

ENST00000581398

ENST00000499685

ENST00000412499

1.48565

28

22

0.3242402

1.48565

28

22

0.3291375

1.41710

94

75

0.3315503

1.06306

7

88

0.3328846

1.33661

13

93

0.3328846

1.33661

13

93

0.3328846

1.33661

13

93

0.3328846

1.33661

13

93

0.3331127

1.88088

87

32

0.3340369

1.46741

96

04

ENST00000525548

ENST00000525548

ENST00000541888

ENST00000541888

NR_034017

ENST00000464866

ENST00000464866

ENST00000549710

Neighboring

upstream

1870

PLA2G16

NM_007069

up

Neighboring

upstream

276

BTG2

NM_006763

Neighboring

down

enhancer

enhancer

down

Neighboring

down

enhancer

down

down

1.99676 37

0.3346709

1.99676

72

37

0.3347956

1.21233

2

46

0.3347956

1.21233

2

46

0.3369990

1.14956

1

99

0.3369990

1.14956

1

99

0.3412640

1.26678

86

37

0.3415308

1.22286

41

88

0.3415308

1.22286

41

88

0.3438398

1.15027

65

16

upstream downstrea

up

72

NM_007069

up

up

0.3346709

PLA2G16

down

down

up

up

m

upstream

Neighboring

enhancer

Neighboring

Neighboring

276

BTG2

7848

9941

NM_006763

BNIP3

LRP1B

NM_004052

NM_018557

upstream

2524

KDM5B

NM_006618

upstream

2524

KDM5B

NM_006618

upstream

upstream

upstream

upstream

2524

2524

1138

KDM5B

KDM5B

CTBP1

NM_006618

NM_006618

NM_001328

283

BTG1

NM_001731

7207

ERCC3

NM_000122

downstrea enhancer

m downstrea

enhancer

m

7207

ERCC3

NM_000122

overlappi down

Neighboring

ng

0

CUL5

NM_003478

overlappi down

Neighboring

ng

0

CUL5

0.220295

1.202331

095

2

0.220295

1.202331

095

2

0.030569

3.416195

T

0.3242402

1870

IP

02

AC

ENST00000412499

55

upstream

SC R

ENST00000451117

1.54279

enhancer

NU

TCONS_00018859

0.3240167

up

MA

ENST00000432511

02

D

ENST00000432511

55

TE

ENST00000542805

1.54279

CE P

ENST00000542805

0.3240167

NM_003478

up

up

33

5

up

0.158242

1.504651

453

6

0.055120

2.004762

082

9

up

0.778402

1.236462

dow

445

7

n

0.017422

1.752506

969

5

0.017422

1.752506

969

5

up

0.296033

1.683092

dow

402

2

n

0.296033

1.683092

dow

402

2

n

0.019939

1.587189

dow

826

8

n

0.003857

3.969065

331

5

0.933321

1.015317

255

9

0.954345

1.022675

72

7

up

0.059279

2.842321

dow

241

8

n

0.237788

1.364390

dow

071

6

n

0.002371

1.645402

dow

596

9

n

up

up

up

up

down

Neighboring

upstream

2338

LTBR

NM_002342

0.046601

1.591276

dow

down

Neighboring

upstream

2338

LTBR

NM_002342

078

7

n

NM_001018

0.345642

049

814

1.285574

n

0.012888

2.427815

dow

416

6

n

0.407862

1.982652

037

2

up

0.693407

1.250044

dow

672

9

n

up

enhancer

upstream

8148

PAEP

downstrea down

enhancer

m

4987

CASP2

NM_032982

downstrea down

up

enhancer

enhancer

m

upstream

68

4987

44503

CASP2

RAB21

NM_032982

NM_014999

dow

ACCEPTED MANUSCRIPT

uc001vfo.1

uc001vfo.1

TCONS_00019627

ENST00000548595

ENST00000548595

ENST00000494116

ENST00000494116

1.24060

57

19

0.3471971

1.24060

57

19

0.3477623

2.04118

85

73

0.3477623

2.04118

85

73

0.3487606

1.14825

34

2

0.3487606

1.14825

34

2

0.3511259

1.47388

89

26

0.3518020

1.08697

8

09

0.3518020

1.08697

8

09

0.3522084

3.58094

81

87

1.79386

49

3

ENST00000423619

ENST00000529722

ENST00000529722

NR_037938

TCONS_00003618

ENST00000419998

ENST00000427151

ENST00000427151

0.3526826

1.79386

49

3

0.3536591

2.52033

77

45

0.3536591

2.52033

77

45

0.3541654

1.69742

04

56

0.3549444

1.38879

28

92

0.3595607

1.11138

63

31

0.3608834

1.23397

59

9

0.3608834

1.23397

59

9

NM_001130

0.827046

1.054677

673

7

0.000109

6.309898

RBP1

992

up

enhancer

upstream

1037

JUN

NM_002228

Neighboring

enhancer

enhancer

up

enhancer

up

enhancer

upstream

upstream

upstream

1037

JUN

31692

31692

RDX

RDX

enhancer

NM_002228

NM_002906

NM_002906

up

up

up

up

up

Neighboring

3

n

0.277464

1.355704

dow

412

9

n

0.043558

2.601926

048

4

NM_001258

0.065445

1.567166

dow

320

696

9

n

0.714312

1.093747

066

2

0.790008

1.085530

969

7

0.000427

1.946118

129

5

0.005960

2.900091

177

9

up

0.047853

1.896928

dow

663

3

n

0.324056

1.207037

dow

NM_005101

335

7

n

NM_001085

0.079912

2.565341

458

874

9

up

NM_001085

0.266896

1.313323

dow

012

1

n

0.315881

1.494115

dow

292

8

n

0.089861

1.213300

dow

NM_199194

032

1

n

NM_001267

0.579303

1.327130

595

652

9

up

0.031376

1.714055

dow

045

4

n

0.218691

1.292565

dow

045

1

n

m

22567

TP53I11

m

1106

ERBB3

NM_001982

downstrea m

1106

ERBB3

NM_001982

upstream

19151

CRYAB

NM_001885

upstream

upstream

5237

5237

ISG15

ISG15

m

47117

CTNND1

NM_005101

47117

CTNND1

458

up

enhancer

upstream

51565

SGK1

NM_005627

upstream

20977

BRE

overlappi ng

0

SENP1

overlappi ng

0

CD81

NM_004356

overlappi Neighboring

915

up

m

down

dow

8

enhancer

Neighboring

1.924788

1.138169

enhancer

down

0.103390

66

NM_001885

Neighboring

up

0.833057

up

down

7

NM_012141

CRYAB

enhancer

321

INTS6

downstrea

down

6.309898

5820

19151

enhancer

0.000109

upstream

downstrea up

up

NM_012141

upstream

enhancer

7

INTS6

enhancer

enhancer

321

5820

downstrea

Neighboring

up

upstream

downstrea

up

0.3526826

n

86

down

87

2

upstream

down

3.58094

121

Neighboring

down

81

NM_014999

up

up

0.3522084

RAB21

dow

T

0.3471971

44503

1.094442

IP

06

AC

ENST00000423619

46

upstream

0.817227

SC R

uc001pkv.1

1.61822

enhancer

NU

uc001pkv.1

0.3442969

up

MA

NR_034014

16

D

NR_034014

65

TE

ENST00000381790

1.15027

CE P

ENST00000549710

0.3438398

ng

69

0

CD81

NM_004356

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000439215

ENST00000439215

ENST00000430660

ENST00000419679

uc001ebn.1

uc001ebn.1

NR_051976

1.29258

56

55

0.3639263

1.29258

56

55

0.3639263

1.29258

56

55

0.3645651

2.12762

64

93

0.3645651

2.12762

64

93

0.3666078

1.47616

96

03

0.3673304

1.76456

02

78

0.3685079

1.45353

54

99

0.3685079

1.45353

54

99

0.3696116

1.28136

68

79

up

Neighboring

down

enhancer

NR_051976

TCONS_00018266

TCONS_00018266

ENST00000439053

ENST00000439053

ENST00000489612

ENST00000489612

enhancer

enhancer

enhancer

up

enhancer

down

enhancer

1.22396

91

96

0.3725218

1.22396

91

96

0.3725218

1.22396

91

96

0.3727744

1.65583

03

76

0.3727744

1.65583

03

76

0.3755251

1.25045

02

92

0.3755251

1.25045

02

92

0.3770888

4.30243

37

79

0.3770888

4.30243

37

79

0

5

NM_005435

12404

CBLC

NM_012116

upstream

m

12404

m

CBLC

5103

21462

BCL3

SLC2A1

21462

SLC2A1

7261

ECT2

downstrea m

Neighboring

Neighboring

down

up

down

down

down

down

Neighboring

Neighboring

m

upstream

upstream

1631

728

728

m

enhancer

enhancer

m

upstream

upstream

0.009466

2.320339

704

5

up

0.040753

MSH5

RAP1A

RAP1A

n

0.213082

1.290504

dow

41

9

n

0.401360

1.333358

745

8

0.005969

2.514336

845

8

0.042071

1.611315

NM_006516

818

3

up

NM_001258

0.597497

1.313175

dow

315

573

1

n

0.267569

1.198356

NM_002441

853

7

up

NM_001010

0.251449

1.288408

dow

935

236

7

n

NM_001010

0.418310

1.419594

935

479

8

NM_012116

NM_005178

NM_006516

0.733829 0

CEP350

NM_014810

51823

SNAI1

NM_005985

51823

39494

39494

SNAI1

UBE2V1

UBE2V1

dow

0.013576

2.878460

dow

228

6

n

0.059188

1.998587

dow

NM_005985

149

6

n

NM_001032

0.550020

1.126520

288

258

7

up

NM_001032

0.650546

1.100089

dow

288

389

3

n

0.017501

4.060444

dow

162

9

n

11184

PTEN

NM_000314

up

enhancer

upstream

11184

PTEN

NM_000314

0.043092

overlappi 0

RAB10

NM_016131

overlappi down

Neighboring

ng

0

RAB10

NM_016131

downstrea up

enhancer

m

RINT1

NM_021930

downstrea up

enhancer

m

70

dow

834

3.311776

0.469058

1.171725

31

1

0.651121

1.122227

001

7

0.027570 14580

14580

RINT1

up

n

upstream

ng

up

1.173257

enhancer

Neighboring

up

622

up

down

up

dow

downstrea enhancer

4

2

downstrea enhancer

292

1.436474

overlappi ng

1.690112

871

downstrea

down

0.3725218

m

downstrea

down

96

m

downstrea up

1.22396

ARHGEF

downstrea

down

91

NM_005435

downstrea

down

0.3725218

ng

5

0.004146

T

0.3639263

0

IP

65

AC

NR_051976

NR_051976

22

ng overlappi

CE P

ENST00000424289

1.92776

Neighboring

SC R

ENST00000425131

0.3637635

up

ARHGEF

NU

ENST00000425131

65

MA

ENST00000425131

22

overlappi

D

ENST00000488041

1.92776

TE

ENST00000488041

0.3637635

NM_021930

n

up

up dow

654

1.883396

0.790821

1.072945

939

5

n

up

ACCEPTED MANUSCRIPT

ENST00000494408

0.3772304

1.34746

43

03

0.3809888

1.35727

21

68

0.3809888

1.35727

21

68

up

Neighboring

up

Neighboring

down

Neighboring

Neighboring

ENST00000562846

ENST00000526220

ENST00000526220

ENST00000396362

57

0.3923344

2.62844

88

17

0.3923344

2.62844

88

17

0.3925832

1.79052

53

34

0.3975528

1.08757

41

07

0.3984139

1.37266

18

11

0.3984139

1.37266

18

11

ENST00000496249

ENST00000507547

ENST00000555766

ENST00000555766

ENST00000435784

ENST00000435784

ENST00000414313

ENST00000414313

Neighboring

enhancer

up

enhancer

up

enhancer

3

0.4016679

2.00944

56

3

0.4017346

1.12111

17

05

0.4030683

3.38157

79

3

0.4032370

1.54582

41

16

0.4032370

1.54582

41

16

0.4047368

1.08799

46

12

0.4047368

1.08799

46

12

0.4082857

1.40170

46

35

0.4082857

1.40170

46

35

0

FOXO3

NM_001455

0

MLH1

NM_000249

m

m

down

down

up

up

up

up

m

Neighboring

Neighboring

Neighboring

Neighboring

upstream

upstream

0

MLH1

0

85452

CDH1

ETV6

m

enhancer

enhancer

m

upstream

upstream

Neighboring

down

Neighboring

ng

enhancer

m

2.302475

dow

831

1

n

0.584391

1.127467

837

7

0.002311

4.045854

151

1

0.069086

2.042737

896

2

0.823139

1.158762

144

8

up

0.605291

1.091933

dow

NM_006565

849

3

n

NM_001142

0.369788

1.236647

dow

930

481

9

n

NM_001142

0.647933

1.124326

dow

478

3

n

0.103844

1.660633

dow

795

7

n

0.151124

1.578109

dow

433

3

n

0.003857

3.969065

331

5

0.054669

3.667628

088

6

NM_004360

NM_001987

NM_018948

30911

ERRFI1

NM_018948

302

97

REL

CTCF

0

API5

NM_002908

0

API5

930

44366

HOXA1

NM_005522

44366

22502

32986

HOXA1

BTG1

EGF

NM_005522

NM_001731

NM_001963

0.326797 0

PAX8

NM_003466

0

PAX8

NM_003466

1724

DIRAS3

NM_004675

downstrea down

Neighboring

m

1724

DIRAS3

NM_004675

overlappi down

Neighboring

ng

Neighboring

ng

71

up

up

up

up

up

up dow

65

1.188004

n

0.688520

1.109148

215

8

0.645544

1.206911

218

6

0.645544

1.206911

218

6

up

568

2.199184

up

0.052517

1.858319

824

8

up

up

0.034490 0

RAP1B

NM_015646

overlappi down

1.217587

0.101752

downstrea down

0.346939

up

overlappi ng

up

6

overlappi down

1.305883

814

NM_000249

downstrea enhancer

849

1.501361

downstrea enhancer

up

0.448652

ERRFI1

overlappi ng

8

1

30911

overlappi ng

916

713

downstrea

down

2.00944

ng

downstrea

up

56

ng

downstrea down

0.4016679

AC

ENST00000396362

88

ng

MA

NR_033980

up

D

ENST00000399343

1.48157

ng

overlappi

TE

ENST00000399343

0.3850557

NM_001455

1.410673

0.647053

overlappi

CE P

NR_033890

95

FOXO3

overlappi

down

0.3815842

0

overlappi

1.48859 ENST00000563916

ng

0.103790

T

03

IP

ENST00000494408

43

overlappi

SC R

ENST00000434672

1.34746

NU

ENST00000434672

0.3772304

0

RAP1B

NM_015646

up

ACCEPTED MANUSCRIPT

TCONS_00004148

TCONS_00012347

TCONS_00012347

ENST00000498163

ENST00000498163

NR_103713

NR_103713

1.19520

14

95

0.4089030

1.19520

14

95

0.4089391

1.36511

32

06

0.4094190

1.46955

46

59

0.4094465

1.24841

68

59

0.4094493

1.63195

33

36

0.4094493

1.63195

33

36

0.4144717

1.95825

68

36

0.4144717

1.95825

68

36

0.4158376

1.99032

42

92

TCONS_00011779

ENST00000448791

TCONS_00021735

NR_047511

NR_047511

ENST00000474780

ENST00000474780

ENST00000431171

downstrea up

enhancer

down

Neighboring

up

Neighboring

Neighboring

Neighboring

down

enhancer

up

enhancer

up

92

0.4173298

1.51372

42

31

0.4173298

1.51372

42

31

0.4191655

1.28982

41

25

0.4253028

1.52352

63

01

0.4287370

1.25830

86

18

0.4287370

1.25830

86

18

0.4306651

1.40720

65

33

0.4306651

1.40720

65

33

0.4319278

1.21618

62

68

19546

1

NM_024310

ng

0

TES

NM_015641

ng

upstream

upstream

enhancer

0

220

96

Neighboring

up

down

down

up

Neighboring

enhancer

TES

S1PR1

m

m

JMY

up

Neighboring

enhancer

up

enhancer

up

Neighboring

m

6

up

0.051935

1.946244

dow

502

2

n

0.007265

1.922694

195

1

0.021214

1.663642

SOD2

437

9

up

945

2.11807

up

0.018342

2.046663

73

3

up

0.799983

1.136320

dow

489

2

n

0.942516

1.029395

dow

859

9

n

0.001089

3.323029

dow

417

1

n

0.003303

6.018866

dow

374

6

n

0.004004

1.262320

294

7

up

0.058970

1.296770

dow

NM_001260

269

8

n

ENST00000

0.119711

1.389135

dow

356956

736

2

n

ENST00000

0.196647

2.114373

dow

356956

157

3

n

0.045355

1.401523

521

1

0.276561

1.262930

304

4

up

0.019403

1.942426

dow

445

9

n

NM_000636

10A

10A

NM_003844

NM_003844

149175

CRYAA

NM_000394

149175

CRYAA

NM_000394

HSPA1B

upstream

upstream

11676

HSPA1B

SFN

104794

CDK8

0

IGF2R

overlappi ng overlappi up

down

down

Neighboring

Neighboring

Neighboring

ng

upstream

upstream

0

54

54

IGF2R

RAB5A

RAB5A

NM_005346

NM_005346

NM_006142

NM_004162

NM_004162

RASL11 down

enhancer

upstream

72

99657

A

up

up

up

up

0.006900

TNFRSF

407

4.183967

957

NM_152405

downstrea up

0.000370

1.787245

TNFRSF

407

n

0.052601

downstrea Neighboring

3

2

downstrea enhancer

771

904

NM_001400

downstrea m

dow

1.030853

NM_000636

0

1.447862

0.912008

SOD2

ng

0.539149

1

86520

overlappi

n

488

NM_015641

upstream

0

1

2.354450

NM_021643

ng

826

0.084418

TRIB2

86520

dow

3

51400

upstream

1.586134

68

upstream

overlappi

up

1.99032

PLEKHF

overlappi

up

42

NM_024310

overlappi

down

0.4158376

m

1

0.111253

T

0.4089030

19546

IP

46

AC

TCONS_00011779

25

m

SC R

ENST00000520855

1.52304

enhancer

PLEKHF

NU

ENST00000432195

0.4086497

up

MA

ENST00000444244

46

D

ENST00000444244

25

downstrea

TE

TCONS_00027288

1.52304

CE P

TCONS_00027288

0.4086497

NM_206827

up

ACCEPTED MANUSCRIPT

ENST00000519655

NR_033708

ENST00000431844

ENST00000431844

NR_033710

ENST00000525320

ENST00000507514

1.15673

01

18

0.4392306

1.20301

11

55

0.4401512

2.05893

36

46

0.4405462

1.28136

16

76

0.4405462

1.28136

16

76

0.4442888

1.13862

95

98

0.4464978

1.31456

43

78

0.4464978

1.31456

43

78

0.4478443

1.30121

23

38

0.4548854

1.21735

5

4

TCONS_00020933

ENST00000405924

ENST00000405924

ENST00000514756

ENST00000514756

ENST00000514756

ENST00000514756

ENST00000426992

overlappi down

Neighboring

down

Neighboring

Neighboring

up

enhancer

Neighboring

up

Neighboring

up

Neighboring

0.4549532

1.33689

82

87

0.4559317

1.23441

64

91

0.4561313

1.79772

15

29

0.4561313

1.79772

15

29

0.4573014

1.36821

99

84

0.4573014

1.36821

99

84

0.4573014

1.36821

99

84

0.4573014

1.36821

99

84

0.4587679

1.15930

33

43

0

R5

NM_006402

0

HBXIP

NM_006402

upstream

m

upstream

136

upstream

ZEB1

NM_030751

62732

19

PTN

RIPK2

NM_002825

NM_003821

19

RIPK2

NM_003821

ng

0

TP73

NM_005427

overlappi

Neighboring

ng

Neighboring

down

up

down

down

Neighboring

enhancer

ng

0

PAX8

NM_003466

upstream

ng

ng

up

enhancer

enhancer

up

enhancer

up

enhancer

m

upstream

upstream

0

PAX8

up

enhancer

upstream

up

0

TP73

Neighboring

ng

73

4

0.275786

2.274973

883

3

up

0.302328

1.563560

dow

829

6

n

0.030772

2.145666

682

1

up

0.157585

1.468559

dow

792

1

n

0.071000

1.798254

dow

952

3

n dow

dow

NM_005427

952

3

n

NM_001142

0.440802

1.126744

784

4

up

0.001628

3.319363

dow

485

3

n

316

0

F2R

NM_001992

0.835145 0

F2R

12080

22257

TBX3

EDN1

NM_001992

NM_016569

NM_001955

22257

EDN1

NM_001955

79372

CXCL13

NM_006419

17703

CCNG2

17703

CCNG2

0

CTSK

up

1.798254

NM_004354

NM_018647

NM_004354

overlappi down

1.111598

569

0.071000

LMO2

19

upstream

0.760509

up

up

36481

ceRNA

enhancer

4

8

TNFRSF up

-05

215

NM_003466

downstrea m

2.437619

1.109148

downstrea up

7.24052E

up

0.688520

overlappi Neighboring

1

1.188004

overlappi Neighboring

564

65

overlappi ng

2.001882

0.326797

overlappi

down

87

LAMTO

overlappi

down

1.33689

ng

downstrea up

82

NM_206827

overlappi

down

0.4549532

ng

A

0.165094

T

0.4389789

99657

IP

18

AC

ENST00000507514

01

upstream

SC R

ENST00000519655

1.15673

enhancer

NU

ENST00000454750

0.4389789

down

MA

ENST00000450834

68

D

ENST00000457535

62

RASL11

TE

ENST00000457535

1.21618

CE P

ENST00000431171

0.4319278

NM_000396

n

dow

901

1.058787

n

0.909978

1.025784

dow

3

8

n

0.006797

2.050123

dow

886

4

n

0.763720

1.069425

dow

215

9

n

0.260267

2.294281

646

4

0.388380

1.403185

588

3

0.683568

1.358837

349

8

0.795661

1.081343

782

3

up

0.002376

2.314030

dow

739

1

n

up

up

up

ACCEPTED MANUSCRIPT

ENST00000454541

NR_038367

NR_038367

ENST00000424041

ENST00000424041

ENST00000424041

0.4609400

1.27580

94

9

0.4609400

1.27580

94

9

0.4609400

1.27580

94

9

0.4609400

1.27580

94

9

0.4616166

1.21972

21

54

0.4616166

1.21972

21

54

0.4617384

1.68963

5

6

0.4617384

1.68963

5

6

0.4617384

1.68963

5

6

0.4617384

1.68963

5

6

NR_002312

0

2A

NM_178031

up

enhancer

upstream

41426

TIAL1

NM_003252

downstrea

ENST00000502787

ENST00000543217

ENST00000543217

ENST00000462623

ENST00000558071

ENST00000424739

ENST00000424739

ENST00000538624

enhancer

enhancer

down

Neighboring

down

Neighboring

1.51954

13

31

0.4623025

1.45530

96

95

0.4661475

1.51361

31

39

0.4661475

1.51361

31

39

0.4666821

1.67402

75

37

0.4675750

1.23281

37

98

0.4676855

1.38989

74

03

0.4676855

1.38989

74

03

0.4678815

1.18487

37

12

upstream

m

12287

BAG3

41426

12287

enhancer

enhancer

TIAL1

BAG3

up

up

up

up

enhancer

0.460683

1.075137

789

6

0.562349

1.260813

935

8

up

0.103844

1.660633

dow

795

7

n

0.151124

1.578109

dow

433

3

n

0.043785

1.941057

dow

NM_005417

148

4

n

NM_001167

0.198429

820

244

1.936424

NM_001167

0.249960

1.600060

820

719

6

0.329568

1.924938

72

9

0.192322

2.770705

109

1

0.623138

1.409979

852

3

up

0.165313

2.554733

dow

419

9

n

0.093112

1.582078

dow

686

4

n

0.870909

1.073649

dow

583

8

n

0.500420

1.313293

59

5

up

0.483050

1.094654

dow

NM_005902

574

2

n

NM_001127

0.006567

2.936307

183

392

9

NM_001127

0.023165

3.591743

183

908

1

up

0.491579

1.191194

dow

596

5

n

NM_003252

NM_004281

NM_005522

BLCAP

BLCAP

downstrea m

39299

SRC

NM_005417

Neighboring

upstream

202

PARP2

NM_005484

upstream

202

PARP2

NM_005484

downstrea up

enhancer

m

22267

FLT4

NM_182925

CDK2AP up

Neighboring

upstream

522

1

NM_004642

CDK2AP up

Neighboring

up

Neighboring

upstream

522

1

NM_004642

0

PTPRG

NM_002841

overlappi

up

enhancer

ng

upstream

6603

SMAD3

overlappi up

Neighboring

ng

0

CFLAR

overlappi up

Neighboring

ng

0

CFLAR

overlappi down

Neighboring

ng

74

0

RAB6A

1.416168

n

enhancer

Neighboring

0.020906

n

8

HOXA1

71882

1.348279

087

NM_004281

87

upstream

621

dow

upstream

SRC

dow

1.168618

NM_005522

71882

n

0.272492

HOXA1

upstream

2

up

87

39299

428

3

upstream

m

dow

659

downstrea

up

0.4617408

m

downstrea

up

31

AC

NR_002312

enhancer

1.439571

0.260752

ng

up

1.51954

TMEM13

Neighboring

up

13

NM_178031

up

up

0.4617408

2A

0.158317

T

13

0

IP

53

ng overlappi

CE P

ENST00000424041

1.26117

Neighboring

SC R

ENST00000454541

0.4595984

up

TMEM13

NU

ENST00000454541

13

MA

ENST00000454541

53

overlappi

D

ENST00000543907

1.26117

TE

ENST00000543907

0.4595984

NM_198896

up

dow n

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000422836

ENST00000531784

ENST00000531784

ENST00000433036

ENST00000433036

ENST00000576021

ENST00000562574

NR_026825

1.73454

79

24

0.4704841

1.73454

79

24

0.4737821

1.45305

48

41

0.4743821

1.46199

67

23

0.4743821

1.46199

67

23

0.4763063

1.55646

21

79

0.4763063

1.55646

21

79

0.4765763

1.28644

96

34

0.4765763

1.28644

96

34

0.4771883

1.40679

84

95

NR_026825

NR_049793

ENST00000406939

ENST00000406939

uc001tdb.1

uc001tdb.1

TCONS_00000918

Neighboring

up

Neighboring

Neighboring

enhancer

Neighboring

up

Neighboring

up

enhancer

1.48319

17

66

0.4824696

1.16052

97

9

0.4824696

1.16052

97

9

0.4833235

1.46149

93

28

0.4844364

1.18721

93

54

0.4844364

1.18721

93

54

0.4860993

1.31989

82

17

0.4860993

1.31989

82

17

0.4948083

1.43494

26

46

DSP

NM_004415

85

THPO

NM_000460

upstream

ng

85

ng

THPO

NM_000460

6334

m

m

up

down

up

up

enhancer

Neighboring

m

ng

ng

Neighboring

ng

Neighboring

ng

Neighboring

up

enhancer

ng

enhancer

m

Neighboring

ng

Neighboring

ng

enhancer

m

75

dow

842

7

n

0.013485

0

93554

93554

7751

7751

0

1.098458

dow

7

511

114

9

n

0.000463

6.740495

ETS1

NM_005238

913

6

0.009170

2.460697

612

2

0.042057

1.723478

75

2

up

0.147362

1.281086

dow

ETS1

NM_005238

ING5

NM_032329

0

0

591

7

n

ARHGDI

NM_001185

0.553977

1.256831

dow

A

077

346

5

n

0.214149

1.219508

293

1

up

158

1.28583

up

0.058326

1.932345

dow

228

7

n

0.108397

1.349757

NM_003483

58

3

up

NM_001270

0.278889

1.425385

dow

508

136

7

n

NM_001243

0.016796

1.889746

186

982

9

NM_001243

0.855350

1.058387

186

039

6

0.004524

1.686237

233

4

0.008475

1.365797

83

8

0.718573

1.176351

498

3

3

3

HMGA2

HMGA2

0

TNFAIP3

78339

PIM1

78339

0

0

13938

up

NM_032329

NM_005187

CBFA2T 0

up

ING5

CBFA2T 0

dow

0.684713

0.485714 NM_005187

NM_003483

PIM1

CRADD

NM_003805

CRADD

NM_003805

downstrea up

1.242954

NM_001113

overlappi up

0.740466

ARHGEF

overlappi up

n

up

downstrea up

dow

4

1.947096

downstrea m

2.297043

658

043

overlappi down

0.016004

511

overlappi up

n

7

overlappi up

4

0.219410

overlappi Neighboring

49

NM_001113

overlappi Neighboring

dow

ARHGEF

overlappi ng

3.220163

n

downstrea m

0.044521

1.866954

downstrea

enhancer

n

543

downstrea

enhancer

1.034119

NM_033084

0

dow

089

FANCD2

downstrea

up

0.4793963

m

overlappi

up

66

m

overlappi up

1.48319

298

downstrea

up

17

NM_198896

downstrea

up

0.4793963

upstream

RAB6A

T

0.4704841

up

0

IP

93

AC

ENST00000562574

56

ng

SC R

ENST00000422836

1.16561

Neighboring

0.883313

NU

uc021wsx.1

0.4690187

down

MA

TCONS_00007321

12

D

TCONS_00007321

37

overlappi

TE

ENST00000561592

1.18487

CE P

ENST00000538624

0.4678815

EDN2

NM_001956

up

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000511039

ENST00000534148

ENST00000440965

ENST00000440965

TCONS_00026503

TCONS_00026503

ENST00000402520

1.25441

49

35

0.5033355

1.31936

76

44

0.5038282

1.13348

34

51

0.5038282

1.13348

34

51

0.5043244

1.26681

89

41

0.5079933

1.11292

53

13

0.5095737

1.24134

1

15

0.5095737

1.24134

1

15

0.5117201

1.12862

02

44

0.5117201

1.12862

02

44

ENST00000402520

ENST00000402520

NR_038359

TCONS_00004015

ENST00000493323

ENST00000493323

TCONS_00016057

TCONS_00016057

up

Neighboring

ng

0

DACH1

NM_004392

down

Neighboring

upstream

71

FANCD2

NM_033084

downstrea Neighboring

Neighboring

Neighboring

1.10868

31

44

0.5139055

1.10868

31

44

0.5139055

1.10868

31

44

0.5185713

1.24584

99

08

0.5202138

1.12529

09

27

0.5278501

1.53501

9

46

0.5278501

1.53501

9

46

0.5283688

1.10797

63

95

0.5283688

1.10797

63

95

ng downstrea

up

enhancer

up

Neighboring

315

m

TNFSF14

NM_003807

0

0

CERS2

CERS2

NM_181746

NM_181746

1.017802

0.802622

1.344726

677

4

ng

ng

down

down

down

down

down

down

enhancer

ng

8

up

0.016461

2.266042

dow

579

7

n

0.017911

1.401720

dow

419

7

n

0.056517

2.230281

921

3

0.056517

2.230281

921

3

0.833542

1.037815

555

5

0.833542

1.037815

555

5

up

0.526049

1.646916

dow

744

5

n

0.606036

1.074557

dow

093

1

n

104919

PIK3C3

NM_002647

2059

2059

2059

UBE2I

UBE2I

UBE2I

NM_194259

NM_194259

NM_194259

down

enhancer

upstream

3523

XRCC5

NM_021141

overlappi

0.260966 0

C12orf5

NM_020375

overlappi 0

48154

downstrea

76

732

1

NM_002257

m

1.043439

908

CFLAR

KLK1

enhancer

0.690502

up

183

0

269

down

7

3.591743

m

upstream

109

0.023165

NM_194259

enhancer

1.019202

NM_001127

Neighboring

down

0.919430

up

9

UBE2I

ng

9

392

CFLAR

2059

Neighboring

824

183

0

up

up

1.177299

2.936307

upstream

ng

0.539878

0.006567

Neighboring

Neighboring

n

NM_001127

downstrea

up

1

2

NM_002647

upstream

978

1.583117

PIK3C3

enhancer

dow

54

104919

upstream

1.460838

0.029153

m

Neighboring

0.432642

NM_003626

downstrea

upstream

n

PPFIA1

enhancer

enhancer

1.866954

0

downstrea m

dow

543

NM_032144

overlappi

Neighboring

up

RAB6C

overlappi

Neighboring

up

9863

overlappi

up

0.5139055

ng overlappi

up

44

m overlappi

down

1.10868

956

0.013485

down

31

NM_001956

overlappi

down

0.5139055

EDN2

T

0.5013873

13938

IP

93

AC

ENST00000402520

14

m

SC R

ENST00000412838

1.18551

enhancer

0.920075

NU

ENST00000412838

0.5011708

up

MA

TCONS_00026873

46

D

ENST00000424471

26

downstrea

TE

ENST00000418340

1.43494

CE P

TCONS_00000918

0.4948083

C12orf5

SEMA4D

NM_020375

NM_006378

GADD45 51309

G

NM_006705

up

up

up

up

up

up

dow

026

1.441445

n

0.538360

1.124161

dow

743

6

n

0.001808

2.074556

dow

989

3

n

0.044751

2.760111

dow

801

5

n

ACCEPTED MANUSCRIPT

NR_023919

NR_023919

ENST00000562040

ENST00000562040

ENST00000431108

ENST00000431108

ENST00000506710

NR_037665

1.52772

78

69

0.5294586

1.36331

66

81

0.5294586

1.36331

66

81

0.5304293

1.15663

27

69

0.5311069

1.07834

7

77

0.5311069

1.07834

7

77

0.5316678

1.28841

56

17

0.5316678

1.28841

56

17

0.5317416

1.10602

52

25

0.5317416

1.10602

52

25

NR_037665

ENST00000447415

ENST00000447415

uc009wog.1

uc009wog.1

ENST00000413068

ENST00000529475

up

Neighboring

upstream

412

CTDSPL

up

Neighboring

upstream

412

CTDSPL

up

up

Neighboring

Neighboring

enhancer

up

enhancer

up

enhancer

04

0.5382881

1.18335

71

04

0.5394303

1.10909

8

44

0.5394303

1.10909

8

44

0.5413575

1.16456

32

78

0.5413575

1.16456

32

78

0.5422915

1.21177

18

44

0.5422915

1.21177

18

44

0.5472283

1.12769

48

98

0.5515691

1.91745

2

79

m

152

m

WASL

152

15672

WASL

IL6

21404

CDC42

21404

CDC42

downstrea

up

1.18335

upstream

downstrea

up

71

upstream

downstrea up

0.5382881

NPR1

down

down

down

down

m

enhancer

enhancer

Neighboring

upstream

upstream

upstream

dow

NM_000906

8

3

n

NM_001008

0.011809

1.464930

dow

392

217

3

n

NM_001008

0.266805 948

1.164969

up

0.001425

2.253232

dow

17

7

n

0.429855

1.985724

259

3

up

0.336218

1.352893

dow

NM_000600

535

1

n

NM_001039

0.328249

1.139651

802

221

5

NM_001039

0.886034

1.045145

802

301

8

0.214149

1.219508

293

1

up

158

1.28583

up

0.188048

1.134232

263

8

up

0.960875

1.009290

dow

604

6

n

0.056141

1.185799

108

7

0.106287

1.719976

465

4

up

0.171853

1.584658

dow

533

7

n

0.188665

1.178119

dow

961

8

n

7.37549E

2.167406

dow

-05

6

n

0.004620

1.763440

dow

613

8

n

0.548270

1.176137

331

8

up

0.802744

1.045250

dow

577

2

n

T

0.5290848

23310

3.542273

392

IP

69

AC

ENST00000506710

78

m

0.001509

NM_003941

SC R

ENST00000444653

1.52772

enhancer

NU

uc003vla.3

0.5290848

down

MA

uc003vla.3

39

D

ENST00000366441

6

downstrea

TE

ENST00000366441

1.22161

CE P

ENST00000454246

0.5288659

NM_003941

CBFA2T 6935

3

NM_005187

CBFA2T 6935

2585

3

EEF1A1

NM_005187

NM_001402

upstream

2585

EEF1A1

NM_001402

Neighboring

upstream

1849

CDC25C

NM_001790

upstream

1849

CDC25C

NM_001790

downstrea up

enhancer

m

27067

PRKAA1

NM_006251

downstrea up

enhancer

m

27067

PRKAA1

NM_006251

SH3GLB down

enhancer

upstream

36728

down

enhancer

upstream

36728

1

NM_016009

SH3GLB 1

NM_016009

overlappi up

Neighboring

ng

0

S100A4

NM_019554

overlappi up

Neighboring

ng

0

S100A4

NM_019554

0.002606 up

enhancer

upstream

76527

ERBB4

NM_005235

overlappi up

Neighboring

ng

77

0

STIM1

up

0.485714

Neighboring

Neighboring

up

NM_003156

up

dow

117

2.412779

n

0.450093

1.403992

dow

407

1

n

ACCEPTED MANUSCRIPT

ENST00000458368

ENST00000458368

ENST00000570072

ENST00000570072

ENST00000454004

ENST00000514270

0.5578324

1.08472

46

95

0.5642689

1.31915

39

45

0.5654868

1.52459

85

63

0.5654868

1.52459

85

63

0.5654868

1.52459

85

63

0.5654868

1.52459

85

63

0.5665142

1.51303

63

01

0.5665142

1.51303

63

01

0.5700892

1.40589

61

24

0.5725254

1.14424

76

03

47

down

Neighboring

down

Neighboring

AC

47

down

down

Neighboring

Neighboring

enhancer

down

Neighboring

down

enhancer

TCONS_00020732

ENST00000454260

ENST00000454260

ENST00000454260

ENST00000454260

ENST00000454260

ENST00000454260

ENST00000454260

1.24890

74

49

0.5886805

1.48144

08

29

0.5886805

1.48144

08

29

0.5886805

1.48144

08

29

0.5886805

1.48144

08

29

0.5886805

1.48144

08

29

0.5886805

1.48144

08

29

0.5886805

1.48144

08

29

NM_003466

ng

0

PAX8

NM_003466

ng

upstream

upstream

0

TP53I3

2971

2971

EEF1A2

EEF1A2

Neighboring

Neighboring

down

up

enhancer

Neighboring

up

up

NM_004881

NM_001958

NM_001958

up

enhancer

1.109148

215

8

up

0.077933

1.910998

dow

463

1

n

0.198714

1.301996

dow

495

9

n

0.198714

1.301996

dow

495

9

n

0.698387

1.193249

939

3

0.698387

1.193249

939

3

ENST00000

0.554774

1.200747

262304

935

5

ENST00000

0.707737

1.069451

262304

871

4

0.797497

1.151929

334

5

0.000302

2.260848

NM_002538

196

1

up

NM_001040

0.113207

1.332821

dow

058

565

9

n

NM_001040

0.794780

1.047878

dow

058

574

3

n

0.054542

1.422898

dow

671

1

n

0.088946

2.917030

dow

354

1

n

0.138636

1.260725

dow

718

7

n

0.210432

1.213820

864

6

0.233072

1.551651

733

2

up

0.239964

2.184424

dow

297

7

n

0.310422

1.374733

dow

418

9

n

0.313305

1.298101

033

4

ng

0

PKD1

ng

0

PKD1

downstrea m

25173

PRUNE2

NM_015225

overlappi ng

0

OCLN

m

81634

SPP1

m

81634

SPP1

m

133570

KRAS

FOS

NM_033360

NM_005252

NM_002005

up

ceRNA

TGFBI

NM_000358

ceRNA

EI24

ceRNA

BTG4

NM_004879

NM_017589

overlappi

up

0.688520

n

NM_001958

ceRNA

Neighboring

1.188004

EEF1A2

FES

up

65

2971

ceRNA

up

dow

upstream

up

up

n

NM_001958

downstrea up

6

EEF1A2

downstrea enhancer

707

2971

downstrea enhancer

dow

upstream

overlappi

down

0.5789492

PAX8

overlappi

down

1.82116

0

overlappi

0.5752634 ENST00000505987

ng

1.118678

0.326797

overlappi

up

1.82116

NM_003156

overlappi

0.5752634 ENST00000505987

STIM1

0.678830

T

95

0

IP

46

ng

SC R

ENST00000458368

1.08472

Neighboring

NU

ENST00000458368

0.5578324

up

MA

ENST00000469867

79

D

ENST00000445745

2

overlappi

TE

ENST00000445745

1.91745

CE P

ENST00000529475

0.5515691

ng

ceRNA

0

STEAP3

KDM4C

78

NM_018234

NM_015061

up

up

up

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000480365

ENST00000480365

ENST00000522844

ENST00000522844

ENST00000449270

ENST00000449270

ENST00000449270

1.48144

08

29

0.5886805

1.48144

08

29

0.5886805

1.48144

08

29

0.5886805

1.48144

08

29

0.5903393

1.23845

75

36

0.5903393

1.23845

75

36

0.5912688

1.45985

32

53

0.5912688

1.45985

32

53

0.5961865

1.09596

95

5

0.5961865

1.09596

95

5

ENST00000528407

ENST00000473808

ENST00000473808

ENST00000478358

ENST00000478358

TCONS_00005946

NR_034094

NR_034094

overlappi up

Neighboring

up

ceRNA

up

up

ceRNA

5

0.5961865

1.09596

95

5

0.5964048

1.26836

4

51

0.5970818

1.11814

13

28

0.5970818

1.11814

13

28

0.5986664

1.10422

96

77

0.5986664

1.10422

96

77

0.6000344

1.12626

22

72

0.6010909

1.26440

89

72

0.6010909

1.26440

89

72

SVIL

ceRNA

NM_018234

Neighboring

ADPRH

down

Neighboring

ng

NM_021738

NM_000460

NM_001125

0

RAB7A

NM_004637

0

RAB7A

NM_004637

overlappi

down

down

down

down

ng

Neighboring

Neighboring

enhancer

upstream

upstream

upstream

322

322

147048

ceRNA

enhancer

upstream

147048

ceRNA

HDAC2

HDAC2

PAK7

NM_001527

NM_001527

NM_020341

EAF2

NM_018456

PAK7

NM_020341

PTTG1

NM_004219

overlappi down

Neighboring

ng

0

FGFR1

NM_023110

downstrea down

enhancer

m

7330

ROCK1

NM_005406

downstrea enhancer

m

7330

ROCK1

NM_005406

up

enhancer

upstream

6184

METAP2

NM_006838

down

enhancer

enhancer

upstream

upstream

6184

36429

METAP2

PPARG

overlappi down

Neighboring

ng

0

MRVI1

overlappi down

Neighboring

ng

79

554

8

0.525165

1.239522

121

6

0

MRVI1

up

up dow

109

1.120492

n

0.617486

1.183261

dow

174

3

n

0.740466

1.242954

dow

842

7

n

0.936375

1.020651

487

9

0.000416

3.425335

428

1

0.013463

3.719975

934

6

up

0.045938

1.999558

dow

265

8

n

0.590835

1.203097

dow

216

9

n

0.003859

1.965775

dow

514

3

n

0.254752

1.928354

356

1

0.341518

2.244439

225

9

up

0.871558

1.020816

dow

201

1

n

0.611333

1.428075

972

5

up

0.009596

2.638948

dow

359

2

n

0.190177

down

up

1.129718

0.611342 NM_139022

THPO

ceRNA

down

up

1.09596

STEAP3

2

overlappi

up

95

0

TSPAN3

up

0.5961865

ng

0.516371

T

0.5886805

NM_005896

IP

29

AC

ENST00000449270

08

IDH1

SC R

ENST00000454260

1.48144

ceRNA

NU

ENST00000454260

0.5886805

up

MA

ENST00000454260

29

D

ENST00000454260

08

TE

ENST00000454260

1.48144

CE P

ENST00000454260

0.5886805

up

up

up

dow

162

1.493846

n

0.002663

5.576112

dow

876

8

n

0.397382

1.292658

dow

809

5

n

0.234835

1.305466

dow

NM_015869

377

2

n

ENST00000

0.255327

1.340035

dow

436272

793

1

n

ENST00000

0.434203

1.172122

436272

255

1

NM_006838

up

ACCEPTED MANUSCRIPT

ENST00000440581

NR_002832

ENST00000446383

ENST00000496868

ENST00000496868

ENST00000465274

ENST00000465274

1.17504

27

88

0.6107889

1.17504

27

88

0.6117774

1.22458

49

51

0.6117774

1.22458

49

51

0.6125389

1.28628

12

07

0.6161266

1.47641

97

39

0.6205157

1.28702

45

27

0.6269282

1.09637

71

3

0.6269282

1.09637

71

3

0.6276295

1.15587

17

59

ENST00000449483

NR_103718

NR_103718

NR_103718

NR_103718

ENST00000560199

ENST00000560199

down

Neighboring

up

enhancer

enhancer

1.49104

11

58

0.6292106

1.49104

11

58

0.6323546

1.24174

24

37

0.6323546

1.24174

24

37

0.6323546

1.24174

24

37

0.6323546

1.24174

24

37

0.6336632

1.18485

3

96

0.6336632

1.18485

3

96

Neighboring

Neighboring

up

enhancer

up

Neighboring

0.6338919

31

MYL9

NM_006097

105686

MTAP

NM_002451

ng

ng

105686

upstream

MTAP

NM_002451

TNFRSF

0

10A

NM_003844

TNFRSF

0

10A

NM_003844

23796

DSP

NM_004415

0

BDNF

NM_170735

overlappi ng

overlappi

Neighboring

ng

0

FGF13

NM_004114

overlappi

Neighboring

up

up

up

up

up

down

Neighboring

enhancer

ng

0

RABL3

NM_173825

overlappi ng

0

RABL3

NM_173825

downstrea m

43783

ACTN1

NM_001102

43783

ACTN1

NM_001102

downstrea enhancer

m

Neighboring

Neighboring

enhancer

upstream

upstream

upstream

53

53

2794

OPA1

OPA1

BID

NM_015560

1.205845

932

1

up

0.000153

2.617340

dow

9

n

872 0.956541 385

dow 1.012681

n

945

2.11807

up

0.018342

2.046663

73

3

up

0.044521

3.220163

dow

49

4

n

0.782380

1.175744

74

1

0.008594

6.686183

527

6

up

0.041312

1.514278

dow

806

7

n

0.277649

1.255401

375

4

0.167669

1.499588

662

8

0.672502

1.079628

266

4

0.006900

n

0.058266

1.463096

dow

034

7

n

0.058266

1.463096

dow

034

7

n

0.641884

1.121956

21

8

0.641884

1.121956

21

8

up

0.009457

2.222940

dow

865

4

n

0.236704

1.247943

dow

NM_004330

355

4

n

NM_001254

0.020325

2.075097

dow

738

195

5

n

NM_001196

upstream

2794

BID

NM_001196

NM_001196

overlappi Neighboring

ng

0

BNIP2

NM_004330

overlappi Neighboring

ng

0

BNIP2

downstrea enhancer

m

80

64836

RND3

dow

9

enhancer

BID

up

058

NM_015560

down

2794

up

dow

NM_001196

upstream

up

1.411091

BID

Neighboring

up

0.482331

2794

up

0.280322

up

n

upstream

up

4

2.533074

Neighboring

up

109

8

down

down

1.505376

0.016092

1.45205 ENST00000441356

m

overlappi

up

0.6292106

m

overlappi

down

59

0

downstrea

up

1.15587

ng downstrea

up

17

NM_006097

overlappi

up

0.6276295

MYL9

0.207236

T

0.6107889

0

IP

32

AC

ENST00000449483

89

ng

SC R

ENST00000517774

1.10854

Neighboring

NU

ENST00000517774

0.6106042

down

MA

ENST00000427983

32

D

ENST00000427983

89

overlappi

TE

ENST00000561134

1.10854

CE P

ENST00000561134

0.6106042

up

ACCEPTED MANUSCRIPT 1.45205

ENST00000433054

ENST00000433054

ENST00000536217

ENST00000536217

ENST00000502188

ENST00000502188

ENST00000422953

NR_033346

NR_033346

ENST00000433644

TCONS_00026823

ENST00000584614

ENST00000584614

NR_046325

NR_046325

1.50970

84

38

0.6350860

1.50970

84

38

0.6378405

1.18636

28

03

0.6378405

1.18636

28

03

0.6388706

1.11284

58

21

0.6388706

1.11284

58

21

0.6393712

1.38114

67

97

0.6393712

1.38114

67

97

0.6421457

1.53805

55

1

0.6421457

1.53805

55

1

0

GAS6

NM_000820

down

Neighboring

upstream

224

UNG

NM_080911

Neighboring

1.20447

8

61

0.6448784

1.37611

73

48

0.6448784

1.37611

73

48

0.6469652

1.34499

63

21

0.6481762

1.07535

13

97

0.6538140

1.48223

1

05

0.6538140

1.48223

1

05

0.6545082

1.13187

18

69

0.6545082

1.13187

18

69

upstream overlappi

Neighboring

ng overlappi

Neighboring

up

enhancer

up

enhancer

ng

224

UNG

NM_080911

0

0

VPS53

VPS53

uc002frn.2

uc002frn.2

upstream

29619

ZAK

NM_016653

upstream

29619

ZAK

NM_016653

downstrea

enhancer

m

61433

HMGA2

NM_003483

downstrea

up

0.6443555

0.170289

ng

up

61

6

Neighboring

down

1.20447

985

down

down

8

738

overlappi

down

0.6443555

1.295406

enhancer

up

up

up

up

Neighboring

Neighboring

m

61433

HMGA2

NM_003483

overlappi ng

0

NUP214

NM_005085

overlappi ng

0

NUP214

NM_005085

0

JAK2

NM_004972

overlappi Neighboring

ng overlappi

Neighboring

ng

0

JAK2

NM_004972

overlappi down

Neighboring

ng

0

BOK

NM_032515

overlappi down

Neighboring

up

enhancer

down

enhancer

ng

upstream

0

BOK

NM_032515

Neighboring

ng

up

up

Neighboring

enhancer

Neighboring

ng

upstream

upstream

81

n

0.129704

2.096481

dow

054

7

n

0.342844

1.563567

392

6

0.029334

1.753156

735

5

up

0.044728

1.502138

dow

947

7

n

17

1.578489

up

0.928508

1.020703

422

8

up

0.058326

1.932345

dow

228

7

n

0.108397

1.349757

58

3

up

0.053482

3.108835

dow

507

2

n

0.627714

1.163603

761

4

up

0.514886

1.118148

dow

75

9

n

0.645113

1.438621

766

9

0.667755

1.079074

999

6

0.670021

1.194409

746

7

up

0.938903

1.015268

dow

915

6

n

up

0.039092

up

up

NM_000264

0.025155

1.781490

dow

5783

SAFB2

NM_014649

121

1

n

ENST00000

0.002181

3.463994

dow

413366

54

8

n

ENST00000

0.007944

2.072423

413366

451

9

0.017422

1.752506

969

5

0.017422

1.752506

969

5

0

PRKCA

overlappi up

2.542615

PTCH1

overlappi up

dow

16185

downstrea m

up

839

T

0.6350860

RND3

0.085924

IP

97

AC

ENST00000422953

32

64836

NM_001254

SC R

ENST00000574008

1.14673

m

NU

ENST00000574008

0.6346089

enhancer

MA

ENST00000541704

up

D

ENST00000541704

31

TE

NR_044995

0.6338919

CE P

ENST00000441356

downstrea

0

2524

2524

PRKCA

KDM5B

KDM5B

NM_006618

NM_006618

up

up

up

ACCEPTED MANUSCRIPT

TCONS_00028433

TCONS_00028433

TCONS_00028433

TCONS_00028433

ENST00000533590

ENST00000531663

ENST00000579522

NR_045484

1.18212

13

27

0.6548326

1.18212

13

27

0.6549847

1.83870

02

95

0.6549847

1.83870

02

95

0.6550407

1.21017

29

93

0.6550407

1.21017

29

93

0.6550407

1.21017

29

93

0.6550407

1.21017

29

93

0.6551938

1.42762

02

02

0.6553744

1.17870

45

73

ENST00000567342

ENST00000420870

ENST00000420870

uc001xvp.3

ENST00000556537

ENST00000556537

ENST00000510807

Neighboring

down

enhancer

1.22854

12

26

0.6607236

1.22854

12

26

0.6610208

1.38070

52

55

0.6623781

1.40269

78

71

0.6623781

1.40269

78

71

0.6625811

1.10485

87

92

0.6673757

1.19463

3

05

0.6673757

1.19463

3

05

0.6677628

1.36121

91

87

m

enhancer

m

enhancer

upstream

enhancer

upstream downstrea

up

enhancer

up

enhancer

28939

EFNA5

NM_001962

28939

EFNA5

NM_001962

24830

IP

NM_017632

24830

m

IP

NM_017632

up

up

up

up

m

enhancer

enhancer

Neighboring

Neighboring

upstream

upstream

upstream

ng

ng

Neighboring

ng

Neighboring

m

5

0.085266

1.817529

484

2

0.729569

1.120161

808

9

up

0.013576

2.878460

dow

228

6

n

up

up

up

NM_001032

0.650546

1.100089

dow

288

389

3

n

0.528658

1.242833

236

7

0.944853

1.025041

124

2

up

0.246949

1.527790

dow

901

9

n

0.032500

2.956789

591

2

0.281253

2.733092

458

2

0.200570

1.444105

NM_001257

311

5

up

NM_001008

0.011809

1.464930

dow

392

217

3

n

NM_001008

0.266805

392

948

1.164969

up

0.560392

1.268549

688

2

up

0.021260

2.695730

dow

795

5

n

50652

593

UBE2V1

UVRAG

NM_003369

0

SYT13

NM_020826

0

MAP2K4

NM_003010

0

BCL10

NM_003921

0

BCL10

NM_003921

625

CDH13

71485

SEL1L

NM_005065

0

PNN

NM_002687

overlappi

82

073

7

overlappi

upstream

1.439986

258

UBE2V1

downstrea

enhancer

0.671920

288

50652

CTDSPL

up

n

1.126520

403

ng

dow

5

0.550020

upstream

Neighboring

3.493195

942

NM_001032

Neighboring

up

0.007285

n

down

ng

n

dow

CTDSPL

Neighboring

2

6

403

up

402

1.998587

upstream

m

dow

149

Neighboring

enhancer

1.683092

0.059188

down

down

0.296033

NM_005985

downstrea up

n

SNAI1

overlappi up

2

36731

overlappi Neighboring

402

NM_005985

overlappi Neighboring

dow

SNAI1

overlappi ng

1.683092

36731

downstrea

up

0.6607236

NM_006618

CDKN2A

up

79

KDM5B

CDKN2A

up

1.14519

2524

downstrea

up

3

NM_006618

downstrea

down

0.6564152

upstream

KDM5B

0.296033

T

0.6548326

up

2524

IP

69

AC

NR_045484

18

upstream

SC R

ENST00000510299

1.13187

enhancer

NU

ENST00000510299

0.6545082

up

MA

ENST00000509458

69

D

ENST00000509458

18

TE

NR_046325

1.13187

CE P

NR_046325

0.6545082

0.087749 0

9105

PNN

CXCL6

NM_002687

NM_002993

up

up

up

dow

675

1.804834

n

0.658265

1.128437

dow

804

4

n

ACCEPTED MANUSCRIPT

ENST00000466502

ENST00000466502

ENST00000466502

ENST00000466502

1.17241

65

77

0.6708393

1.23831

9

73

0.6708393

1.23831

9

73

0.6773045

1.16381

56

92

0.6773045

1.16381

56

92

0.6773045

1.16381

56

92

0.6773045

1.16381

56

92

Neighboring

0.6785413

down

Neighboring

up

enhancer

down

down

enhancer

Neighboring

enhancer

down

enhancer

down

Neighboring

down

enhancer

36

down

ENST00000445429

72

TE

0.6786063 1.06798

0.6786063

NR_040058

ENST00000538101

uc003bus.3

ENST00000528210

ENST00000528210

NR_026948

ENST00000441264

ENST00000441264

ENST00000425312

1.06798

0.6795435

1.22553

48

02

0.6816665

1.15278

41

91

AC

ENST00000538101

72

down

down

CE P

ENST00000445429

enhancer

D

0.6785413

0.6816665

1.15278

41

91

0.6834204

1.05668

9

76

0.6849710

1.11880

71

38

0.6849710

1.11880

71

38

0.6851458

1.21386

9

42

0.6865967

1.14637

2

56

0.6865967

1.14637

2

56

0.6869308

1.14060

18

8

ng

NM_001184

0

ATR

NM_001184

m

14885

GPRC5A

NM_003979

downstrea

1.14606 TCONS_00004454

ATR

downstrea

up

36

0

overlappi

1.14606 TCONS_00004454

ng

down

down

m

upstream

upstream

Neighboring

14885

GPRC5A

2083

2083

ATR

ATR

CTDSPL

5

n

0.002972

2.153672

dow

031

5

n

0.811831

1.094515

243

1

0.811831

1.094515

243

1

up

0.030378

1.814644

dow

246

2

n

0.090023

2.776684

NM_002410

331

8

up

NM_001008

0.011809

1.464930

dow

392

217

3

n

NM_001008

0.266805 948

1.164969

up

0.418519

1.163009

dow

598

3

n

0.016211

2.113358

dow

798

4

n

0.028067

2.110905

dow

895

5

n

NM_001184

NM_002410

CTDSPL

392

Neighboring

upstream

23

RAD51

NM_002875

overlappi AHNAK

NM_001620

overlappi down

Neighboring

ng

0

AHNAK

2.890761

031

NM_001184

449

0

0.002074

NM_001620

0.013485 up

Neighboring

upstream

292

FANCD2

NM_033084

overlappi up

Neighboring

up

Neighboring

ng

0

PARP2

NM_005484

0

PARP2

NM_005484

overlappi ng downstrea up

up

up

enhancer

enhancer

enhancer

m

upstream

upstream

4905

41997

41997

FAIM2

PARP1

PARP1

NM_012306

NM_001618

NM_001618

downstrea down

enhancer

m

83

14978

MDH1

up

dow

upstream

ng

1

2.153672

Neighboring

Neighboring

243

0.002972

NM_001184

449

1.094515

up

ATR

upstream

0.811831

6

2083

MGAT5

n

943

NM_003979

upstream

222984

5

2.629595

NM_001184

upstream

031

0.002600

ATR

MGAT5

dow

8

2083

222984

2.153672

078

upstream

upstream

0.002972

T

0.6683414

down

IP

NR_003932

77

SC R

NR_003932

65

overlappi

NU

ENST00000481134

1.17241

MA

ENST00000481134

0.6683414

NM_005917

up

up

dow

543

1.866954

n

0.192322

2.770705

109

1

0.623138

1.409979

852

3

0.989182

1.004552

77

4

up

0.242680

1.418953

dow

341

8

n

0.399226

1.245985

dow

522

5

n

0.022138

1.366483

dow

943

8

n

up

up

ACCEPTED MANUSCRIPT

ENST00000411780

ENST00000411780

ENST00000526635

8

0.6883115

1.07988

17

44

0.6883115

1.07988

17

44

0.6883115

1.07988

17

44

0.6883115

1.07988

17

44

0.6893851

1.20078

38

94

down

enhancer

m

up

enhancer

m

87038

SRC

up

enhancer

upstream

8185

BLCAP

up

enhancer

upstream downstrea

up

down

enhancer

Neighboring

ENST00000413839

ENST00000413839

ENST00000451639

m

upstream

1.20148

31

18

0.6983789

1.20148

31

18

0.6995919

1.36422

75

81

0.6995919

1.36422

75

81

ENST00000477848

ENST00000477848

ENST00000561409

ENST00000561409

ENST00000569249

ENST00000569249

TCONS_00012265

TCONS_00012265

up

enhancer

1.26708 27

0.7060866

1.14835

66

5

0.7062613

1.44123

32

81

0.7062613

1.44123

32

81

0.7070407

1.14339

47

74

0.7070407

1.14339

47

74

0.7095906

1.30932

76

96

0.7095906

1.30932

76

96

0.7099724

1.09930

1

96

0.7099724

1.09930

1

96

2

n

0.043785

1.941057

dow

NM_005417

148

4

n

NM_001167

0.198429

BLCAP

87038

30

SRC

RAD51

enhancer

244

1.936424

NM_001167

0.249960

1.600060

820

719

6

0.329568

1.924938

72

9

up

0.418519

1.163009

dow

598

3

n

0.196679

2.084116

012

5

up

0.031608

3.217272

dow

948

9

n

0.010671

2.297847

dow

013

9

n

0.349520

1.695178

dow

907

8

n

5.82491E

9.128950

-06

1

up

3.588262

up

NM_005417

NM_002875

3996

GNMT

NM_018960

upstream

5457

MMP12

NM_002426

m

61253

CUL1

enhancer

down

down

down

down

enhancer

enhancer

m

61253

CUL1

NM_003592

NM_003592

downstrea m

67295

IGFBP1

NM_000596

downstrea m

Neighboring

ng

upstream

67295

IGFBP1

NM_000596

0

ERBB4

NM_005235

Neighboring

ng

656

DBP

NM_001352

0

LAMA5

NM_005560

overlappi down

Neighboring

ng

0

LAMA5

NM_005560

overlappi up

Neighboring

up

Neighboring

ng

0

AKAP13

NM_007200

0

AKAP13

NM_007200

overlappi ng overlappi down

Neighboring

ng

CBFA2T 0

overlappi down

up

up

Neighboring

enhancer

enhancer

ng

upstream

upstream

84

006 0.002606

overlappi down

n

up

0.003301

overlappi Neighboring

dow

820

downstrea

up

3

678

NM_005917

downstrea

up

0.7060734

8185

NU

0.6983789

dow

upstream

MA

72

AC

NR_004401

1.06873

52

enhancer

D

ENST00000392885

0.6974219

down

TE

ENST00000392885

1.0518

CE P

ENST00000530713

18

MDH1

1.017365

downstrea

0.6898693 ENST00000326586

14978

0.922601

T

ENST00000411780

18

downstrea

IP

ENST00000411780

1.14060

SC R

ENST00000425312

0.6869308

3

NM_005187

CBFA2T 0

268424

268424

3

HSF2

HSF2

dow

117

2.412779

n

0.832027

1.105325

417

7

up

8.58074E

2.928353

dow

-05

4

n

0.185805

1.626521

dow

161

5

n

0.611888

1.142217

849

2

0.752861

1.085370

293

3

0.214149

1.219508

293

1

up

158

1.28583

up

0.127121

1.747453

dow

568

3

n

0.213366

2.182183

dow

085

2

n

up

up

0.485714 NM_005187

NM_004506

NM_004506

ACCEPTED MANUSCRIPT

NR_038885

NR_038885

NR_038885

ENST00000415716

ENST00000415716

ENST00000491837

ENST00000491837

1.09130

39

63

0.7136029

1.15775

19

46

0.7136029

1.15775

19

46

0.7153210

1.18291

93

99

0.7153210

1.18291

93

99

0.7153210

1.18291

93

99

0.7153210

1.18291

93

99

0.7173904

1.19095

57

38

0.7173904

1.19095

57

38

0.7176283

1.17333

4

89

ENST00000553425

ENST00000433810

ENST00000433810

TCONS_00019532

TCONS_00019532

TCONS_00020260

TCONS_00020260

ENST00000448289

Neighboring

up

Neighboring

enhancer

enhancer

1.30270

88

98

0.7251171

1.30270

88

98

0.7292260

1.24329

33

9

0.7292260

1.24329

33

9

0.7304132

1.12999

63

76

0.7304132

1.12999

63

76

0.7310815

1.23221

42

19

0.7310815

1.23221

42

19

0.7321996

1.09656

27

95

m

Neighboring

m downstrea

up

enhancer

up

Neighboring

0

SHPRH

3669

m

HSF2

m

3669

2929

HSF2

RUNX1

2929

RUNX1

2929

RUNX1

downstrea

enhancer

m

NM_025047

815

3

up

ENST00000

0.024546

1.530404

dow

355072

606

7

n

NM_001042

0.066474

2.052910

dow

586

1

n

0.127121

1.747453

dow

568

3

n

0.213366

2.182183

dow

NM_004506

085

2

n

NM_001001

0.461399

1.504377

890

471

8

NM_001001

0.461399

1.504377

890

471

8

up

NM_001001

0.536768

1.278740

dow

890

256

6

n

NM_001001

0.536768

1.278740

dow

890

256

6

n

0.595632

1.150273

dow

454

9

n

up

683

downstrea

NM_004506

2929

RUNX1

downstrea

down

0.7251171

m

downstrea

up

89

ng

downstrea

up

1.17333

HTT

downstrea

down

4

166

overlappi

down

0.7176283

upstream

ARL14

T

0.7130965

down

91372

3.147124

IP

64

AC

ENST00000553425

77

m

0.001599

SC R

NR_038885

1.15062

enhancer

NU

uc003pyw.1

0.7124059

down

MA

uc003pyw.1

67

enhancer

D

NR_038244

44

downstrea

TE

NR_045414

1.08016

down

up

CE P

ENST00000490136

0.7110868

up

up

enhancer

enhancer

m

31292

MAL

downstrea m

0.664757 31292

MAL

downstrea m

10502

FAIM

10502

FAIM

downstrea enhancer

enhancer

m

upstream

30067

FOXA1

downstrea up

enhancer

NM_002371

m

4898

MIPOL1

NM_002371

079

1.090555

NM_001033

0.016126

1.964272

032

83

3

up

NM_001033

0.803640

1.220490

dow

032

988

1

n

0.000787

2.922341

dow

NM_004496

664

3

n

NM_001195

0.355590

1.775805

dow

296

301

9

n

0.000615

10.89733

dow

777

81

n

0.540193

1.261414

dow

935

6

n

0.000463

6.740495

913

6

0.009170

2.460697

612

2

up

0.195321

1.392810

dow

545

9

n

0.220451

3.308575

814

9

0.004786

2.074211

408

9

downstrea up

enhancer

m

4543

MYCN

NM_005378

downstrea up

enhancer

down

enhancer

m

4543

MYCN

NM_005378

165292

ETS1

NM_005238

downstrea m downstrea down

enhancer

m

165292

ETS1

NM_005238

downstrea up

Neighboring

m

128

BRI3BP

NM_080626

downstrea up

Neighboring

m

128

BRI3BP

NM_080626

overlappi down

Neighboring

ng

85

up

0

MTOR

NM_004958

up

up

up

ACCEPTED MANUSCRIPT

ENST00000429986

ENST00000583377

ENST00000533146

uc003xew.3

uc003xew.3

ENST00000557223

ENST00000547902

1.05535

69

17

0.7332880

1.05535

69

17

0.7334285

1.26955

79

73

0.7334285

1.26955

79

73

0.7345239

1.13230

42

07

0.7346782

1.17689

27

3

0.7358936

1.04444

42

97

0.7385589

1.17860

32

36

0.7385589

1.17860

32

36

0.7405530

1.04543

81

29

ENST00000512245

NR_047570

NR_047570

TCONS_00029702

ENST00000525992

ENST00000531701

ENST00000531701

ENST00000563394

up

enhancer

m

17650

MAPK1

NM_002745

up

Neighboring

upstream

270

RBMS1

NM_016836

up

up

Neighboring

enhancer

enhancer

up

enhancer

down

Neighboring

91

0.7406189

1.05863

27

91

0.7409486

1.09385

03

82

0.7409952

1.12822

22

71

0.7409952

1.12822

22

71

0.7425359

1.25330

18

77

0.7501655

1.37561

6

11

0.7521330

1.10269

54

74

0.7521330

1.10269

54

74

0.7522153

1.11243

86

56

upstream

upstream

270

m

RBMS1

25538

25538

MCM5

MCM5

74715

XIAP

0

NF1

overlappi

down

1.05863

upstream

downstrea

down

27

NM_002745

downstrea

up

0.7406189

MAPK1

down

down

up

up

up

ng

Neighboring

Neighboring

Neighboring

Neighboring

upstream

upstream

upstream

32

53

53

RAD51

BNIP3L

BNIP3L

m

enhancer

m

upstream

Neighboring

ng

2

up

0.001125

0.651763

1.152899

dow

575

2

n

0.081589

1.259346

dow

327

4

n

0.148635

1.548010

dow

364

5

n

0.863760

1.041854

NM_001167

027

3

up

NM_001042

0.226162

1.591247

dow

492

935

6

n

0.418519

1.163009

dow

598

3

n

0.154775

1.439896

171

3

0.782329

1.057633

224

7

up

0.005987

1.765190

dow

4

9

n

0.989182

1.004552

77

4

0.989182

1.004552

77

4

up

0.458841

1.166353

dow

366

5

n

NM_016836

NM_006739

NM_006739

NM_002875

NM_004331

NM_004331

NM_005163

1150

FAIM2

NM_012306

FAIM2

UNC5A

NM_012306

NM_133369

overlappi down

15

n

AKT1

71100

1.288615

dow

0

1150

0.519318

1

downstrea Neighboring

0.326797 0

PAX8

NM_003466

overlappi

65

1.188004

0.688520

1.109148

215

8

Neighboring

ng

0

PAX8

NM_003466

down

enhancer

upstream

8867

PDGFB

NM_002608

095

1.107795

NM_001197

0.141958

1.570765

104

606

7

0.006759

13.45544

581

72

0.022072

3.993339

147

4

0.110350

2.046070

675

5

0.694329

up

Neighboring

ng

0

KMT2A

overlappi down

Neighboring

ng

0

DEFB1

NM_005218

overlappi down

up

Neighboring

Neighboring

ng

upstream

86

0

2241

DEFB1

UBTF

NM_005218

NM_014233

up

up

dow

down

overlappi

up

2.683909

downstrea enhancer

1.440335

726

overlappi ng

781

T

0.7332880

17650

IP

17

AC

ENST00000547902

95

m

SC R

TCONS_00029585

1.07340

enhancer

0.108608

NU

TCONS_00029585

0.7328699

up

MA

ENST00000459712

17

D

ENST00000459712

95

downstrea

TE

ENST00000435222

1.07340

CE P

ENST00000435222

0.7328699

n

up dow n

up

up

up

up

ACCEPTED MANUSCRIPT

uc003kor.1

ENST00000560481

ENST00000560481

ENST00000426577

ENST00000484005

ENST00000484005

ENST00000523225

1.12450

58

08

0.7580265

1.11237

59

56

0.7580265

1.11237

59

56

0.7589851

1.03410

01

92

0.7596793

1.08218

7

08

0.7623165

1.11919

18

08

0.7623165

1.11919

18

08

0.7639375

1.09770

83

1

0.7648144

1.14281

89

85

0.7648144

1.14281

89

85

ENST00000445082

ENST00000436616

uc002umb.1

ENST00000447680

ENST00000447680

ENST00000393804

ENST00000393804

ENST00000559021

down

enhancer

down

enhancer

Neighboring

1.11157

09

86

0.7674554

1.13586

85

07

0.7714856

1.06460

5

24

0.7722480

1.24243

14

94

0.7731014

1.08469

54

74

0.7731014

1.08469

54

74

0.7896787

1.08179

33

11

0.7896787

1.08179

33

11

0.7977334

1.06047

81

31

ng

Neighboring

ng downstrea

enhancer

down

enhancer

down

Neighboring

MAP3K8

NM_005204

55782

MAP3K8

NM_005204

m

0

upstream

SEPT4

0

7902

SEPT4

TFAP2A

ng

ng

up

up

up

up

enhancer

enhancer

ng

upstream

upstream

6594

MAPK9

0

MCPH1

overlappi Neighboring

ng overlappi

Neighboring

ng

0

MCPH1

2.101547

2.082510

dow

167

4

n

0.534984

1.616829

dow

234

6

n

0.744662

1.277230

549

5

0.539878

1.177299

824

9

0.919430

1.019202

109

7

0.024198

2.571680

521

1

0.370937

1.476251

353

7

up

0.376471

1.607054

dow

NM_002752

87

1

n

NM_001172

0.300285

1.086093

574

127

9

up

NM_001172

0.932313

574

704

1.030957

up

NM_004574

NM_003220

NM_181746

MAPK9

0.022792

NM_181746

NM_004484

NM_002752

0.013485 down

Neighboring

upstream

102

FANCD2

NM_033084

overlappi up

Neighboring

ng

0

PRKRA

NM_003690

overlappi up

Neighboring

up

enhancer

ng

0

PRKRA

NM_003690

71454

DKK1

NM_012242

downstrea m downstrea up

enhancer

m

DKK1

NM_012242

up

up

up

up

up

dow

543

1.866954

n

0.030974

1.552535

dow

603

3

n

0.030974

1.552535

dow

603

3

n

0.007273

2.808621

dow

56

6

n

0.113159 71454

up

0.333108

CERS2

6594

7

up

0

GPC3

529

9

NM_005246

0

3.005260

582

NM_004574

overlappi

Neighboring

0.002977

up

1.511408

FER

CERS2

9

0.171981

4682

0

597

5

overlappi

Neighboring

1.710016

037

overlappi

down

0.7672334

m

overlappi

down

86

55782

overlappi

up

1.11157

m downstrea

down

09

NM_014233

downstrea

down

0.7672334

UBTF

0.571636

T

0.7525977

2241

IP

08

AC

ENST00000523225

58

upstream

SC R

ENST00000420389

1.12450

Neighboring

NU

ENST00000580769

0.7525977

up

MA

ENST00000580769

56

D

ENST00000396326

86

TE

ENST00000396326

1.11243

CE P

ENST00000563394

0.7522153

414

dow 1.487361

n

377

1.459005

up

0.378091

1.198925

dow

238

8

n

0.088946

2.917030

dow

354

1

n

0.191874 down

down

enhancer

enhancer

upstream

upstream

31021

31021

SOD1

SOD1

NM_000454

NM_000454

downstrea down

enhancer

m

87

9892

FOS

NM_005252

ACCEPTED MANUSCRIPT

ENST00000487421

ENST00000530690

ENST00000530690

ENST00000530690

TCONS_00018285

ENST00000576554

ENST00000231383

1.06972

84

83

0.7988942

1.06972

84

83

0.7988942

1.06972

84

83

0.7990896

1.25182

56

6

0.7990896

1.25182

56

6

0.8004109

1.10847

94

03

0.8004109

1.10847

94

03

0.8004109

1.10847

94

03

0.8021988

1.20904

01

2

0.8063742

1.18082

47

59

ENST00000231383

ENST00000231383

ENST00000421648

ENST00000456685

ENST00000456685

ENST00000563981

ENST00000505151

ENST00000505151

Neighboring

up

Neighboring

Neighboring

Neighboring

Neighboring

up

Neighboring

down

Neighboring

1.03284

73

94

0.8140193

1.03284

73

94

0.8140193

1.03284

73

94

0.8170647

1.21763

81

11

0.8172428

1.04869

12

25

0.8172428

1.04869

12

25

0.8179980

1.10374

14

79

0.8186350

1.05713

52

83

0.8186350

1.05713

52

83

1944

BCL2L13

NM_015367

0

BID

NM_001196

ng

1944

ng

BCL2L13

NM_015367

0

0

BID

LAMA5

NM_001196

NM_005560

0

LAMA5

NM_005560

0

PPFIA1

NM_003626

overlappi

down

0.8140193

ng

overlappi

down

94

upstream

overlappi up

1.03284

ng

overlappi up

73

NM_130469

overlappi

up

0.8140193

upstream

JDP2

up

down

down

down

down

ng

Neighboring

Neighboring

Neighboring

upstream

upstream

143

143

CTTN

CTTN

NM_005231

NM_005231

downstrea m

557

overlappi

down

Neighboring

Neighboring

ng

down

down

Neighboring

Neighboring

Neighboring

ng

upstream

upstream

88

2.205736

475

6

0.641884

1.121956

21

8

up

8.58074E

2.928353

dow

-05

4

n

0.185805

1.626521

dow

161

5

n

0.029153

1.583117

54

2

0.091330

2.165875

634

7

0.742569

1.121800

32

3

up

0.003320

2.340029

dow

0.272492

1.168618

dow

087

8

n

0.460683

1.075137

789

6

0.562349

1.260813

935

8

0.368187

1.546336

28

9

BAG3

TIAL1

NM_004281

NM_003252

BAG3

NM_004281

NM_005232

0

PAX8

NM_003466

0.326797

2994

2994

up

up

EPHA1

0

up

3

0

0

up

1.416168

PAX8

NM_003466

overlappi up

0.084680

659

overlappi down

n

0.020906

overlappi ng

dow

7

n

overlappi ng

1.463096

034

5

downstrea

Neighboring

0.058266

346

NM_003252

down

up

dow

TIAL1

29489

7

1.256831

24038

m

742

0.553977

upstream

enhancer

2.944520

NM_001185

downstrea down

0.001862

ARHGDI

enhancer

24038

n

n

077

upstream

5

3

A

enhancer

325

929

0

29489

dow

NM_025235

ng

m

1.225722

TNKS2

Neighboring

enhancer

0.513860

T

0.7988942

up

135861

IP

83

AC

ENST00000231383

84

upstream

SC R

ENST00000487421

1.06972

enhancer

NU

uc002znb.3

0.7988942

down

MA

uc002znb.3

31

D

uc002znb.3

81

TE

uc002znb.3

1.06047

CE P

ENST00000559021

0.7977334

CDH13

GNB2L1

GNB2L1

NM_001257

NM_006098

NM_006098

up

up

up dow

65

1.188004

n

0.688520

1.109148

215

8

0.200570

1.444105

311

5

0.451332

1.127489

786

7

up

0.725742

1.060917

dow

271

4

n

up

up

ACCEPTED MANUSCRIPT

TCONS_00024123

ENST00000555967

ENST00000555967

uc003myy.1

ENST00000528578

ENST00000415809

ENST00000415809

1.16858

49

62

0.8305408

1.05875

31

79

0.8305408

1.05875

31

79

0.8305408

1.05875

31

79

0.8305408

1.05875

31

79

0.8331020

1.02761

9

04

0.8331020

1.02761

9

04

0.8334549

1.06750

39

54

0.8335604

1.16951

2

59

0.8348060

1.04158

34

5

ENST00000517454

ENST00000520175

ENST00000520175

uc003vdd.1

uc003vdd.1

uc002vsa.3

uc002vsa.3

NR_027067

MTUS1

924

up

Neighboring

upstream

141

ZEB1

NM_030751

downstrea Neighboring

1.03824

4

37

0.8358775

1.03824

4

37

0.8409112

1.07508

33

99

0.8409112

1.07508

33

99

0.8544890

1.19275

87

86

0.8544890

1.19275

87

86

0.8589569

1.05240

2

39

0.8589569

1.05240

2

39

0.8658299

1.05643

64

91

m downstrea

enhancer

m downstrea

enhancer

m downstrea

down

Neighboring

down

enhancer

2301

2301

2301

m

2301

downstrea m

6775

downstrea

enhancer

m

BCL2L10

BCL2L10

BCL2L10

BCL2L10

Neighboring

up

up

up

down

Neighboring

ng

0

B

TFAP2A

overlappi ng

0

KMT2A

1.384504

up

0.275786

2.274973

1.607061

57

3

0.212356

1.607061

57

3

up

0.619623

1.153773

dow

857

7

n

0.619623

1.153773

dow

857

7

n

0.114680

1.465556

dow

766

5

n

0.924961

1.042882

907

9

up

0.534984

1.616829

dow

NM_003220

234

6

n

NM_001197

0.141958

1.570765

104

606

7

up

0.450093

1.403992

dow

407

1

n

NM_020396

NM_020396

NM_020396

NM_020396

NM_015316

NM_015316

STIM1

NM_003156

0.678830

1.118678

dow

Neighboring

upstream

193

STIM1

NM_003156

707

6

n

NM_001001

0.020697

924

358

NM_001001

0.424203

924

overlappi Neighboring

ng

0

MTUS1

Neighboring

ng

0

MTUS1

Neighboring

ng

0

STK3

NM_006281

up

Neighboring

ng

0

STK3

NM_006281

up

Neighboring

upstream

17

RINT1

NM_021930

dow 2.159611

n

514

1.384504

up

0.357412

1.279931

dow

356

4

n

0.745203

1.127397

447

5

0.027570

down

down

Neighboring

Neighboring

Neighboring

upstream

upstream

upstream

17

1524

1524

RINT1

PTMA

PTMA

downstrea down

up

193

overlappi

up

up

upstream

overlappi up

514

Neighboring

overlappi down

n

0.212356

PPP1R13 6775

2.159611

3

PPP1R13 B

dow

883

overlappi

up

0.8358775

0.424203

8293

down

5

NM_001001 upstream

down

1.04158

358

enhancer

down

34

924

down

down

0.8348060

MTUS1

T

0.8301367

8293

0.020697

IP

49

AC

ENST00000517454

09

upstream

NM_001001

SC R

TCONS_00024123

1.14861

enhancer

NU

TCONS_00024123

0.8294698

down

MA

TCONS_00024123

49

D

uc021pov.1

09

TE

ENST00000520156

1.14861

CE P

ENST00000520156

0.8294698

enhancer

m

89

78287

ERG

up dow

654

1.883396

0.790821

1.072945

NM_021930

939

5

NM_001099

0.019698

1.497883

285

364

4

NM_001099

0.770573

1.134662

285

035

2

NM_001243

0.039709

1.381228

428

964

6

n

up

up

up

up

ACCEPTED MANUSCRIPT

ENST00000520129

ENST00000553698

ENST00000553698

TCONS_00004557

NR_038453

NR_046365

ENST00000550617

1.05643

64

91

0.8658850

1.06538

78

81

0.8658850

1.06538

78

81

0.8677572

1.05977

89

87

0.8677572

1.05977

89

87

0.8736259

1.03219

18

29

0.8736259

1.03219

18

29

0.8737912

1.05142

62

91

0.8743763

1.09119

97

22

0.8747561

1.07114

79

99

ENST00000566904

TCONS_00004641

TCONS_00004641

ENST00000426353

ENST00000426353

ENST00000526906

ENST00000526906

ENST00000526906

downstrea

1.03952

67

61

0.8895008

1.03952

67

61

0.8898972

1.05564

74

68

0.8898972

1.05564

74

68

0.8933557

1.04194

55

39

0.8933557

1.04194

55

39

0.8948225

1.03255

92

91

0.8948225

1.03255

92

91

0.8948225

1.03255

92

91

NM_001243

0.516659

1.247078

dow

705

2

n

0.774102

1.180842

ERG

428

down

enhancer

upstream

53573

ETS2

NM_005239

enhancer

enhancer

upstream

upstream overlappi

Neighboring

ng overlappi

up

Neighboring

down

enhancer

enhancer

91563

AKR1B1

NM_001628

91563

0

AKR1B1

E2F5

NM_001628

NM_001951

ng

0

E2F5

NM_001951

upstream

28562

PNN

NM_002687

upstream

enhancer

up

down

down

up

Neighboring

m

28562

PNN

NM_002687

18490

FZD7

NM_003507

overlappi ng

0

UNC5B

NM_170744

downstrea

enhancer

m

5251

BIRC8

NM_033341

enhancer

upstream

3703

DRAM1

NM_018370

downstrea enhancer

m

Neighboring

m

2259

CEP350

NM_014810

Neighboring

m

2259

CEP350

NM_014810

2532

ING5

NM_032329

downstrea down

Neighboring

m

2532

ING5

NM_032329

down

enhancer

upstream

3178

EPHA2

NM_004431

down

up

up

up

enhancer

Neighboring

enhancer

Neighboring

upstream

upstream

upstream

upstream

90

up

0.002953

2.116394

dow

083

4

n

0.026971

1.176406

dow

166

7

n

0.161523

1.334539

dow

227

6

n

0.338913

1.403581

dow

82

8

n

0.021260

2.695730

dow

795

5

n dow

675

1.804834

n

0.171809

1.667668

dow

485

9

n

0.001373

5.295865

959

5

up

0.120773

2.031873

dow

916

8

n

0.002330

3.256912

489

9

622

3178

1390

1390

1390

EPHA2

ADM

ADM

ADM

NM_004431

NM_001124

NM_001124

NM_001124

up dow

1.173257

0.733829

downstrea down

3

0.733829

downstrea up

538

0.087749

downstrea

down

0.8895008

up

78287

down

19

1.54486

m

up

1.06326

259

enhancer

up

31

NM_005239

down

up

0.8847217

ETS2

T

0.8658299

53573

IP

91

AC

ENST00000566904

64

upstream

SC R

ENST00000520129

1.05643

enhancer

NU

ENST00000453087

0.8658299

down

MA

ENST00000453087

91

D

NR_027067

64

0.466980

TE

NR_027067

1.05643

CE P

NR_027067

0.8658299

n dow

622

1.173257

n

0.042057

1.723478

75

2

up

0.147362

1.281086

dow

591

7

n

0.166329

2.101499

dow

861

5

n

0.186313

1.620362

543

9

0.006697

2.402708

185

5

0.006697

2.402708

185

5

up

0.237297

1.405979

dow

221

4

n

up

up

ACCEPTED MANUSCRIPT

ENST00000472521

TCONS_00004240

NR_046268

NR_046268

ENST00000450044

ENST00000433633

ENST00000420367

1.01653

79

02

0.8977650

1.10878

08

21

0.8983767

1.11648

81

86

0.9003349

1.07237

15

46

0.9003349

1.07237

15

46

0.9075986

1.01830

6

03

0.9156007

1.00627

48

53

0.9156007

1.00627

48

53

0.9265981

1.02967

43

93

0.9280668

1.03546

73

53

1.02426

15

08

ENST00000569039

ENST00000569039

ENST00000555261

ENST00000555261

NR_026763

NR_026763

ENST00000403956

ENST00000403956

0.9290871

1.01643

69

79

0.9290871

1.01643

69

79

0.9305985

1.05534

17

02

0.9305985

1.05534

17

02

0.9322041

1.02825

63

53

0.9322041

1.02825

63

53

0.9374152

1.04681

47

29

0.9374152

1.04681

47

29

n

0.035249

1.259212

dow

525

9

n

YY1

NM_003403

up

Neighboring

upstream

209

YY1

NM_003403

702

1.513715

up

NM_001024

0.229157

1.272163

dow

630

605

5

n

0.080677

1.961162

817

9

0.000416

3.425335

428

1

0.013463

3.719975

934

6

0.198648

1.168872

691

6

0.339136

enhancer

Neighboring

upstream

upstream overlappi

Neighboring

ng overlappi

up

Neighboring

down

Neighboring

114368

RUNX2

518

0

ITGA5

RAB7A

NM_002205

NM_004637

ng

0

RAB7A

NM_004637

upstream

1078

PRKCE

NM_005400

overlappi

Neighboring

ng

0.107080 0

TGFB2

NM_003238

overlappi

up

0.9287900

4

209

up

08

221

upstream

up

1.02426

dow

Neighboring

up

15

NM_001124

1.405979

up

down

0.9287900

ADM

0.237297

T

0.8970213

1390

IP

02

AC

ENST00000420367

79

upstream

SC R

ENST00000472521

1.01653

enhancer

NU

ENST00000552053

0.8970213

up

MA

TCONS_00011820

91

Neighboring

D

ENST00000554537

92

TE

ENST00000554537

1.03255

down

down

CE P

ENST00000526906

0.8948225

up

up

Neighboring

enhancer

ng

0

TGFB2

NM_003238

downstrea m

upstream

72

PRKRA

NM_003690

5011

TCF20

NM_005650

0

PDCD4

NM_014456

overlappi Neighboring

ng overlappi

Neighboring

ng

0

PDCD4

NM_014456

up

Neighboring

Neighboring

upstream

upstream

27

27

MVP

MVP

NM_017458

NM_017458

overlappi up

Neighboring

up

Neighboring

ng

Neighboring

ng

666

1.773473

n

0.426105

1.101603

dow

543

8

n

0.030974

1.552535

dow

603

3

n

0.304367

1.150928

dow

735

3

n

0.131988

2.644989

105

4

0.848332

1.056179

765

9

down

down

Neighboring

enhancer

enhancer

ng

upstream

upstream

91

up

up dow

169

1.674119

n

0.672384

1.078094

dow

928

5

n

919

1.444281

up

MAX

NM_002382

0.927466

1.030207

0

MAX

NM_002382

657

7

NM_001001

0.792408

1.019802

419

6

9

NM_001001

0.818688

1.054148

419

731

6

up

0.017603

3.772780

dow

304

7

n

0.969904

1.020225

703

1

0

SMAD5

overlappi up

up

0

overlappi up

up

0.008384

overlappi ng

up

dow

0.049874 up

up

0

28109

28109

SMAD5

BCLAF1

BCLAF1

NM_014739

NM_014739

up

up

up

ACCEPTED MANUSCRIPT

ENST00000419283

ENST00000419283

ENST00000471720

TCONS_00016117

NR_033992

NR_033992

ENST00000560221

uc003hws.1

1.02489

57

83

0.9399056

1.02489

57

83

0.9400037

1.01190

46

14

0.9400037

1.01190

46

14

0.9400037

1.01190

46

14

0.9400037

1.01190

46

14

0.9412711

1.03921

51

66

0.9412963

1.01967

12

32

0.9418113

1.02801

89

33

0.9418113

1.02801

89

33

ENST00000456721

ENST00000456721

ENST00000418183

ENST00000557518

ENST00000557518

ENST00000454488

ENST00000450125

up

Neighboring

up

enhancer

enhancer

1.01747

36

69

0.9470755

1.01606

15

58

0.9493045

1.02106

75

24

0.9493045

1.02106

75

24

0.9499466

1.02072

41

03

0.9524515

1.02070

92

54

0.9524515

1.02070

92

54

0.9541535

1.01176

97

76

0.9552487

1.07397

54

19

m

Neighboring

m downstrea

enhancer

m downstrea

down

Neighboring

down

enhancer

NQO1

NM_000903

7910

RAB2A

NM_002865

7910

m

RAB2A

NM_002865

2814

2814

DPP4

DPP4

NM_001935

NM_001935

2814

DPP4

NM_001935

2814

DPP4

NM_001935

downstrea m

Neighboring

upstream

2759

TRIM59

NM_173084

downstrea

up

0.9444916

m

downstrea

down

69

0

downstrea

down

1.01747

ng downstrea

down

36

NM_000903

overlappi

up

0.9444916

NQO1

enhancer

down

down

down

down

up

Neighboring

m

27638

RAD23B

NM_002874

overlappi ng

0

TOPORS

NM_005802

overlappi 0

TOPORS

NM_005802

enhancer

upstream

2160

IGF1R

NM_000875

Neighboring

upstream

2160

185

IGF1R

UBE2D3

NM_000875

NM_181886

overlappi down

Neighboring

ng

0

LAMA5

NM_005560

overlappi down

Neighboring

down

Neighboring

ng

0

LAMA5

NM_005560

0

TOP3A

NM_004618

overlappi ng downstrea down

enhancer

m

46761

TMX1

NM_030755

downstrea down

enhancer

m

Neighboring

ng

46761

TMX1

NM_030755

0

PRKRA

NM_003690

downstrea down

enhancer

m

92

4

up

0.797413

1.056814

dow

19

7

n

0.110644

1.556456

dow

411

7

n

0.882708

1.042715

dow

303

2

n

0.127734

1.359031

675

6

0.127734

1.359031

675

6

0.985446

1.004849

279

2

0.985446

1.004849

279

2

up

0.030740

2.648690

dow

546

6

n

0.562557

1.270166

536

2

489

up

up

up

up dow

2.248732

n

301

1.120601

up

0.226243

1.359237

dow

703

2

n

0.226243

1.359237

dow

703

2

n

0.018625

1.581976

449

6

up

8.58074E

2.928353

dow

-05

4

n

0.185805

1.626521

dow

161

5

n

0.038386

1.643122

52

8

up

0.121872

1.632220

dow

46

6

n

0.839219

overlappi up

751

0.322926

ng

upstream

1.917295

0.010835

Neighboring

Neighboring

0.032061

T

0.9399056

0

IP

79

AC

ENST00000560221

09

ng

SC R

ENST00000419283

1.02393

Neighboring

NU

ENST00000419283

0.9386898

up

MA

ENST00000526470

79

D

ENST00000526470

09

overlappi

TE

ENST00000562696

1.02393

CE P

ENST00000562696

0.9386898

35387

PAX7

NM_002584

dow

287

1.042745

n

0.030974

1.552535

dow

603

3

n

0.146130

1.478466

dow

159

4

n

ACCEPTED MANUSCRIPT

NR_026876

TCONS_00027488

TCONS_00027488

ENST00000437118

ENST00000437118

ENST00000580267

ENST00000580267

NR_045215

1.01297

84

45

0.9612938

1.00730

3

67

0.9640651

1.00629

46

98

0.9675042

1.02472

71

06

0.9675042

1.02472

71

06

0.9682422

1.02894

83

65

0.9682422

1.02894

83

65

0.9686595

1.03317

4

63

0.9686595

1.03317

4

63

0.9704052

1.01605

29

02

ENST00000515178

ENST00000515178

ENST00000548270

ENST00000548270

ENST00000453082

ENST00000429532

ENST00000429532

Neighboring

down

enhancer

up

enhancer

Neighboring

enhancer

up

enhancer

up

Neighboring

0.9722870

1.00416

69

17

0.9722870

1.00416

69

17

0.9725521

1.00933

39

43

0.9725521

1.00933

39

43

0.9747074

1.00744

72

79

0.9747074

1.00744

72

79

0.9798296

1.00295

14

82

0.9830851

1.00674

38

82

0.9830851

1.00674

38

82

NM_002467

m

80021

TGFBR3

NM_003243

m

upstream

upstream

34922

upstream

CD5

115

190705

RABL2B

TPD52L1

m

Neighboring

m

enhancer

up

down

down

down

enhancer

Neighboring

m

m

167112

RND3

overlappi ng

0

RAB12

0

RAB12

overlappi Neighboring

ng overlappi

Neighboring

ng

0

TAGLN

overlappi down

Neighboring

ng

0

TAGLN

Neighboring

m

802

HPGD

2

NM_001130

0.865573

1.065539

922

015

3

0.391403

1.079271

167

9

0.831170

1.048304

026

4

up

0.000141

2.195804

dow

922

6

n

0.650833

1.185010

NM_052876

694

9

up

NM_001254

0.020325

2.075097

dow

738

195

5

n

NM_001254

0.085924

1.295406

738

985

6

up

NM_001025

0.186004

1.625141

dow

300

235

6

n

NM_001025

0.838573

1.135175

300

136

7

up

NM_001001

0.348487

1.276627

dow

522

554

9

n

NM_001001

0.467157

1.248484

522

105

5

up

0.798586

1.054176

dow

061

3

n

0.799989

1.070383

08

4

0.004524

1.686237

233

4

0.008475

1.365797

83

8

NM_003287

NM_000860

down

Neighboring

m

802

HPGD

NM_000860

up

enhancer

upstream

35788

CRADD

NM_003805

enhancer

upstream

35788

CRADD

NM_003805

overlappi down

up

up

Neighboring

Neighboring

Neighboring

ng

upstream

upstream

93

0.493435

328

downstrea

up

up

NM_014207

downstrea down

9

1.125454

NM_052876

downstrea

685

0.718375

NACC1

RND3

2.558130

n

130

167112

0.065265

9.08527E 0

457

457

UBE3A

CTDSPL

CTDSPL

up

dow

NM_003287

downstrea

4

8

TPD52L1

NACC1

673

1.628950

190705

130

2.301847

472

downstrea

up

02

MYC

downstrea

up

1.01605

2101

downstrea

up

29

NM_002467

downstrea

up

0.9704052

upstream

MYC

0.004613

T

0.9608127

down

2101

IP

88

AC

NR_045215

91

upstream

SC R

NR_026876

1.01984

Neighboring

NU

ENST00000463325

0.9591144

down

MA

ENST00000536495

88

D

ENST00000439897

91

TE

ENST00000519071

1.01984

CE P

ENST00000519071

0.9591144

up

up

up

up

up

up dow

NM_000462

-05

2.950597

n

NM_001008

0.011809

1.464930

dow

392

217

3

n

NM_001008

0.266805

392

948

1.164969

up

ACCEPTED MANUSCRIPT

ENST00000472161

0.9854225

1.00558

07

74

0.9938365

1.00235

85

74

0.9942663

1.00149

52

52

0.9942663

1.00149

52

52

down

Neighboring

down

Neighboring

down

enhancer

upstream

upstream

500

CCNG2

NM_004354

500

CCNG2

NM_004354

218245

SGK1

NM_005627

downstrea

down

down

enhancer

enhancer

m

upstream

upstream

245269

245269

AC

CE P

TE

D

MA

NU

ENST00000472161

74

94

0.388380

1.403185

588

3

0.795661

1.081343

782

3

up

0.315881

PMAIP1

NM_021127

PMAIP1

NM_021127

up

1.494115

dow

292

8

n

0.002638

2.554357

487

4

0.008034

1.764963

348

4

T

ENST00000418701

07

IP

TCONS_00008508

1.00558

SC R

TCONS_00008508

0.9854225

up

up

ACCEPTED MANUSCRIPT Table 4 Correlation between four identified lncRNA expression levels and clinicopathologic variables in 57 HCC patients ENST00000518376

ENST00000502804

high

low

high

high

n=27 value

n=30

P

n=27 value

low n=30

23

Female

425

254

Age(years)

5

5

<=50

15

>50

12 16

HBsAg

14

Positive

26

Negative

128

Liver cirrhosis

2

Presence

23

Absence

284

AFP(ug/L)

2

12

11

0.62

24

23

22

26

0.25

263

3

6

15

16

13

13

0.90

n=32

22

446

0.49

14

0.83

11 17 15

27

27

0.57

25

1

2

0.51

290

25

26

0.96

23

3

3

0.100.10

282

0.12 3

00.17

9

18

19

Multiple

238

227

7

8

>5cm

1413

19 20

Vascular invasion

16

10 9

No

718

18 7

Tumor

23

23

15

0.67

0.95

8

Yes

15

21

18

0.29

7

11

17

0.95

228

0.29

21

21

7

8

0.83

17

0.39

258 7

14

0.40

0.15

20

<5cm

0.70

0.28

10

Single

0.59

0.58

4

11

0.38

0.32

2

Tumor number

12 Differentiation

0.06

284

219

Incomplete

n=25 value

D TE

CE P

0.32

197

15

n=29

P

0

Negative <=20

complete encapsulation

high low NR_073453

22

303

20

*Tumor size

0.15

MA

15 19

0.85

NU

0.87

23

>20

AC

Positive

0.85

n=28

low P value

SC R

Gender Male

P

T

ENST00000438347

IP

Variables

0.005

12

16

16

23

0.35

11

0.49

1714 15

9

0.40

8

8

20

21

0.93

7

0.99

918 23

13

0.91

14 16

13

17

15

12

0.36

10 2015 12

95

0.09

ACCEPTED MANUSCRIPT I-II 22

27

III-IV

0.36

3

20

0.01

297

25

24

3

5

0.48

23

0.25

262

AC

CE P

TE

D

MA

NU

SC R

IP

T

Data were given as the median (range). 5 1 6 * Diameter of multiple tumors was calculated as the sum of the size of every single tumor. HBsAg: hepatitis B surface antigen; AFP: α-fetoprotein;

96

ACCEPTED MANUSCRIPT Table 5 Univariate and multivariate analyses of prognostic factors associated with overall survival OS 1-year

3-year

OS 5-year

Univariate Multivariate Multivariate P P HR 95%CI

T

Clinicopathological characteristics

78.8%

44.3%

24.2%

female

67.6%

33.3%

0%

Age 80.0%

48.2%

12.8%

>50

72.9%

44.5%

23.2%

HBsAg

NU

≤50

75.6%

43.0%

25.5%

negative

100.0%

50.0%

0%

MA

positive

Liver cirrhosis 80.0%

47.8%

23.8%

absence

50.0%

25.0%

D

presence

25.0%

≤20ug/L

72.2%

55.6%

27.5%

>20ug/L

79.2%

41.2%

25.8%

CE P

TE

AFP

Tumor number single

AC

multiple

0.64

80.5%

54.1%

28.4%

66.7%

26.7%

0%

0.81

NS

0.11

NS

0.27

NS

0.46

NS

0.07

NS

0.16

NS

0.004

0.02

0.0

NS

0.5

NS

Tumor size ≤5cm

82.0%

53.9%

26.5%

>5cm

72.1%

39.1%0%

12.4%

NS

SC R

male

IP

Gender

Vascular invasion Yes

62.5%

21.1%

13.2%

No

82.5%

55.8%

27.4%

Tumor encapsulation complete

90.0%

57.6%

30.2%

incomplete

62.2%

33.5%

10.9%

Tumor differentiation I-II

77.3%

47.7%

20.6%

III-IV

75.0%

25.0%

25.0%

3

2

ENST00000438347 97

2.67 1.21-5.88

0.001

0.003

3.28 1.48-7.24

low

86.7%

65.1%

65.1%

high

65.4%

24.5%

0%

low

80.0%

57.8%

57.8%

high

73.4%

16.8%

0%

72.3%

39.1%

18.9%

high

81.9%

53.8%

29.0%

0.04

0.16

0.06

NR_073453

81.2%

50.2%

25.9%

high

72.0%

41.2%

19.5%

NU

low

1.69 1.31-3.69

NS

SC R

ENST00000502804

low

0.02

T

ENST00000518376

IP

ACCEPTED MANUSCRIPT

NS

MA

Note: AFP alpha-fetoprotein; OS overall survival; NS not significant; HR hazard ratio;

AC

CE P

TE

D

CI confidential interval.

98

ACCEPTED MANUSCRIPT Highlights 1、 Our results revealed the expression profile in oxaliplatin-resistant HCC and a series of

IP

T

lncRNAs play important roles in HCC oxaliplatin resistance and progression.

SC R

2、 We identified 120 differentially expressed lncRNAs with underlying pathways related to cell death, proliferation, cellular response to stimulus, including p53 pathway, ErbB pathway and MAPK pathway.

NU

3、 We found that ENST00000438347, NR_073453 and ENST00000502804 were up-regulated

MA

in chemo-resistant HCC cells and tissues. Moreover, high expression of ENST00000438347

AC

CE P

TE

D

and ENST00000518376 were associated with poor prognosis in HCC patients.

99

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