Gene expression profiles in the common marmoset brain determined using a newly developed common marmoset-specific DNA microarray

Neuroscience Research 66 (2010) 62–85

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Gene expression profiles in the common marmoset brain determined using a newly developed common marmoset-specific DNA microarray Toshifumi Fukuoka a,*, Kayo Sumida b, Toru Yamada a, Chihiro Higuchi c, Keiko Nakagaki d, Katsuki Nakamura d, Shinichi Kohsaka d, Koichi Saito b, Kenji Oeda b a

Safety Research Laboratories, Dainippon Sumitomo Pharma Co., Ltd., 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-8558, Japan Genomic Science Laboratories, Dainippon Sumitomo Pharma Co., Ltd., 3-1-98 Kasugade-naka, Konohana-ku, Osaka 554-0022, Japan d National Institute of Neuroscience, National Center of Neurology and Psychiatry, Japan, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan b c

A R T I C L E I N F O

A B S T R A C T

Article history: Received 3 June 2009 Received in revised form 28 August 2009 Accepted 28 September 2009 Available online 4 October 2009

To facilitate common marmoset brain research, we produced a DNA microarray with 7557 probe sets derived from the common marmoset brain. Gene expression profiles in the frontal lobe, hippocampus, cerebellum and amygdaloid nucleus were then analyzed and the top 100 probe sets expressed in each structure were compared. The three lists for the frontal lobe, hippocampus and amygdaloid nucleus were very similar but the probe sets for the cerebellum demonstrated specific differences. Some of the genes specifically expressed in cerebellum were analyzed by real-time quantitative PCR to verify the DNA microarray results. Of examined genes, 5 showed extremely strong expression in cerebellum in comparison with the other structures. The results of real-time quantitative PCR were well consistent with the microarray findings, validating our newly developed DNA microarray as a useful tool for brain research with the common marmoset. ß 2009 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

Keywords: Common marmoset DNA microarray Gene expression Cerebellum

1. Introduction Various animal species have been utilized in biomedical research. In particular, nonhuman primates have been playing important roles as models for the human, especially for the central nerve system (CNS) due to the high similarities in function and morphology. Macaca species, i.e. rhesus monkey (Macaca mulatta) and cynomolgus monkey (Macaca fascicularis) have been widely used for this purpose. Another nonhuman primate species, the common marmoset (Callithrix jacchus) has also found application for research into reproductive physiology, neuroscience, infectious disease and drug efficacy and safety (Mansfield, 2003). Recently, common marmosets have been increasingly employed as an alternative to traditionally used nonhuman primate species. They offer a number of advantages compared with Macaca species, including a small adult body size, ease of handling, avoidable zoonotic issues, early sexual maturation, a short gestation period, and production of 4–6 offspring per year (Mansfield, 2003; Abbott et al., 2003; Tardif et al., 2003). Various models are available related to changes in the CNS including, for example, multiple sclerosis (t’Hart et al., 2000), Huntington’s disease (Kendall et al., 1998), Alzheimer’s disease (Baker et al., 1993; Maclean et al.,

* Corresponding author. Tel.: +81 6 6466 5332; fax: +81 6 6466 5443. E-mail address: [email protected] (T. Fukuoka).

2000), Parkinson’s disease (Gnanalingham et al., 1993; Roeling et al., 1995) and aging (Leuner et al., 2007). Behavioral and histological analyses using common marmosets have thus become mainstream in the field. Many useful tools have also been developed to understand functional and morphological aspects of the common marmoset brain, such as single photon emission computed tomography (SPECT) (Saji et al., 2006) and diffusion tensor tractography (DTT) (Fujiyoshi et al., 2007). Gene expression analysis using DNA microarrays also has great advantages for identification of genes, pathways and networks involved in different diseases or disorders, since expression of thousands of genes can be simultaneously assessed. However, gene expression profiling of nonhuman primates is hampered by the fact that most simian genomes have not been sequenced and only a few microarrays are available. Gene expression profiles of nonhuman primates including the common marmoset have been reported (Marvanova´ et al., 2003), but there are problems with species differences with use of microarrays designed for human studies to obtain data for other primates (Karssen et al., 2006; Jacquelin et al., 2007). Our aim in the present study was to develop a useful tool for gene expression profiling of common marmoset brain and to evaluate its performance. There, we created our own common marmoset DNA microarray and carried out a validation with real-time quantitative PCR. In this paper, we document analysis of gene expression profiles of 4 typical structures, the frontal lobe, hippocampus, cerebellum and

0168-0102/$ – see front matter ß 2009 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved. doi:10.1016/j.neures.2009.09.1709

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

amygdaloid nucleus, of the common marmoset brain. In addition we confirmed compatibility between microarray findings and realtime quantitative PCR, using examples of genes already reported to be specifically expressed in cerebellum. 2. Materials and methods

63

control probe sets, for glyceraldehyde-3-phosphate dehydrogenase, beta-actin, hypoxanthine guanine phosphoribosyltransferase, cyclosporin A and 18S ribosomal RNA, were included. In the microarray, we further tiled 2163 human-derived probe sets selected from those in the Affymetrix human U133Plus 2.0 array to compare responses between common marmoset and human probe sets. The resultant array was named the Marmoa520295F array.

2.1. Animals and tissue preparation 2.4. High-density oligonucleotide microarray analysis Adult 3 male common marmosets (309–379 g, aged 4–8 years) were used in this study. All experimental and animal care procedures were performed in accordance with the guidelines outlines in the Guide for the Care and Use of Laboratory Animals of the National Research Council (1996), and by the Guide for Care and Use of Laboratory Primates published by the National Institute of Neuroscience, National Center of Neurology and Psychiatry (2005, 2008). 2.2. Tissue preparations The animals were anesthetized with ketamine (10 mg/kg, im) and with pentobarbital sodium (25 mg/kg, iv) or isoflurane (3– 5%) and perfused with cold PBS buffer. The ventral portion of the frontal cortex located around A12, the hippocampus, the amygdala, and the cerebellum were identified and obtained. The total RNA was extracted using an RNeasy Mini Kit (Qiangen Inc., Hilden, Germany) according to the manufacturer’s instructions. Concentrations of total RNA samples were measured by Amersham-Pharmacia spectrophotometer, model Ultraspec 3100pro (Amersham Pharmacia Biotech, Uppsala, Sweden) with quantification and assessment of ribosomal RNA integrity using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). 2.3. Generation of common marmoset cDNA sequences and construction of the microarray To obtain cDNA clones expressed preferentially in the brain, total RNA was isolated from whole brain and reverse-transcribed. Then, a normalized cDNA library was constructed with the pCMVSPORT6 vector. A total of 17,280 clones randomly picked up from the library were sequenced at their 30 loci using an oligo-dT primer and 12,000 sequences longer than 300 bp in length with high phred scores (Q320) were subjected to homology search by BLAST2.2.10 and ClustalW to remove redundancy. The resultant 7001 sequences were selected as representative clones. In addition, the RT-PCR method was also employed to clone fragments of specific common marmoset cDNAs of pharmacological or toxicological importance. The primers were designed based on sequence homology among the human and other mammals. Publicly available information on the common marmoset sequences was also employed. Genomic sequences were obtained from the pilot phase of ENCODE project (Birney et al., 2007) and cDNA sequences were assembled based on the homology to human orthologous cDNA sequences. Known common marmoset mRNA or cDNA sequences available in GenBank were also utilized. As a result, a total of 7470 sequences were used for the construction of microarray. The microarray was constructed according to the GeneChip1 CustomExpress1 Array Program (Affymetrix Inc., CA, USA.). And probe sets were designed after the GeneChip1 Custom Expression Array Design Guide. For evaluation of array performance and scaling of intensity data, several control probe sets were also tiled on the microarray. Apart from noneukaryotic Affymetrix hybridization controls (bioB, bioC, bioD and cre) and polyA probe sets (dap, lys, phe and thr), 6 common marmoset-specific housekeeping

Total RNA samples were prepared with an RNeasy Mini Kit (Qiangen Inc., Hilden, Germany) according to the manufacturer’s instructions and concentrations were measured using an Amersham-Pharmacia spectrophotometer, model Ultraspec 3100pro. Ribosomal RNA integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). For microarray probing, reverse transcription, second-strand synthesis, and probe generation were all accomplished with One-Cycle Target Labeling and Control Reagents (Affymetrix) following the manufacturer’s protocol. Briefly, from 3 mg of total RNA, the first-strand cDNA was synthesized with SuperScript II reverse transcriptase and a T7oligo (dT) primer, and then double-strand cDNA was synthesized with E. coli RNase H, E. coli DNA polymerase I and E. coli DNA ligase. From the double-strand cDNA, biotin-labeled cRNA was prepared and 20 mg of labeled cRNA was fragmented. The Marmoa520295F arrays were hybridized as described in the Gene Chip Expression Analysis Technical Manual (Affymetrix). The arrays were stained and washed with R-Phycoerythrin Streptavidin (Molecular Probes, Eugene, OR) and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix), while the fluorescence was intensified by the antibody-amplification method. The arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) and the obtained image files were analyzed with the Affymetrix data suite system, Gene Chip Operating Software (GCOS) version 1.4. We then obtained tabdelimited files containing data regarding the relative levels of expression of transcripts (Signal) and the reliability of detection (Detection Call). The derived Signal values were globally normalized and targeted to all probe sets equal to 100. 2.5. Microarray data analysis To examine genes specifically expressed in different brain structures, average Signal values of three biological replicates for each were calculated. The magnitude and direction of change in expression of a transcript was obtained as the ratio from the average Signal values of three replicates for the structure and those of other structures. Furthermore, Signal data were similarly analyzed by the Student’s t-test. To find the genes which were specifically expressed in the structure (Table 5), at p < 0.05, probe sets showing ratios greater than ‘‘1’’ and ‘‘P (present)’’ Detection Calls in the structure were selected. 2.6. Real-time quantitative PCR Measurement of selected gene transcripts was carried out by quantitative PCR (qPCR) with reverse-transcribed cDNA. One microgram of each DNase-treated RNA sample was reversetranscribed with random hexamer primers using PrimeScriptTM RT reagent Kit (Takara, Bio Inc., Shiga, Japan) according to manufacturer’s instructions. cDNA from each reaction was diluted to a concentration of 10 ng/mL and 2 mL aliquots were used for each qPCR reaction. In addition, cDNA from each reaction was used at serial 10-fold dilution for generation of calibration curves. cDNA samples were mixed with SYBR Premix Ex TaqTM II (Takara, Bio Inc.) and amplified according to the manufacturer’s instructions. qPCR was performed with an Applied Biosystems 7900HT Fast

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

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Real-Time PCR System (Applied Biosystems, Carlsbad, CA, USA). All samples were run in triplicate sets within the same plate for each assay, using the same RNA samples used in the microarray analysis. Primers were as follows: calbindin 1 [forward primer gaaatgagatctgccaaaaactaaaa, reverse primer catttacacgctaaaggcaaagc]; aldolase C, fructose-bisphosphate [forward primer tccttttctcccctccctttc, reverse primer gcaccctatcctcccatcct]; gamma-aminobutyric acid (GABA) A receptor, alpha 6 [forward primer attcaaccttgtgtactggatagtttatct, reverse primer tgtcctggatgcaagctattca]; neurogenic differentiation 1 [forward primer cagaataagagctgtttgagatgtga, reverse primer tgcattacaccataatatacaggattaca]; carbonic anhydrase 8 [forward primer tgaatgcaaagtgaatgatgagtaaa, reverse

primer tggcaatccagcctaacaatt]; GAPDH [forward primer ccacccatggcaaattcc, reverse primer tgggatttccattgatgacaag]. The abundance of these mRNAs was calculated from threshold cycle values using each standard curve and then normalized to the amount of GAPDH. Data are reported as averages of triplicate assays. 3. Results 3.1. Probe sets expressed in each structure of brain Lists of the top 100 probe sets expressed in each examined brain structure are shown in Table 1A–D. For example, in List A, the top

Table 1 Lists of top 100 probe sets expressed in each structure of brain. Probe sets

FLa_AVEb

FLa_SDc

Symbol

Description

(A) Frontal lobe CJB04967_at CJB10548_at CJD00108_s_at CJB05145_s_at CJA00056_at CJD00128_at CJD00015_at CJD00144_s_at CJB09303_at CJB02035_s_at CJB01130_s_at CJA00017_s_at CJD00025_s_at CJB01231_at

7059.1 5936.1 5812.5 5805.4 5769.6 5213.1 5208.5 5132.8 5114.4 4825.2 4691.3 4190.9 4186.8 3498.8

1387.9 1274.3 665.2 1278.2 664.0 973.2 1228.8 348.7 827.0 123.7 779.0 448.3 127.9 713.8

MT-ATP6 MT-CO3 MT-CYB MT-ND4

Mitochondrially Mitochondrially Mitochondrially Mitochondrially

encoded encoded encoded encoded

ATP synthase 6 cytochrome c oxidase III cytochrome b NADH dehydrogenase 4

MT-RNR1 MT-CYB MT-RNR2 MT-ND1 MT-RNR2 MT-CO2

Mitochondrially Mitochondrially Mitochondrially Mitochondrially Mitochondrially Mitochondrially

encoded encoded encoded encoded encoded encoded

12S RNA cytochrome b 16S RNA NADH dehydrogenase 1 16S RNA cytochrome c oxidase II

Mitochondrially encoded cytochrome c oxidase II Thymosin-like 3/thymosin beta 4, X-linked

CJA00069_at CJB01642_at CJB05136_at CJB00780_at CJB03798_at CJA00036_at CJB09795_at CJB06346_at CJC00003_ GAPDH-3_s_at CJB03140_at CJB11352_at CJB10533_at CJB02174_at CJB01755_at CJB05477_at CJB05570_at CJB03587_at CJB02082_at CJB05646_at CJB03135_at

3366.2 3264.6 3202.1 3013.3 2842.0 2755.4 2739.5 2665.4 2614.1

248.9 625.5 416.3 681.3 171.8 433.0 636.9 652.1 833.2

MT-CO2 TMSL3/ TMSB4X MT-ND5 GNAS UBC FTL SNAP25 FTH1 HSP90AA1 TPT1 GAPDH

2606.7 2572.9 2565.4 2559.9 2558.0 2526.9 2523.0 2463.5 2446.1 2398.9 2365.0

1077.1 51.5 77.5 507.4 494.5 452.0 243.3 140.9 49.7 641.0 146.1

PEBP1 GPM6B SLC1A2 VSNL1 ITM2B CHN1 GLUL EEF1A1 TUBA1A TSC22D1 YWHAG

CJC00004_ CYCA_s_at CJB02035_at CJB07092_at CJB00322_at CJB09730_at CJB07556_at CJB01204_at CJB04173_at CJB01539_at CJB11816_at CJB06125_at

2356.4

372.8

PPIA

Phosphatidylethanolamine binding protein 1 Glycoprotein M6B Solute carrier family 1 (glial high affinity glutamate transporter), member 2 Visinin-like 1 Integral membrane protein 2B Chimerin (chimaerin) 1 Glutamate-ammonia ligase (glutamine synthetase) Eukaryotic translation elongation factor 1 alpha 1 Tubulin, alpha 1a TSC22 domain family, member 1 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide Peptidylprolyl isomerase A (cyclophilin A)

2313.7 2239.0 2141.1 2113.8 2100.9 2100.7 2049.3 2046.4 2046.3 2020.9

881.3 430.5 712.0 221.1 262.3 122.9 569.7 815.4 145.1 228.8

MT-RNR2 RPS3 LDHB NDRG2 FBXL16 EIF4A2 ATP1A2 UCHL1 OLFM1 PGAM1/ PGAM4

Mitochondrially encoded 16S RNA Ribosomal protein S3 Lactate dehydrogenase B NDRG family member 2 F-box and leucine-rich repeat protein 16 Eukaryotic translation initiation factor 4A, isoform 2 ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) Olfactomedin 1 Phosphoglycerate mutase 1 (brain)/family member 4

CJB06122_at CJB05295_at CJB10024_at CJB03293_at CJB03621_at CJB05372_at CJB03371_at CJB02131_at

1995.9 1992.7 1981.7 1965.6 1963.9 1951.1 1922.2 1887.0

229.9 439.0 157.0 524.1 400.7 105.5 225.7 340.2

RTN1 TTC3 BEX1 SLC1A3 ENC1 GFAP PNMA2

Reticulon 1 Tetratricopeptide repeat domain 3 Brain expressed, X-linked 1 Solute carrier family 1 (glial high affinity glutamate transporter), member 3 Ectodermal-neural cortex (with BTB-like domain) Glial fibrillary acidic protein Paraneoplastic antigen MA2

Mitochondrially encoded NADH dehydrogenase 5 GNAS complex locus Ubiquitin C Ferritin, light polypeptide Synaptosomal-associated protein, 25 kDa Ferritin, heavy polypeptide 1 Heat shock protein 90 kDa alpha (cytosolic), class A member 1 Tumor protein, translationally controlled 1 Glyceraldehyde-3-phosphate dehydrogenase

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

65

Table 1 (Continued ) Probe sets

FLa_AVEb

FLa_SDc

Symbol

Description

CJB01175_at CJB04667_at CJB01944_at CJB04608_at CJB06097_at CJB04235_at CJB05454_at CJB03857_at CJB02965_at CJB01004_at CJB07223_at CJB11702_at CJB11634_at CJB02150_at CJB06143_s_at CJB03230_at CJB05043_at CJB10740_at CJB04772_at CJB12057_at CJB01455_at CJB04745_at CJC00001_ ACT-3_at CJB05936_at CJB01619_at CJB09450_at CJB03734_at CJB02996_at CJB11894_at CJB12081_at CJB06172_at CJB08956_at CJB12035_at CJB01454_at CJB09976_at CJB09260_at CJB08453_at CJB02863_at CJB01728_at CJB03481_at CJB01880_at CJB08145_at CJB11644_at CJB05054_at CJB05121_at

1875.7 1854.0 1849.4 1835.5 1800.6 1797.9 1791.7 1776.6 1752.9 1730.8 1722.1 1705.3 1702.7 1691.6 1669.1 1668.3 1658.3 1652.5 1645.7 1640.1 1613.3 1598.2 1586.7

384.7 225.3 96.2 379.3 231.5 167.9 443.3 83.5 80.6 122.6 443.1 195.5 107.1 322.1 157.5 62.3 490.9 302.9 301.3 182.9 368.9 40.3 442.3

MRFAP1 GPM6A SPTBN1 PTGDS GPM6A APLP1 PNMA1 RPL14 TSPAN7 GNB1 HSP90AB1 RPL3 KLC1 PRNP YWHAH CTNND2 SEPT7 EEF2 YWHAB CPE ENO2 NDRG4 ACTB

Mof4 family associated protein 1 Glycoprotein M6A Spectrin, beta, non-erythrocytic 1 Prostaglandin D2 synthase 21 kDa (brain) Glycoprotein M6A Amyloid beta (A4) precursor-like protein 1 Paraneoplastic antigen MA1 Ribosomal protein L14 Tetraspanin 7 Guanine nucleotide binding protein (G protein), beta polypeptide 1 Heat shock protein 90 kDa alpha (cytosolic), class B member 1 Ribosomal protein L3 Kinesin light chain 1 Prion protein Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide Catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein) Septin 7 Eukaryotic translation elongation factor 2 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide Carboxypeptidase E Enolase 2 (gamma, neuronal) NDRG family member 4 Actin, beta

1557.3 1546.5 1542.5 1521.4 1519.7 1514.2 1512.3 1509.3 1493.6 1492.5 1489.3 1489.1 1485.6 1476.1 1463.0 1462.5 1447.2 1446.5 1446.0 1442.9 1432.6 1430.8

300.8 181.5 290.3 188.8 503.4 507.4 89.5 171.2 21.1 383.0 273.1 363.4 40.6 262.4 91.3 48.8 357.0 629.4 173.0 153.7 581.3 387.5

SEPT5 NPTN TTC3 HTRA1 CKB

Septin 5 Neuroplastin Tetratricopeptide repeat domain 3 HtrA serine peptidase 1 Creatine kinase, brain

SPTAN1 PEA15 DNER ACTG1 CPLX2 RAC1 PSAP AES IDS GJA1 DNM1 RPS15

Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) Phosphoprotein enriched in astrocytes 15 Delta/notch-like EGF repeat containing Actin, gamma 1 Complexin 2 ras-Related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) prosaposin Amino-terminal enhancer of split Iduronate 2-sulfatase Gap junction protein, alpha 1, 43 kDa Dynamin 1 Ribosomal protein S15

CLTC CAMK2A YWHAQ

CJB07294_at CJB07522_at

1410.6 1409.4

190.9 560.2

Clathrin, heavy chain (Hc) Calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide Ribosomal protein L13a Calmodulin 3 (phosphorylase kinase, delta)

Probe sets

Hid_AVEb

Hid_SDc

Symbol

Description

(B) Hippocampus CJB04967_at CJB10548_at CJB05145_s_at CJA00056_at CJD00108_s_at CJB09303_at CJD00128_at CJB02035_s_at CJD00015_at CJB01130_s_at CJD00144_s_at CJA00017_s_at CJB01231_at

5999.9 5323.6 5138.8 5073.7 5056.9 4574.1 4537.4 4442.6 4436.0 4270.1 4209.9 3829.0 3643.0

1354.5 1086.2 1076.7 548.0 752.6 899.8 892.9 618.5 755.3 860.5 367.1 736.9 655.4

MT-ATP6 MT-CO3 MT-ND4

Mitochondrially encoded ATP synthase 6 Mitochondrially encoded cytochrome c oxidase III Mitochondrially encoded NADH dehydrogenase 4

MT-CYB MT-ND1 MT-RNR1 MT-RNR2 MT-CYB MT-CO2 MT-RNR2

Mitochondrially Mitochondrially Mitochondrially Mitochondrially Mitochondrially Mitochondrially Mitochondrially

Thymosin-like 3/thymosin beta 4, X-linked

3628.6 3236.9 3035.2 2966.2 2855.4 2829.5 2751.7 2680.2

294.4 153.2 443.8 321.8 751.8 265.6 984.6 321.2

TMSL3/ TMSB4X MT-CO2 TUBA1A MT-ND5 UBC HSP90AA1 GNAS PEBP1 PPIA

2645.2 2602.5

207.7 691.1

ENC1 ITM2B

Ectodermal-neural cortex (with BTB-like domain) Integral membrane protein 2B

CJD00025_s_at CJB02082_at CJA00069_at CJB05136_at CJB09795_at CJB01642_at CJB03140_at CJC00004_ CYCA_s_at CJB05372_at CJB01755_at

RPL13A CALM3

encoded encoded encoded encoded encoded encoded encoded

cytochrome b NADH dehydrogenase 1 12S RNA 16S RNA cytochrome b cytochrome c oxidase II 16S RNA

Mitochondrially encoded cytochrome c oxidase II Tubulin, alpha 1a Mitochondrially encoded NADH dehydrogenase 5 ubiquitin C Heat shock protein 90 kDa alpha (cytosolic), class A member 1 GNAS complex locus Phosphatidylethanolamine binding protein 1 Peptidylprolyl isomerase A (cyclophilin A)

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

66 Table 1 (Continued ) Probe sets

Hid_AVEb

Hid_SDc

Symbol

Description

CJB03135_at

2585.4

153.0

YWHAG

CJB03798_at CJA00036_at CJB01539_at CJB06346_at CJB11894_at CJB03293_at CJC00003_ GAPDH-3_s_at CJB05477_at CJB03587_at CJB05454_at CJB04745_at CJB05646_at CJB10533_at CJB11352_at CJB00780_at CJB02131_at CJB06125_at

2581.8 2581.6 2581.5 2481.6 2479.9 2448.4

271.1 314.9 838.0 657.8 477.1 615.7

SNAP25 FTH1 UCHL1 TPT1

Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide Synaptosomal-associated protein, 25 kDa Ferritin, heavy polypeptide 1 Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) Tumor protein, translationally controlled 1

BEX1

Brain expressed, X-linked 1

2440.2 2370.5 2306.9 2230.6 2214.9 2200.3 2175.9 2118.1 2112.7 2104.5 2056.1

1421.1 414.8 162.4 489.1 183.2 342.2 239.3 169.9 577.4 267.6 338.9

Glyceraldehyde-3-phosphate dehydrogenase Chimerin (chimaerin) 1 Eukaryotic translation elongation factor 1 alpha 1 Paraneoplastic antigen MA1 NDRG family member 4 TSC22 domain family, member 1 Solute carrier family 1 (glial high affinity glutamate transporter), member 2 Glycoprotein M6B Ferritin, light polypeptide Paraneoplastic antigen MA2 Phosphoglycerate mutase 1 (brain)/family member 4

CJB01204_at CJB04667_at CJB11816_at CJB05295_at CJB11634_at CJB02035_at CJB07092_at CJB06143_s_at CJB09976_at CJB10024_at CJB07083_at CJB02965_at CJB06097_at CJC00001_ ACT-3_at CJB04772_at CJB09730_at CJB07223_at CJB08236_at CJB01944_at CJB06172_at CJB01175_at CJB05570_at CJB04249_at CJB00533_at CJB01454_at CJB09260_at CJB03481_at CJB02863_at CJB07410_at CJB01475_at CJB11644_at CJB12057_at CJB11702_at CJB12081_at CJB01604_at CJB04235_at CJB09450_at CJB06639_at CJB02150_at CJB12035_at CJB01926_at CJB05121_at CJB06070_at CJB05054_at CJB00322_at CJB06122_at CJB04488_at CJB05160_at CJB07556_at CJB07808_at CJB06407_at CJB07343_at CJB01847_at CJB01619_at CJB08983_at

2011.7 1996.6 1994.2 1971.3 1919.2 1912.0 1881.4 1881.3 1870.6 1868.2 1810.5 1808.2 1784.9

160.8 342.6 271.0 336.2 214.3 735.4 448.4 62.5 407.6 246.5 554.4 131.3 101.2

GAPDH CHN1 EEF1A1 PNMA1 NDRG4 TSC22D1 SLC1A2 GPM6B FTL PNMA2 PGAM1/ PGAM4 EIF4A2 GPM6A OLFM1 RTN1 KLC1 MT-RNR2 RPS3 YWHAH RAC1 TTC3 PNMAL1 TSPAN7 GPM6A

1784.8 1773.3 1723.8 1720.0 1698.3 1679.5 1678.3 1674.9 1672.4 1670.6 1667.3 1665.4 1650.2 1645.5 1643.7 1640.0 1635.2 1633.0 1632.8 1616.1 1607.4 1603.1 1603.1 1601.0 1573.4 1567.6 1558.6 1557.1 1554.7 1528.5 1513.2 1509.3 1503.3 1501.0 1499.7 1498.2 1479.1 1468.2 1463.3 1462.1 1453.8 1452.2

519.2 297.3 172.1 363.4 90.1 55.2 327.7 126.5 166.1 666.2 558.4 298.4 158.1 413.2 284.5 259.3 581.7 440.6 138.7 226.4 160.8 407.3 198.4 480.9 213.1 351.6 350.6 291.2 372.0 358.1 735.6 361.4 255.3 187.3 371.7 293.4 281.4 297.3 226.3 322.3 133.3 211.2

ACTB YWHAB NDRG2 HSP90AB1 SLC17A7 SPTBN1 PEA15 MRFAP1 GLUL MOAP1 NPTX1 CPLX2 PSAP DNM1 IDS THY1 GNAO1 CLTC CPE RPL3 SPTAN1 ADCY1 APLP1 TTC3 INPP5F PRNP ACTG1 PFN2 YWHAQ SERINC1 CAMK2A LDHB

Actin, beta Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide NDRG family member 2 Heat shock protein 90 kDa alpha (cytosolic), class B member 1 Solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7 Spectrin, beta, non-erythrocytic 1 Phosphoprotein enriched in astrocytes 15 Mof4 family associated protein 1 Glutamate-ammonia ligase (glutamine synthetase) Modulator of apoptosis 1 Neuronal pentraxin I Complexin 2 Prosaposin Dynamin 1 Iduronate 2-sulfatase Thy-1 cell surface antigen Guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O Clathrin, heavy chain (Hc) Carboxypeptidase E Ribosomal protein L3 Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) Adenylate cyclase 1 (brain) Amyloid beta (A4) precursor-like protein 1 Tetratricopeptide repeat domain 3 Inositol polyphosphate-5-phosphatase F Prion protein Actin, gamma 1 Profilin 2 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide Serine incorporator 1 Calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha Lactate dehydrogenase B

BTBD3 ATP5B FBXL16 HSPA8 MAP1B TMEM66 CLTA NPTN TSPYL4

BTB (POZ) domain containing 3 ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide F-box and leucine-rich repeat protein 16 Heat shock 70 kDa protein 8 Microtubule-associated protein 1B Transmembrane protein 66 Clathrin, light chain (Lca) Neuroplastin TSPY-like 4

Eukaryotic translation initiation factor 4A, isoform 2 Glycoprotein M6A Olfactomedin 1 Reticulon 1 Kinesin light chain 1 Mitochondrially encoded 16S RNA Ribosomal protein S3 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide ras-Related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) Tetratricopeptide repeat domain 3 PNMA-like 1 Tetraspanin 7 Glycoprotein M6A

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

67

Table 1 (Continued ) Probe sets CJB06845_at CJB08145_at CJB03857_at CJB00401_at Probe sets (C) Cerebellum CJB04967_at CJB10548_at CJD00108_s_at CJB05145_s_at CJA00056_at CJB01130_s_at CJD00128_at CJB09303_at CJB02035_s_at CJD00015_at CJD00144_s_at CJD00025_s_at CJB05136_at CJA00017_s_at CJB01755_at CJB09795_at CJB03798_at CJB11894_at CJB01231_at

Hid_AVEb 1445.0 1438.6 1435.8 1434.0 Cbe_AVEb

Hid_SDc 185.3 168.2 241.4 207.7 Cbe_SDc

5032.9 4639.6 4414.3 4297.9 4202.6 3902.3 3808.2 3700.2 3682.6 3653.7 3409.8 2982.5 2940.0 2879.8 2848.7 2782.4 2778.7 2628.8 2546.2

1666.0 1426.8 999.5 1439.5 772.9 939.9 1006.1 670.9 571.5 896.0 197.5 178.2 327.9 496.6 684.4 850.1 467.1 696.2 654.0

CJB02082_at CJB03140_at CJC00004_ CYCA_s_at CJB01642_at CJB01564_at CJB01204_at CJB00780_at CJB03587_at CJB09730_at CJB07092_at CJB05454_at CJB02174_at CJA00036_at CJB06346_at CJC00003_ GAPDH-3_s_at CJB05121_at CJB11352_at CJB11629_at CJA00069_at CJB05295_at CJB00322_at CJB07808_at CJB06122_at CJB11634_at CJB11119_at CJB03293_at CJB05160_at CJB07844_at CJB08956_at CJB04173_at CJB06097_at CJB04745_at CJB11702_at CJB01455_at CJB01175_at CJB06070_at CJB06125_at

2523.4 2507.0 2368.7

135.7 995.9 197.7

2315.1 2199.9 2149.1 2119.3 2112.0 2100.7 2068.6 2057.2 2041.6 2015.0 1996.9 1980.1

462.6 340.5 120.9 604.1 12.9 308.7 691.1 531.3 168.3 347.5 706.0 1145.4

1978.5 1968.5 1916.6 1880.9 1871.8 1865.2 1863.7 1836.8 1828.5 1815.1 1806.4 1781.2 1768.2 1734.1 1728.5 1721.9 1714.5 1712.7 1711.8 1701.0 1698.2 1672.9

468.7 352.5 307.1 224.5 361.1 624.3 217.0 277.6 340.2 386.5 588.2 163.8 146.1 228.8 488.7 188.8 157.9 392.6 159.5 242.3 271.7 375.8

CJB06229_at CJB07547_at CJB08174_at CJB03135_at CJB06845_at CJB02965_at CJB01475_at CJB04435_at CJB01604_at CJB02035_at

1662.4 1657.8 1657.3 1652.4 1629.5 1626.3 1596.6 1596.0 1594.6 1577.5

89.0 220.7 186.7 196.3 115.0 147.9 441.2 451.8 110.8 753.8

Symbol

Description

MORF4L1

Mortality factor 4 like 1

RPL14 BEX4

Ribosomal protein L14 BEX family member 4

Symbol

Description

MT-ATP6 MT-CO3 MT-CYB MT-ND4

Mitochondrially Mitochondrially Mitochondrially Mitochondrially

encoded encoded encoded encoded

ATP synthase 6 cytochrome c oxidase III cytochrome b NADH dehydrogenase 4

MT-CO2 MT-RNR1 MT-ND1 MT-RNR2 MT-CYB MT-RNR2 MT-CO2 UBC

Mitochondrially Mitochondrially Mitochondrially Mitochondrially Mitochondrially Mitochondrially Mitochondrially Ubiquitin C

encoded encoded encoded encoded encoded encoded encoded

cytochrome c oxidase II 12S RNA NADH dehydrogenase 1 16S RNA cytochrome b 16S RNA cytochrome c oxidase II

ITM2B HSP90AA1 SNAP25

Integral membrane protein 2B Heat shock protein 90 kDa alpha (cytosolic), class A member 1 Synaptosomal-associated protein, 25 kDa

TMSL3/ TMSB4X TUBA1A PEBP1 PPIA

Thymosin-like 3/thymosin beta 4, X-linked

GNAS ALDOC EIF4A2 FTL EEF1A1 NDRG2 RPS3 PNMA1 VSNL1 FTH1 TPT1 GAPDH

GNAS complex locus Aldolase C, fructose-bisphosphate Eukaryotic translation initiation factor 4A, isoform 2 Ferritin, light polypeptide Eukaryotic translation elongation factor 1 alpha 1 NDRG family member 2 Ribosomal protein S3 Paraneoplastic antigen MA1 Visinin-like 1 Ferritin, heavy polypeptide 1 Tumor protein, translationally controlled 1 Glyceraldehyde-3-phosphate dehydrogenase

YWHAQ GPM6B NEUROD1 MT-ND5 RTN1 LDHB HSPA8

Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide Glycoprotein M6B Neurogenic differentiation 1 Mitochondrially encoded NADH dehydrogenase 5 Reticulon 1 Lactate dehydrogenase B Heat shock 70 kDa protein 8

KLC1 HPCAL1 BEX1 ATP5B EIF1 DNER ATP1A2 GPM6A NDRG4 RPL3 ENO2 MRFAP1 SERINC1 PGAM1/ PGAM4 TIAM1 CALM1 TMEM178 YWHAG MORF4L1 TSPAN7 GNAO1 NACA ADCY1 MT-RNR2

Kinesin light chain 1 Hippocalcin-like 1 Brain expressed, X-linked 1 ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide Eukaryotic translation initiation factor 1 Delta/notch-like EGF repeat containing ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide Glycoprotein M6A NDRG family member 4 Ribosomal protein L3 Enolase 2 (gamma, neuronal) Mof4 family associated protein 1 Serine incorporator 1 Phosphoglycerate mutase 1 (brain)/family member 4

Tubulin, alpha 1a Phosphatidylethanolamine binding protein 1 Peptidylprolyl isomerase A (cyclophilin A)

T-cell lymphoma invasion and metastasis 1 Calmodulin 1 (phosphorylase kinase, delta) Transmembrane protein 178 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide Mortality factor 4 like 1 Tetraspanin 7 Guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O Nascent polypeptide-associated complex alpha subunit Adenylate cyclase 1 (brain) Mitochondrially encoded 16S RNA

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

68 Table 1 (Continued ) Probe sets CJB07223_at CJB03621_at CJB11644_at CJB01093_at CJB02150_at CJB05163_at CJB05646_at CJB03500_at CJB09577_at CJB05043_at CJB01619_at CJB03857_at CJB06143_s_at CJB03506_at CJB12057_at CJB06639_at CJB06880_at CJB04667_at CJB09976_at CJB12081_at CJB00533_at CJB05355_at CJB10024_at CJB12001_at CJB01857_at CJB04608_at CJB10180_at CJB03487_at CJB07294_at CJB05570_at CJB01059_at CJB04497_at CJB01944_at CJB04249_at Probe sets

Cbe_AVEb

CJB01539_at CJB03587_at CJB00780_at CJC00003_ GAPDH-3_s_at CJA00036_at CJB02035_at CJB11894_at CJB04745_at

Symbol

Description

HSP90AB1 SLC1A3 CLTC GABRA6 PRNP NHP2L1 TSC22D1 CALB1 CALB1 SEPT7 NPTN RPL14 YWHAH DPYSL2 CPE INPP5F CBLN1 GPM6A RAC1 SPTAN1 NPTX1 EIF4H TTC3 CA8 ABLIM1 PTGDS MBP CAMKK2 RPL13A GLUL C5orf13 HSPA1A SPTBN1 MOAP1

Heat shock protein 90 kDa alpha (cytosolic), class B member 1 Solute carrier family 1 (glial high affinity glutamate transporter), member 3 Clathrin, heavy chain (Hc) Gamma-aminobutyric acid (GABA) A receptor, alpha 6 Prion protein NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae) TSC22 domain family, member 1 Calbindin 1, 28 kDa Calbindin 1, 28 kDa Septin 7 Neuroplastin Ribosomal protein L14 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide Dihydropyrimidinase-like 2 Carboxypeptidase E Inositol polyphosphate-5-phosphatase F Cerebellin 1 precursor Glycoprotein M6A ras-Related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) Spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) Neuronal pentraxin I Eukaryotic translation initiation factor 4H Tetratricopeptide repeat domain 3 Carbonic anhydrase VIII Actin binding LIM protein 1 Prostaglandin D2 synthase 21 kDa (brain) Myelin basic protein Calcium/calmodulin-dependent protein kinase kinase 2, beta Ribosomal protein L13a Glutamate-ammonia ligase (glutamine synthetase) Chromosome 5 open reading frame 13 Heat shock 70 kDa protein 1A Spectrin, beta, non-erythrocytic 1 Modulator of apoptosis 1

1573.7 1568.6 1560.3 1558.6 1554.1 1543.7 1541.7 1541.3 1527.9 1526.0 1520.9 1520.0 1496.5 1491.6 1489.9 1476.5 1464.0 1460.7 1432.1 1426.8 1421.5 1418.9 1418.5 1413.1 1402.2 1390.6 1380.7 1378.2 1376.7 1360.1 1345.0 1344.3 1341.9 1321.6

225.7 229.5 323.1 453.7 293.0 539.1 527.3 253.3 54.7 295.1 177.0 502.2 30.7 305.9 122.9 73.5 432.2 48.1 241.4 165.6 477.9 446.8 307.0 282.9 239.5 569.4 198.4 87.2 295.6 164.4 112.2 89.2 28.6 497.8

ANf_AVEb

ANf_SDc

Symbol

Description

2742.1 2236.0 1648.3 2190.8 1458.7 1722.0 1840.0 1485.5 1105.4 1622.2 570.9 1498.4

MT-ATP6 MT-CO3 MT-CYB MT-ND4

Mitochondrially Mitochondrially Mitochondrially Mitochondrially

MT-RNR1 MT-CYB MT-ND1 MT-RNR2 MT-CO2 MT-RNR2 TMSL3/ TMSB4X

Mitochondrially encoded 12S RNA Mitochondrially encoded cytochrome b Mitochondrially encoded NADH dehydrogenase 1 Mitochondrially encoded 16S RNA Mitochondrially encoded cytochrome c oxidase II Mitochondrially encoded 16S RNA Thymosin-like 3/thymosin beta 4, X-linked

(D) Amygdaloid nucleus CJB04967_at 6351.5 CJB10548_at 5429.7 CJD00108_s_at 5129.2 CJB05145_s_at 5117.8 CJA00056_at 5052.8 CJD00128_at 4638.1 CJD00015_at 4574.2 CJB09303_at 4525.4 CJB02035_s_at 4352.1 CJB01130_s_at 4271.8 CJD00144_s_at 4025.6 CJB01231_at 3761.9 CJA00017_s_at CJD00025_s_at CJB05136_at CJA00069_at CJB09795_at CJB02082_at CJB01642_at CJC00004_ CYCA_s_at CJB03140_at CJB01755_at CJB11352_at CJB06346_at CJB03798_at CJB10533_at CJB03293_at CJB03135_at

Cbe_SDc

encoded encoded encoded encoded

ATP synthase 6 cytochrome c oxidase III cytochrome b NADH dehydrogenase 4

3688.5 3643.0 3153.7 3090.5 3027.7 2977.7 2938.0

1001.1 515.2 717.7 553.1 1181.1 267.2 587.5

MT-CO2 UBC MT-ND5 HSP90AA1 TUBA1A GNAS

Mitochondrially encoded cytochrome c oxidase II Ubiquitin C Mitochondrially encoded NADH dehydrogenase 5 Heat shock protein 90 kDa alpha (cytosolic), class A member 1 Tubulin, alpha 1a GNAS complex locus

2781.6 2725.0 2632.5 2595.8 2551.2 2550.4 2486.2 2481.2 2415.8

449.1 1321.6 662.1 767.0 1045.9 495.6 531.4 899.0 524.5

PPIA PEBP1 ITM2B GPM6B TPT1 SNAP25 SLC1A2 BEX1 YWHAG

2328.1 2285.6 2273.5 2244.4

984.8 194.8 617.4 1426.0

UCHL1 EEF1A1 FTL GAPDH

Peptidylprolyl isomerase A (cyclophilin A) Phosphatidylethanolamine binding protein 1 Integral membrane protein 2B Glycoprotein M6B Tumor protein, translationally controlled 1 Synaptosomal-associated protein, 25 kDa Solute carrier family 1 (glial high affinity glutamate transporter), member 2 Brain expressed, X-linked 1 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) Eukaryotic translation elongation factor 1 alpha 1 Ferritin, light polypeptide Glyceraldehyde-3-phosphate dehydrogenase

2225.4 2216.4 2172.9 2139.6

260.7 551.0 770.8 428.4

FTH1 MT-RNR2

Ferritin, heavy polypeptide 1 Mitochondrially encoded 16S RNA

NDRG4

NDRG family member 4

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

69

Table 1 (Continued ) Probe sets

a b c d e f

ANf_AVEb

ANf_SDc

Symbol

Description

PNMA1 RTN1 PGAM1/ PGAM4 GFAP RAC1 CPE NDRG2 RPS3 PNMA2 ATP1A2 CHN1 IDS GPM6A TSPAN7 KLC1 TSC22D1 PNMAL1 GLUL EIF4A2 SPTBN1 GPM6A INPP5F PRNP MOAP1 YWHAQ

Paraneoplastic antigen MA1 Reticulon 1 Phosphoglycerate mutase 1 (brain)/family member 4

CJB05454_at CJB05295_at CJB06125_at

2137.1 2122.0 2119.1

582.9 675.5 654.1

CJB03371_at CJB09976_at CJB12057_at CJB09730_at CJB07092_at CJB02131_at CJB04173_at CJB05477_at CJB02863_at CJB04667_at CJB02965_at CJB11634_at CJB05646_at CJB07083_at CJB05570_at CJB01204_at CJB01944_at CJB06097_at CJB06639_at CJB02150_at CJB04249_at CJB05121_at CJC00001_ ACT-3_at CJB11644_at CJB05160_at CJB00322_at CJB10529_at CJB08145_at CJB04772_at CJB11702_at CJB06172_at CJB04608_at CJB06070_at CJB00401_at CJB01175_at CJB08956_at CJB06143_s_at CJB12035_at CJB05372_at CJB07808_at CJB07223_at CJB03621_at CJB07343_at CJB05043_at CJB01475_at CJB02174_at CJB05163_at CJB09926_at CJB11816_at CJB09260_at CJB06845_at CJC00001_ ACT-M_at CJC00003_ GAPDH-3_at CJB10024_at CJB04070_at CJB01728_at CJB03857_at CJB10180_at CJB05464_at CJB04307_at CJB04435_at

2116.9 2002.4 1989.5 1967.6 1946.0 1944.8 1927.7 1906.7 1906.5 1880.6 1843.6 1838.5 1826.5 1802.0 1801.4 1776.1 1761.6 1751.6 1725.8 1725.4 1722.1 1707.1

491.6 403.9 214.6 138.4 614.5 102.1 333.8 496.3 438.6 217.1 448.8 305.4 416.2 765.2 138.4 156.4 86.4 22.8 179.4 529.2 674.7 643.9

1703.0 1689.1 1677.3 1665.9 1625.1 1624.8 1624.4 1621.5 1607.4 1587.5 1568.1 1563.7 1559.9 1552.2 1552.0 1551.7 1547.5 1546.8 1544.7 1542.3 1536.4 1519.1 1514.1 1487.8 1460.4 1457.4 1453.4 1449.7 1424.3 1422.9

426.1 445.0 223.7 575.4 281.3 83.9 513.3 356.5 435.7 1226.6 217.7 388.6 232.4 313.6 138.0 433.6 82.4 268.3 206.8 346.2 57.3 461.7 660.5 275.7 577.6 245.2 156.5 144.6 205.5 1050.8

ACTB CLTC ATP5B LDHB HLA-A

Actin, beta Clathrin, heavy chain (Hc) ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide Lactate dehydrogenase B Major histocompatibility complex, class I, A

YWHAB RPL3 PEA15 PTGDS SERINC1 BEX4 MRFAP1 DNER YWHAH ACTG1 ENC1 HSPA8 HSP90AB1 SLC1A3 TMEM66 SEPT7 GNAO1 VSNL1 NHP2L1 NDN OLFM1 PSAP MORF4L1 ACTB

Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide Ribosomal protein L3 Phosphoprotein enriched in astrocytes 15 Prostaglandin D2 synthase 21 kDa (brain) Serine incorporator 1 BEX family member 4 Mof4 family associated protein 1 Delta/notch-like EGF repeat containing Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide Actin, gamma 1 Ectodermal-neural cortex (with BTB-like domain) Heat shock 70 kDa protein 8 Heat shock protein 90 kDa alpha (cytosolic), class B member 1 Solute carrier family 1 (glial high affinity glutamate transporter), member 3 Transmembrane protein 66 Septin 7 Guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O Visinin-like 1 NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae) Necdin homolog (mouse) Olfactomedin 1 Prosaposin Mortality factor 4 like 1 Actin, beta

1422.9

1105.1

GAPDH

Glyceraldehyde-3-phosphate dehydrogenase

1416.5 1414.5 1411.5 1398.2 1386.1 1378.4 1375.9 1370.5

277.6 179.5 226.8 413.7 568.7 241.1 377.1 327.1

TTC3 ENO1 GJA1 RPL14 MBP DBI TIMP2 NACA

Tetratricopeptide repeat domain 3 Enolase 1 (alpha) Gap junction protein, alpha 1, 43 kDa Ribosomal protein L14 Myelin basic protein Diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A binding protein) TIMP metallopeptidase inhibitor 2 Nascent polypeptide-associated complex alpha subunit

Glial fibrillary acidic protein ras-Related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) Carboxypeptidase E NDRG family member 2 Ribosomal protein S3 Paraneoplastic antigen MA2 ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide Chimerin (chimaerin) 1 Iduronate 2-sulfatase Glycoprotein M6A Tetraspanin 7 Kinesin light chain 1 TSC22 domain family, member 1 PNMA-like 1 Glutamate-ammonia ligase (glutamine synthetase) Eukaryotic translation initiation factor 4A, isoform 2 Spectrin, beta, non-erythrocytic 1 Glycoprotein M6A Inositol polyphosphate-5-phosphatase F Prion protein Modulator of apoptosis 1 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide

FL, frontal lobe. AVE, average Signal values of three common marmosets. SD, standard deviation of Signal values of three common marmosets. Hi, hippocampus. Cb, cerebellum. AN, amygdaloid nucleus.

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

70 Table 2 Number of probe sets categorized by the function. Function

The number of annotated probe sets (%) a

FL Transport Metabolism Nervous system development Translation Signal transduction Cytoskeleton Regulation of transcription Protein modification Protein folding Neurotransmitter uptake Apoptosis Cytokinesis Response to stress Others Unclassified Total a b c d

Table 3 Similarity of top 100 probe sets expressed in each structure among 4 structures.

b

Hi

Cb

c

Structure

The number of annotated probe sets (%)

d

FLa

AN

11 9 8 8 8 5 4 4 3 2 2 2 0 9 25

14 8 7 5 6 5 3 4 4 0 3 0 0 13 28

12 8 9 8 7 3 5 3 4 2 2 0 2 11 24

12 9 9 5 7 5 6 3 4 2 3 0 0 9 26

100

100

100

100

FL, H, Cb and AN in common FL, Hi and Cb in common FL, Hi and AN in common FL, Cb and AN in common Hi, Cb and AN in common FL and Hi in common FL and Cb in common FL and AN in common Hi and AN in common Hi and Cb in common Cb and AN in common FL only Hi only Cb only AN only

56 2 12 6 0 6 2 2 0 0 0 9 0 0 0

Total

95 (100)

a

FL, frontal lobe. Hi, hippocampus. Cb, cerebellum. AN, amygdaloid nucleus.

Hib

b c d

(59) (2) (12) (6) (0) (6) (2) (2) (0) (0) (0) (9) (0) (0) (0)

56 2 12 0 7 6 0 0 3 2 0 0 7 0 0

(59) (2) (12) (0) (7) (6) (0) (0) (3) (2) (0) (0) (7) (0) (0)

95 (100)

Cbc

ANd

56 2 0 6 7 0 2 0 0 2 3 0 0 18 0

56 0 12 6 7 0 0 2 3 0 3 0 0 0 7

(58) (2) (0) (6) (7) (0) (2) (0) (0) (2) (3) (0) (0) (18) (0)

96 (100)

(58) (0) (13) (6) (7) (0) (0) (2) (3) (0) (3) (0) (0) (0) (7)

96 (100)

FL, frontal lobe. Hi, hippocampus. Cb, cerebellum. AN, amygdaloid nucleus.

Table 4 Lists of probe sets. Probe sets

FLa_AVEb

FLa_SDc

Hid_AVEb

Hid_SDc

ANe_AVEb

(A) Probe sets expressed in frontal lobe, in hippocampus and in amygdaloid nucleus CJB10533_at 2565.4 77.5 2175.9 239.3 2486.2

c d e f

Description

531.4

SLC1A2

Solute carrier family 1 (glial high affinity glutamate transporter), member 2 Chimerin (chimaerin) 1 Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) Olfactomedin 1 Ectodermal-neural cortex (with BTB-like domain) Paraneoplastic antigen MA2 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide Actin, beta Phosphoprotein enriched in astrocytes 15 Actin, gamma 1 Prosaposin Iduronate 2-sulfatase

2526.9 2046.4

452.0 815.4

2370.5 2581.5

414.8 838.0

1906.7 2328.1

496.3 984.8

CHN1 UCHL1

CJB11816_at CJB05372_at CJB02131_at CJB04772_at

2046.3 1951.1 1887.0 1645.7

145.1 105.5 340.2 301.3

1994.2 2645.2 2104.5 1773.3

271.0 207.7 267.6 297.3

1453.4 1547.5 1944.8 1624.4

156.5 82.4 102.1 513.3

OLFM1 ENC1 PNMA2 YWHAB

CJC00001_ACT-3_at CJB06172_at CJB12035_at CJB09260_at CJB02863_at

1586.7 1509.3 1492.5 1485.6 1463.0

442.3 171.2 383.0 40.6 91.3

1784.8 1678.3 1558.6 1650.2 1643.7

519.2 327.7 350.6 158.1 284.5

1703.0 1607.4 1551.7 1449.7 1906.5

1050.8 435.7 433.6 144.6 438.6

ACTB PEA15 ACTG1 PSAP IDS

Cbf_AVEb

(B) Probe sets expressed only in cerebellum CJB01564_at 2199.9 CJB11629_at 1916.6 CJB11119_at 1815.1 CJB07844_at 1768.2 CJB06229_at 1662.4 CJB07547_at 1657.8 CJB08174_at 1657.3 CJB01093_at 1558.6 CJB03500_at 1541.3 CJB09577_at 1527.9 CJB03506_at 1491.6 CJB06880_at 1464.0 CJB05355_at 1418.9 CJB12001_at 1413.1 CJB01857_at 1402.2 CJB03487_at 1378.2 CJB01059_at 1345.0 CJB04497_at 1344.3 b

Symbol

CJB05477_at CJB01539_at

Probe sets

a

ANe_SDc

Cbf_SDc

Symbol

Description

340.5 307.1 386.5 146.1 89.0 220.7 186.7 453.7 253.3 54.7 305.9 432.2 446.8 282.9 239.5 87.2 112.2 89.2

ALDOC NEUROD1 HPCAL1 EIF1 TIAM1 CALM1 TMEM178 GABRA6 CALB1 CALB1 DPYSL2 CBLN1 EIF4H CA8 ABLIM1 CAMKK2 C5orf13 HSPA1A

Aldolase C, fructose-bisphosphate Neurogenic differentiation 1 Hippocalcin-like 1 Eukaryotic translation initiation factor 1 T-cell lymphoma invasion and metastasis 1 Calmodulin 1 (phosphorylase kinase, delta) Transmembrane protein 178 Gamma-aminobutyric acid (GABA) A receptor, alpha 6 Calbindin 1, 28 kDa Calbindin 1, 28 kDa Dihydropyrimidinase-like 2 Cerebellin 1 precursor Eukaryotic translation initiation factor 4H Carbonic anhydrase VIII Actin binding LIM protein 1 Calcium/calmodulin-dependent protein kinase kinase 2, beta Chromosome 5 open reading frame 13 Heat shock 70 kDa protein 1A

FL, frontal lobe. AVE, average Signal values of three common marmosets. SD, standard deviation of Signal values of three common marmosets. Hi, hippocampus. AN, amygdaloid nucleus. Cb, cerebellum.

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

71

Fig. 1. Comparison of gene expression profiling. The number of probe sets for analysis was shown in parentheses. (A) Scattered plots between the individual samples in the same structure. (B) Scattered plots among the frontal lobe, cerebellum, hippocampus and amygdaloid nucleus with the average of the normalized Signal values.

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

72

structures. Twelve probe sets, over 10%, were common among 3 structures other than the cerebellum (Table 4A). Furthermore, of the top 100 probe sets expressed in cerebellum, 18% (18 probe sets) were cerebellum-specific (Table 4B). The normalized data obtained by microarray analysis were drawn in a scatter plot (Fig. 1A and B). The number of probe sets for analysis was shown in parentheses, which showed more than one ‘‘P (present)’’ of the three Detection Call of the individual samples in either of comparison groups.

100 probe sets sorted by average Signal values in frontal lobe of brain are given. Standard deviations of the three biological replicates were also calculated. Furthermore, the top 100 probe sets were categorized from the point of gene function, according to gene ontology information (Table 2). Twelve probe sets, which were common among the 3 structures other than the cerebellum, were not categorized to a particular kind of function. Furthermore, this was the case for 18 probe sets which were to some extent cerebellum-specific. Similarity of the top 100 probe sets expressed in each structure among 4 structures is indicated in Table 3. Of the top 100 probe sets, 95, 95, 96 and 96 probe sets were annotated in the frontal lobe, hippocampus, cerebellum, amygdaloid nucleus, respectively. About 60% (56 probe sets) were common among all 4

3.2. Probe sets specifically expressed in each area of brain Lists of probe sets specifically expressed in each structure of brain are shown in Table 5A–D. The ratio and p value by the

Table 5 Lists of probe sets specifically expressed in each structure of brain. Probe sets

FLa_AVEb

FLa_SDc

Fold change

p value

Fold change

p value

Fold change

p value

FLa/Hid

FLa/Hid

FLa/Cbe

FLa/Cbe

FLa/ANf

FLa/ANf

Symbol

Description

Glutamate-ammonia ligase (glutamine synthetase) Guanine nucleotide binding protein (G protein), beta polypeptide 1 Catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein) HtrA serine peptidase 1 Chemokine (C-X-C motif) ligand 14 Protein kinase C, beta Cyclic AMP phosphoprotein, 19 kD (EntrezGene) Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 Chromosome 7 open reading frame 41

(A) Frontal lobe CJB05570_at

2523.0

243.3

1.5

0.010

1.9

0.004

1.4

0.019

GLUL

CJB01004_at

1730.8

122.6

1.2

0.047

1.3

0.030

1.4

0.045

GNB1

CJB03230_at

1668.3

62.3

2.0

0.001

2.6

0.005

2.3

0.033

CTNND2

CJB03734_at CJB05559_at CJB01597_at CJB06822_at

1521.4 1167.7 1143.4 1084.0

188.8 107.9 106.6 157.3

1.7 3.1 1.6 3.4

0.016 0.004 0.007 0.004

1.4 9.5 4.9 5.0

0.035 0.003 0.000 0.007

1.5 2.6 2.7 3.2

0.035 0.002 0.002 0.004

HTRA1 CXCL14 PRKCB (ARPP-19)

CJB05920_at

1075.3

61.0

3.4

0.000

1.9

0.000

2.1

0.000

SERPINE2

CJB00279_at CJB05336_at CJB07796_at CJB02660_at

1007.6 950.1 873.9 844.2

134.8 217.0 53.9 61.1

1.9 2.1 1.7 1.3

0.017 0.035 0.021 0.011

1.9 2.1 2.7 1.5

0.018 0.040 0.000 0.005

1.8 1.9 1.8 1.7

0.013 0.050 0.041 0.002

C7orf41 PCDH9 MAPK8IP3

CJB08889_at

754.3

60.9

1.4

0.049

1.9

0.025

1.8

0.049

TPPP

CJB04008_at

712.0

40.1

1.5

0.008

1.9

0.002

2.7

0.000

KCNQ2

CJB02607_at CJB09897_at CJB04998_at

682.2 646.3 641.8

96.2 58.8 157.6

2.8 1.3 5.7

0.014 0.041 0.023

3.6 1.7 24.1

0.012 0.005 0.021

2.7 1.3 8.4

0.005 0.042 0.025

R3HDM1 SULT4A1 NGEF

CJB11062_at CJB06080_at CJB05528_at

640.3 602.7 598.2

139.4 71.1 91.8

3.1 2.6 17.5

0.020 0.002 0.008

3.3 5.7 4.2

0.025 0.006 0.003

4.5 4.0 10.5

0.021 0.001 0.009

CABP1

CJB09180_at CJB03989_at

561.7 531.8

68.7 33.8

2.4 1.4

0.010 0.033

4.3 1.9

0.003 0.006

3.5 1.4

CJB02875_at CJB05714_at CJB09477_at CJB03970_at CJB08348_at

523.6 514.5 502.3 497.1 466.9

15.6 72.9 31.9 59.3 114.5

1.1 2.2 1.2 1.6 3.5

0.018 0.007 0.017 0.040 0.025

1.5 6.3 1.5 2.5 12.2

0.000 0.008 0.002 0.020 0.021

CJB01982_at CJB12038_at

466.9 413.4

28.0 51.1

1.2 8.2

0.040 0.005

2.0 6.2

CJB10772_at CJB06746_at

409.5 403.9

19.0 55.8

1.5 2.2

0.012 0.010

CJB10692_at CJB10298_at

392.9 390.6

75.4 9.3

6.2 1.8

CJB09056_at CJB03498_at

374.9 371.8

39.4 49.1

2.0 1.9

Protocadherin 9 Mitogen-activated protein kinase 8 interacting protein 3 Tubulin polymerization promoting protein Potassium voltage-gated channel, KQT-like subfamily, member 2 R3H domain containing 1 Sulfotransferase family 4A, member 1 Neuronal guanine nucleotide exchange factor Calcium binding protein 1

RIMS3

Regulating synaptic membrane exocytosis 3

0.002 0.047

KCNMA1

1.3 2.7 1.5 1.9 5.2

0.005 0.004 0.003 0.028 0.021

SAE1 KALRN CNTNAP1 ACTN1 (ARPP-21)

0.005 0.007

1.4 4.8

0.019 0.007

ATCAY CIT

2.7 3.5

0.000 0.010

1.8 2.2

0.000 0.011

KIAA0284 CMTM4

0.010 0.000

2.9 2.5

0.011 0.005

8.4 3.2

0.013 0.006

RPH3A PPP1R16B

0.004 0.010

3.2 68.0

0.003 0.006

1.8 4.6

0.006 0.003

TUBG2 TBR1

Potassium large conductance calcium-activated channel, subfamily M, alpha member 1 SUMO1 activating enzyme subunit 1 Kalirin, RhoGEF kinase Contactin associated protein 1 Actinin, alpha 1 Cyclic AMP-regulated phosphoprotein, 21 kD (EntrezGene) Ataxia, cerebellar, Cayman type Citron (rho-interacting, serine/ threonine kinase 21) KIAA0284 CKLF-like MARVEL transmembrane domain containing 4 Rabphilin 3A homolog (mouse) Protein phosphatase 1, regulatory (inhibitor) subunit 16B Tubulin, gamma 2 T-box, brain, 1

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Table 5 (Continued ) Probe sets

FLa_AVEb

FLa_SDc

Fold change

p value

Fold change

p value

Fold change

p value

FLa/Hid

FLa/Hid

FLa/Cbe

FLa/Cbe

FLa/ANf

FLa/ANf

Symbol

Description

Isocitrate dehydrogenase 2 (NADP+), mitochondrial Protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched) TYRO3 protein tyrosine kinase Dishevelled, dsh homolog 1 (Drosophila) Immunoglobin superfamily, member 21 Cordon-bleu homolog (mouse) Syntaxin 1A (brain) Actin binding LIM protein family, member 2 Wolfram syndrome 1 (wolframin) Meningioma (disrupted in balanced translocation) 1 Calcium/calmodulin-dependent protein kinase IG Agrin Mitogen-activated protein kinase 3 SH2 domain containing 5 Cholecystokinin B receptor Chromosome 1 open reading frame 21 Ras association (RalGDS/AF-6) domain family member 2 IQ motif and Sec7 domain 3 ADP-ribosylation factor-like 4D

CJB02319_at

368.3

15.7

1.7

0.000

1.8

0.000

1.4

0.003

IDH2

CJB01808_at

356.7

22.9

1.6

0.002

5.4

0.000

1.7

0.004

PTPN5

CJB05627_at CJB03509_at CJB03229_at CJB11578_at CJB06355_at CJB02364_at

355.9 348.5 332.8 319.2 317.1 299.8

12.1 9.1 43.1 48.1 31.5 32.1

1.9 1.4 2.8 5.4 1.3 2.2

0.004 0.014 0.006 0.007 0.040 0.010

2.1 1.3 1.7 8.5 13.5 2.6

0.004 0.000 0.019 0.006 0.003 0.003

1.6 1.6 3.1 4.3 1.8 2.8

0.009 0.000 0.006 0.003 0.030 0.002

TYRO3 DVL1 IGSF21 COBL STX1A ABLIM2

CJB07251_at CJB06686_at

286.4 275.1

27.8 17.9

2.1 2.9

0.002 0.001

6.1 8.3

0.003 0.001

1.8 2.3

0.005 0.002

WFS1 MN1

CJB09408_at

270.4

48.0

3.6

0.018

2.5

0.015

3.1

0.021

CAMK1G

CJB02799_at CJB10512_at CJB05720_at CJB03244_at CJB07191_at CJB03277_at

270.1 261.2 250.0 236.0 229.3 222.6

18.6 20.0 32.2 56.2 4.9 13.1

3.8 1.6 2.6 3.0 1.4 1.8

0.000 0.006 0.004 0.026 0.036 0.001

5.2 2.9 15.3 8.5 1.4 1.2

0.001 0.001 0.006 0.023 0.015 0.013

2.9 1.4 1.7 2.3 1.8 1.1

0.000 0.021 0.014 0.033 0.039 0.050

AGRN MAPK3 SH2D5 CCKBR C1orf21 RASSF2

CJB02379_at CJB06761_at CJB01375_at CJB12002_at CJB02462_at CJB02344_at CJB08359_at CJB07941_at CJB04121_at CJB01533_at

221.5 209.1 184.4 181.3 169.8 168.9 163.8 163.3 154.0 144.6

24.3 8.8 11.0 20.1 17.7 9.7 2.9 21.6 33.5 7.9

1.8 1.7 1.2 1.6 1.5 1.2 1.5 2.9 3.9 2.9

0.017 0.005 0.045 0.029 0.031 0.012 0.045 0.011 0.024 0.000

2.0 2.3 5.8 3.4 3.5 1.2 1.9 2.4 2.2 2.5

0.009 0.000 0.000 0.001 0.004 0.032 0.016 0.007 0.040 0.000

1.9 2.4 1.7 2.1 2.0 1.3 2.0 3.6 2.9 2.1

0.009 0.009 0.003 0.014 0.008 0.034 0.014 0.006 0.032 0.000

IQSEC3 ARL4D RAB11FIP4 ZDHHC8 TMEM214 FBXL15 KIAA1522 LGI3 PLEKHA6

CJB11350_at CJB01163_at

137.2 137.0

11.6 10.8

3.3 2.5

0.001 0.001

2.2 2.4

0.009 0.002

1.7 2.0

0.027 0.007

AFAP1 TNFSF12

CJB06587_at CJB10858_at CJB01385_at CJB03800_at CJB07193_at CJB08778_at CJB09921_at CJB08094_at CJB00879_at CJB00713_at CJB00262_at CJB09476_at CJB00006_at CJB02226_at CJB06342_at CJB02909_at CJB02232_at

129.0 126.3 125.8 125.7 125.2 123.2 119.0 112.9 109.4 107.7 101.0 98.9 98.4 94.6 93.0 92.6 89.6

15.9 20.4 11.9 7.3 25.0 12.9 18.3 18.7 21.3 16.6 2.4 18.6 10.2 6.5 19.3 2.5 11.8

1.6 2.3 1.6 1.9 2.0 1.5 1.5 11.5 13.5 2.1 1.8 4.6 1.3 1.9 3.5 7.4 2.3

0.036 0.020 0.017 0.005 0.028 0.033 0.042 0.007 0.013 0.015 0.004 0.009 0.041 0.004 0.022 0.000 0.005

8.9 1.6 2.2 1.5 1.7 2.6 2.0 3.0 26.3 2.0 1.3 3.3 1.8 1.7 4.2 11.3 3.6

0.001 0.035 0.004 0.002 0.050 0.005 0.022 0.006 0.013 0.019 0.024 0.009 0.007 0.002 0.022 0.000 0.004

2.0 1.6 1.4 1.8 2.3 1.9 1.8 12.5 15.0 1.7 1.6 2.0 1.5 2.3 2.3 4.4 1.8

0.019 0.048 0.020 0.001 0.037 0.005 0.020 0.008 0.014 0.022 0.010 0.028 0.032 0.008 0.027 0.000 0.022

YJEFN3 DOK5 TPST2 ANKRD27 POU6F1 RHOBTB2 SLC45A4 HR KIAA0748 GPC1 SLC22A23 FBLN5 BRSK2 JAG2 COL4A2 COBL RPS6KA2

CJB04135_at CJB00410_at

88.0 87.2

3.6 5.8

2.5 2.1

0.000 0.005

1.7 1.9

0.000 0.001

1.9 2.0

0.002 0.001

ZBED1 MAFK

CJB04280_at CJB10917_at CJB08193_at

81.5 80.9 80.4

19.8 7.0 9.6

6.3 6.9 1.5

0.024 0.000 0.022

2.6 27.0 2.2

0.046 0.001 0.006

4.3 2.2 1.8

0.030 0.001 0.010

FBLN7 CBLN4 DLGAP4

CJB02228_at CJB09000_at CJB02112_at

80.0 79.5 78.3

27.9 12.0 8.1

20.2 2.0 1.7

0.040 0.012 0.017

13.7 6.2 1.8

0.042 0.007 0.006

19.4 2.0 1.3

0.041 0.012 0.048

KIAA0748 MFGE8 ARPC1B

CJB06592_at CJB07980_at CJB01890_at

72.4 70.6 63.2

9.5 18.2 7.4

1.6 4.0 2.0

0.022 0.037 0.008

2.0 3.3 6.7

0.020 0.034 0.001

1.6 5.0 2.2

0.020 0.022 0.011

TSPAN14

CJB07166_at CJB02709_at CJB09182_at CJB00159_x_at

57.9 57.4 56.3 54.6

4.7 8.9 11.1 10.1

1.5 1.6 2.4 2.8

0.036 0.033 0.020 0.017

1.4 2.2 4.2 1.9

0.018 0.010 0.011 0.027

1.6 2.0 2.4 1.8

0.025 0.019 0.025 0.037

FBXO10

N-terminal EF-hand calcium binding protein 3 F-box protein 10

STAC2 PCP4L1

SH3 and cysteine-rich domain 2 Purkinje cell protein 4 like 1

NECAB3

RAB11 family interacting protein 4 (class II) Zinc finger, DHHC-type containing 8 Transmembrane protein 214 F-box and leucine-rich repeat protein 15 KIAA1522 Leucine-rich repeat LGI family, member 3 Pleckstrin homology domain containing, family A member 6 Actin filament associated protein 1 Tumor necrosis factor (ligand) superfamily, member 12 YjeF N-terminal domain containing 3 Docking protein 5 Tyrosylprotein sulfotransferase 2 Ankyrin repeat domain 27 (VPS9 domain) POU class 6 homeobox 1 Rho-related BTB domain containing 2 Solute carrier family 45, member 4 Hairless homolog (mouse) KIAA0748 Glypican 1 Solute carrier family 22, member 23 Fibulin 5 BR serine/threonine kinase 2 Jagged 2 Collagen, type IV, alpha 2 Cordon-bleu homolog (mouse) Ribosomal protein S6 kinase, 90 kDa, polypeptide 2 Zinc finger, BED-type containing 1 v-maf musculoaponeurotic fibrosarcoma oncogene homolog K (avian) Fibulin 7 Cerebellin 4 precursor Discs, large (Drosophila) homologassociated protein 4 KIAA0748 Milk fat globule-EGF factor 8 protein Actin related protein 2/3 complex, subunit 1B, 41 kDa Tetraspanin 14

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

74 Table 5 (Continued ) Probe sets

FLa_AVEb

FLa_SDc

Fold change

p value

Fold change

p value

Fold change

p value

FLa/Hid

FLa/Hid

FLa/Cbe

FLa/Cbe

FLa/ANf

FLa/ANf

Symbol

Description

Endothelin converting enzyme 1 Leucine-rich repeat containing 32 Nuclear receptor subfamily 4, group A, member 1 Pleckstrin homology domain containing, family A member 6

CJB11945_at CJB01003_at CJB06747_at

49.6 49.0 46.3

10.1 5.9 9.2

3.0 3.7 3.1

0.016 0.002 0.026

2.5 2.2 2.0

0.023 0.006 0.027

2.0 2.2 2.2

0.039 0.004 0.028

ECE1 LRRC32 NR4A1

CJB01221_at

44.1

6.9

2.3

0.019

2.3

0.010

1.9

0.023

PLEKHA6

CJB03097_at CJG00050_at CJB01580_at CJB02840_at CJB00998_at

43.7 42.8 41.6 40.3 39.1

7.8 9.8 2.5 7.3 3.8

2.5 4.2 4.0 2.0 1.4

0.012 0.021 0.000 0.039 0.021

3.0 9.1 2.5 2.6 3.2

0.010 0.013 0.001 0.020 0.001

2.7 3.0 4.9 1.7 1.4

0.010 0.035 0.000 0.036 0.027

RUNX2 RGS6 (DKFZP566E164) PPM1M

CJB08563_at CJB02497_at CJB09041_at

36.9 35.1 33.3

8.4 4.9 4.9

2.4 3.6 1.7

0.046 0.011 0.020

11.3 8.0 1.9

0.014 0.002 0.016

5.7 2.9 1.5

0.013 0.004 0.039

CLEC14A

C-type lectin domain family 14, member A

CJB08232_at CJB12088_at

31.8 31.6

1.2 5.9

1.8 2.3

0.011 0.017

2.9 2.1

0.000 0.021

2.5 1.8

0.003 0.045

ID2

Inhibitor of DNA binding 2, dominant negative helix-loop-helix protein (intron-containing)

CJB04022_at CJB09896_at CJB01832_at CJB01800_at

29.2 29.1 28.7 19.3

3.3 4.0 2.7 3.5

2.9 3.9 2.8 2.1

0.002 0.004 0.001 0.033

3.2 26.5 4.1 3.5

0.002 0.007 0.002 0.016

1.7 4.7 2.3 2.1

0.022 0.006 0.002 0.048

STYK1 TMEM44

Serine/threonine/tyrosine kinase 1 Transmembrane protein 44

Probe sets

Hid_AVEb

(B) Hippocampus CJB05372_at 2645.2

Hid_SDc

CALHM2

Fold change

p value

Fold change

p value

Fold change

p value

Hid/FLa

Hid/FLa

Hid/Cbe

Hid/Cbe

Hid/ANf

Hid/ANf

207.7

1.4

0.014

106.2

0.002

1.7

runt-Related transcription factor 2 Regulator of G-protein signaling 6 DKFZP566E164 protein (EntrezGene) Protein phosphatase 1M (PP2C domain containing) Calcium homeostasis modulator 2

Symbol

Description

0.006

ENC1

Ectodermal-neural cortex (with BTB-like domain) Fibroblast growth factor 13 Synapsin II Neuronal pentraxin receptor CAP, adenylate cyclase-associated protein, 2 (yeast) Phosphofructokinase, platelet piggyBac transposable element derived 5 Transmembrane protein 130 Neuritin 1 Mitogen-activated protein kinase kinase 1

CJB03408_at CJB02135_at CJB07567_at CJB05049_at

1361.0 1349.4 1325.3 1101.4

111.2 28.4 185.2 85.5

2.3 1.8 2.0 1.3

0.002 0.004 0.011 0.017

24.6 2.7 5.7 2.3

0.002 0.000 0.006 0.005

1.2 1.4 1.4 1.2

0.046 0.001 0.048 0.030

FGF13 SYN2 NPTXR CAP2

CJB00289_at CJB06075_at

1050.9 958.1

19.3 74.6

2.0 2.3

0.001 0.001

1.3 2.0

0.016 0.001

1.3 1.4

0.007 0.010

PFKP PGBD5

CJB03925_at CJB03407_at CJB11224_at

940.5 857.8 762.8

36.9 55.8 79.3

1.7 1.7 1.6

0.000 0.004 0.013

4.5 1.6 2.6

0.000 0.003 0.008

1.5 1.7 1.6

0.005 0.002 0.008

TMEM130 NRN1 MAP2K1

CJB00808_at CJB07670_at

687.8 609.9

88.0 74.0

7.0 1.4

0.005 0.043

6.9 1.8

0.007 0.010

1.7 1.3

0.012 0.046

PRRT1

CJB10354_at

520.1

30.2

1.6

0.002

2.1

0.002

1.4

0.029

GARNL4

CJB01042_at

428.7

50.4

2.5

0.003

2.3

0.004

1.6

0.019

PCLO

CJB08715_at

403.7

38.0

1.5

0.011

2.2

0.003

1.5

0.021

C16orf45

CJB05865_at CJB00469_at CJB01368_at CJB02204_at CJB00234_at CJB11095_at

338.2 318.0 299.4 293.8 266.6 255.7

50.4 18.5 20.8 24.2 36.3 45.3

6.6 2.0 2.6 1.4 1.6 1.8

0.009 0.003 0.001 0.010 0.027 0.032

8.6 2.1 2.2 2.4 2.4 3.8

0.008 0.001 0.001 0.003 0.007 0.016

2.1 1.4 1.5 1.4 1.6 2.7

0.020 0.013 0.033 0.018 0.031 0.011

DOCK10 MAOB PELI1

CJB07386_at CJB05608_at CJB11657_at CJB02852_at CJB05107_at CJB02594_at

233.9 201.7 173.9 167.4 163.2 150.1

46.7 29.0 9.2 11.9 19.7 26.5

1.7 1.7 1.3 1.6 2.4 2.1

0.044 0.025 0.013 0.012 0.004 0.022

12.1 2.6 3.2 3.9 3.9 1.9

0.014 0.011 0.000 0.001 0.002 0.044

2.1 1.5 1.3 2.5 1.5 1.6

CJB08235_at CJB00425_at

138.3 106.5

13.5 11.4

1.5 3.0

0.031 0.002

1.5 2.4

0.014 0.003

CJB08958_at

97.1

16.4

4.0

0.012

5.4

CJB09592_at

88.6

5.4

1.2

0.028

1.6

Proline-rich transmembrane protein 1 GTPase activating Rap/RanGAP domain-like 4 Piccolo (presynaptic cytomatrix protein) Chromosome 16 open reading frame 45 Dedicator of cytokinesis 10 Monoamine oxidase B Pellino homolog 1 (Drosophila)

UNC13A CAMK1

unc-13 homolog A (C. elegans) Calcium/calmodulin-dependent protein kinase I

0.025 0.050 0.008 0.012 0.050 0.043

FMNL1 SYN2 PTPRE

1.4 1.5

0.032 0.016

DAGLB ANKRD29(i)

0.012

1.5

0.048

C22orf23

0.006

1.2

0.046

TBCD

Formin-like 1 Synapsin II Protein tyrosine phosphatase, receptor type, E Diacylglycerol lipase, beta Ankyrin repeat domain 29 (intron) Chromosome 22 open reading frame 23 Tubulin folding cofactor D

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

75

Table 5 (Continued ) Probe sets

CJB02453_at

CJB05302_at Probe sets

Hid_AVEb

67.9

33.8 Cbe_AVEb

Hid_SDc

3.7

6.4 Cbe_SDc

Fold change

p value

Fold change

p value

Fold change

p value

Hid/FLa

Hid/FLa

Hid/Cbe

Hid/Cbe

Hid/ANf

Hid/ANf

1.1

0.040

0.018

1.2

1.7

0.042

1.3

4.2

0.019

2.4

Symbol

Description

0.050

B4GALT7

0.016

LAMA3

Xylosylprotein beta 1,4-galactosyltransferase, polypeptide 7 (galactosyltransferase I) Laminin, alpha 3

Fold change

p value

Fold change

p value

Fold change

p value

Cbe/FLa

Cbe/FLa

Cbe/Hid

Cbe/Hid

Cbe/ANf

Cbe/ANf

Symbol

Description

Aldolase C, fructose-bisphosphate Neurogenic differentiation 1 Eukaryotic translation initiation factor 1 T-cell lymphoma invasion and metastasis 1 Transmembrane protein 178 Gamma-aminobutyric acid (GABA) A receptor, alpha 6 Calbindin 1, 28 kDa Calbindin 1, 28 kDa Cerebellin 1 precursor Carbonic anhydrase VIII Actin binding LIM protein 1 Calcium/calmodulin-dependent protein kinase kinase 2, beta Chromosome 5 open reading frame 13 Heat shock 70 kDa protein 1A Eukaryotic translation initiation factor 1 ATPase, Na+/K+ transporting, alpha 1 polypeptide KIAA1576 protein (EntrezGene) Chromosome 5 open reading frame 13 B-cell translocation gene 1, anti-proliferative Tyrosine 3-monooxygenase/ tryptophan 5-monooxygenase activation protein, theta polypeptide Mitochondrial tumor suppressor 1 Calmodulin binding transcription activator 1 CXXC finger 5 Reelin Zic family member 4 Chimerin (chimaerin) 2 Vacuolar protein sorting 26 homolog A (S. pombe) Family with sequence similarity 21, member A/B/C

(C) Cerebellum CJB01564_at CJB11629_at CJB07844_at

2199.9 1916.6 1768.2

340.5 307.1 146.1

1.9 12.8 1.3

0.017 0.010 0.026

1.7 4.5 1.6

0.026 0.013 0.005

1.9 4.7 1.5

0.017 0.012 0.006

ALDOC NEUROD1 EIF1

CJB06229_at

1662.4

89.0

2.7

0.002

2.2

0.028

2.9

0.001

TIAM1

CJB08174_at CJB01093_at

1657.3 1558.6

186.7 453.7

3.0 730.6

0.002 0.027

2.2 2750.5

0.004 0.027

3.0 792.5

0.005 0.027

TMEM178 GABRA6

CJB03500_at CJB09577_at CJB06880_at CJB12001_at CJB01857_at CJB03487_at

1541.3 1527.9 1464.0 1413.1 1402.2 1378.2

253.3 54.7 432.2 282.9 239.5 87.2

15.0 9.7 86.5 89.8 4.0 2.0

0.009 0.000 0.028 0.013 0.014 0.005

7.5 5.7 84.8 53.3 5.7 5.2

0.011 0.000 0.028 0.014 0.014 0.000

12.5 15.3 49.9 54.8 7.3 7.4

0.009 0.000 0.029 0.013 0.013 0.001

CALB1 CALB1 CBLN1 CA8 ABLIM1 CAMKK2

CJB01059_at

1345.0

112.2

4.6

0.001

3.7

0.004

7.0

0.002

C5orf13

CJB04497_at CJB01899_at

1344.3 1299.2

89.2 164.2

2.3 1.6

0.003 0.018

1.5 1.8

0.003 0.010

1.9 1.4

0.002 0.036

HSPA1A EIF1

CJB04985_at

1294.7

119.1

1.7

0.006

1.6

0.018

1.9

0.010

ATP1A1

CJB02138_at CJA00018_s_at

1240.8 1170.5

230.7 323.4

6.2 3.4

0.014 0.041

3.4 3.0

0.017 0.048

2.2 5.7

0.025 0.029

(KIAA1576) C5orf13

CJB07044_at

1058.4

81.6

5.1

0.002

2.6

0.005

2.9

0.005

BTG1

CJB05166_at

1027.3

105.4

2.4

0.019

2.1

0.029

1.7

0.009

YWHAQ

CJB06755_s_at CJB00226_at

976.7 947.2

187.1 63.9

3.1 1.8

0.019 0.001

3.7 2.1

0.021 0.004

3.5 2.9

0.021 0.001

MTUS1 CAMTA1

CJB07886_at CJB06569_at CJB09870_at CJB11031_at CJB00538_at

929.7 889.8 880.0 831.6 829.2

57.0 38.1 44.3 116.6 56.8

2.1 4.3 33.2 6.5 2.8

0.000 0.000 0.001 0.009 0.001

2.2 11.5 71.7 2.0 2.4

0.001 0.000 0.001 0.013 0.001

2.7 6.3 26.3 4.2 2.3

0.001 0.000 0.001 0.009 0.001

CXXC5 RELN ZIC4 CHN2 VPS26A

CJB09131_at

823.6

136.6

2.8

0.015

2.6

0.010

2.2

0.022

CJB03514_at

798.1

33.5

2.8

0.000

2.2

0.000

4.2

0.001

FAM21A/ FAM21B/ FAM21C KCNK1

CJB05463_at

780.6

125.8

1.7

0.041

1.9

0.020

1.6

0.041

DDX3X

CJB03242_at

778.2

32.7

1.2

0.046

1.1

0.045

1.2

0.015

NONO

CJB03124_at CJB10402_at

725.8 725.8

157.1 48.2

4.8 8.5

0.022 0.001

7.7 2.6

0.020 0.000

4.9 5.8

0.020 0.002

SEPT4 ALS2

CJB11381_at CJB07593_at

718.8 718.6

30.0 108.4

2.9 1.7

0.001 0.038

2.7 1.8

0.001 0.033

2.4 1.6

0.000 0.028

RNF146 PAIP2

CJB00701_at

702.6

86.2

2.3

0.012

4.2

0.004

5.5

0.005

VAMP1

CJB01785_at CJB07885_at

684.9 678.4

64.2 97.0

2.1 2.8

0.004 0.012

2.2 3.5

0.004 0.011

1.9 3.9

0.009 0.007

DST SYNE1

CJB01438_at CJB11978_at CJB00314_at

669.8 654.3 652.0

43.8 157.4 116.7

2.6 59.5 5.9

0.000 0.019 0.013

3.6 80.1 4.7

0.000 0.019 0.011

3.4 58.9 3.4

0.000 0.019 0.019

BCL6 CBLN3 MTSS1

Potassium channel, subfamily K, member 1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked Non-POU domain containing, octamer-binding Septin 4 Amyotrophic lateral sclerosis 2 (juvenile) Ring finger protein 146 Poly(A) binding protein interacting protein 2 Vesicle-associated membrane protein 1 (synaptobrevin 1) Dystonin Spectrin repeat containing, nuclear envelope 1 B-cell CLL/lymphoma 6 Cerebellin 3 precursor Metastasis suppressor 1

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

76 Table 5 (Continued ) Probe sets

Cbe_AVEb

Cbe_SDc

Fold change

p value

Fold change

p value

Fold change

p value

Cbe/FLa

Cbe/FLa

Cbe/Hid

Cbe/Hid

Cbe/ANf

Cbe/ANf

Symbol

Description

Erythrocyte membrane protein band 4.1-like 3 Nicotinamide nucleotide adenylyltransferase 2 Protein phosphatase 1, catalytic subunit, gamma isoform Actin binding LIM protein 1 SON DNA binding protein KIAA1279 forkhead box N3 KIAA0746 protein (EntrezGene)

CJB09546_at

645.5

21.4

2.2

0.000

3.8

0.000

3.5

0.000

EPB41L3

CJB02027_at

644.0

87.1

1.9

0.010

1.5

0.044

1.6

0.024

NMNAT2

CJB03633_at

635.7

108.6

2.6

0.022

2.3

0.025

1.9

0.025

PPP1CC

CJB04733_at CJB02937_s_at CJB02298_at CJB01387_at CJB05597_at CJB04739_at CJB07546_at

630.5 628.0 627.9 622.8 615.5 600.4 599.5

67.4 95.7 63.7 168.7 71.1 40.9 12.3

3.5 1.5 2.9 3.3 8.0 4.2 2.9

0.013 0.044 0.001 0.043 0.006 0.000 0.005

9.0 1.5 2.0 5.4 8.4 8.3 2.1

0.004 0.042 0.006 0.026 0.005 0.002 0.011

9.7 1.6 1.7 5.1 8.4 14.6 2.0

0.003 0.040 0.006 0.031 0.005 0.001 0.004

ABLIM1 SON KIAA1279 FOXN3 (KIAA0746) PNRC1

CJB03225_at

592.4

50.1

1.3

0.037

1.3

0.034

1.3

0.021

PSMC5

CJB00968_at

587.5

21.0

1.3

0.011

1.6

0.002

1.4

0.047

HNRNPD

CJB02050_at CJB09350_at

585.2 577.3

81.7 25.4

3.0 1.9

0.012 0.000

3.8 1.6

0.011 0.001

3.3 1.6

0.010 0.000

ATP11A TAF7

CJB06673_at CJB08525_at

576.3 563.2

139.2 25.7

3.7 1.3

0.028 0.005

7.8 3.0

0.025 0.000

3.9 3.9

0.029 0.000

FGFR1 ATP2B2

CJB11889_at

557.9

24.4

1.9

0.006

1.7

0.000

1.3

0.019

CHL1

CJB07750_at CJB07253_at CJB04027_at CJB03022_at

557.5 555.8 552.0 547.4

83.7 72.8 24.4 88.0

12.8 4.8 1.3 5.7

0.008 0.002 0.003 0.010

82.0 19.2 1.5 5.7

0.008 0.006 0.002 0.010

20.7 17.6 1.6 4.4

0.006 0.006 0.001 0.012

INADL ANK1

CJB02645_at CJB06755_at CJB01309_at CJB06974_at CJB08735_at CJB00206_at CJB01038_at CJB01100_at CJB11649_at CJB06753_at CJB08842_at CJB05481_at CJB10226_at CJB07016_at CJB01201_s_at CJB12080_at CJB10041_at CJB06547_at

546.4 545.0 528.6 520.5 515.9 515.6 485.9 482.0 476.6 476.4 463.9 459.8 455.4 450.4 450.2 433.0 418.3 414.8

116.7 57.5 39.7 49.1 49.6 65.4 59.7 81.4 51.3 27.6 83.8 45.0 16.4 37.3 53.8 31.8 38.6 37.1

17.9 3.4 2.7 2.9 2.0 1.8 3.1 15.0 1.5 2.0 17.4 1.4 1.9 1.7 2.1 1.6 2.0 1.6

0.016 0.005 0.002 0.003 0.007 0.015 0.006 0.011 0.016 0.001 0.012 0.050 0.010 0.006 0.006 0.003 0.005 0.013

109.3 3.7 1.7 15.8 1.7 1.7 2.2 7.3 4.4 8.4 24.2 3.7 1.9 1.8 2.0 1.9 2.0 1.3

0.015 0.004 0.006 0.003 0.005 0.030 0.008 0.012 0.005 0.000 0.011 0.002 0.000 0.003 0.009 0.001 0.004 0.027

36.0 3.4 2.2 14.1 1.7 1.7 2.0 31.4 4.8 3.3 16.1 2.5 2.2 1.3 2.3 1.8 1.6 1.9

0.016 0.006 0.003 0.003 0.007 0.024 0.009 0.010 0.005 0.002 0.011 0.006 0.000 0.015 0.009 0.002 0.013 0.019

INADL MTUS1 CA10 KIAA0802 GPBP1 ARGLU1 NFIA EXPH5 DAB2IP LHFP ZNF521 DUSP1 NCOR1

SLIT-ROBO Rho GTPase activating protein 2 InaD-like (Drosophila) Mitochondrial tumor suppressor 1 Carbonic anhydrase X KIAA0802 GC-rich promoter binding protein 1 Arginine and glutamate rich 1 Nuclear factor I/A Exophilin 5 DAB2 interacting protein Lipoma HMGIC fusion partner Zinc finger protein 521 Dual specificity phosphatase 1 Nuclear receptor co-repressor 1

PISD

Phosphatidylserine decarboxylase

SFRS3 PLEKHH1

CJB09493_at CJG00032_at CJB02786_at

413.9 405.1 397.7

98.2 45.7 22.3

4.1 2.6 2.2

0.029 0.003 0.000

3.5 1.9 1.6

0.031 0.009 0.003

3.9 1.9 1.6

0.030 0.006 0.009

FKBP4 SON RAB21

CJB04553_at CJB07374_at

390.5 387.7

94.4 49.4

2.6 1.8

0.031 0.022

2.5 1.7

0.034 0.021

2.4 1.4

0.033 0.049

KIAA0247 PNRC2

CJB09379_at

384.8

28.5

6.0

0.000

91.6

0.002

24.6

0.002

SCN4B

CJB06821_at

382.7

58.8

27.1

0.008

59.2

0.008

33.0

0.007

ZIC1

Splicing factor, arginine/serine-rich 3 Pleckstrin homology domain containing, family H (with MyTH4 domain) member 1 FK506 binding protein 4, 59 kDa SON DNA binding protein RAB21, member RAS oncogene family KIAA0247 Proline-rich nuclear receptor coactivator 2 Sodium channel, voltagegated, type IV, beta Zic family member 1 (odd-paired homolog, Drosophila)

CJB06918_at CJB01357_at CJB03189_at CJB10198_at

382.0 374.1 369.1 366.7

39.0 19.9 69.0 28.7

1.7 1.7 7.5 1.7

0.011 0.005 0.009 0.006

2.0 1.6 5.9 2.0

0.010 0.002 0.015 0.002

1.8 1.5 8.6 1.7

0.004 0.016 0.010 0.016

CLIP1

SRGAP2

Proline-rich nuclear receptor coactivator 1 Proteasome (prosome, macropain) 26S subunit, ATPase, 5 Heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37 kDa) ATPase, class VI, type 11A TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 55 kDa Fibroblast growth factor receptor 1 ATPase, Ca++ transporting, plasma membrane 2 Cell adhesion molecule with homology to L1CAM (close homolog of L1) InaD-like (Drosophila) Ankyrin 1, erythrocytic

CAP-GLY domain containing linker protein 1

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

77

Table 5 (Continued ) Probe sets

Cbe_AVEb

Cbe_SDc

Fold change

p value

Fold change

p value

Fold change

p value

Cbe/FLa

Cbe/FLa

Cbe/Hid

Cbe/Hid

Cbe/ANf

Cbe/ANf

Symbol

Description

Homer homolog 3 (Drosophila) Family with sequence similarity 123A Transducer of ERBB2, 2 NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49 kDa (NADH-coenzyme Q reductase) Paired box 6 Ring finger and CHY zinc finger domain containing 1 Glucocorticoid induced transcript 1 Fibronectin type III domain containing 5

CJB05354_at CJB08596_at

366.1 365.0

60.6 36.6

11.6 1.3

0.011 0.038

1.9 1.4

0.030 0.020

4.9 1.6

0.012 0.016

HOMER3 FAM123A

CJB09257_at CJB02356_at

357.2 352.2

61.2 17.8

2.4 1.3

0.021 0.014

3.0 1.2

0.014 0.024

2.6 1.2

0.023 0.015

TOB2 NDUFS2

CJB01285_at CJB00190_at

345.0 337.8

92.1 40.3

4.6 1.7

0.032 0.013

5.8 1.7

0.025 0.011

4.6 1.7

0.028 0.016

PAX6 RCHY1

CJB06723_at CJB11560_at

336.5 332.7

69.7 27.3

4.0 5.2

0.022 0.003

4.4 3.6

0.019 0.001

6.8 4.5

0.016 0.001

GLCCI1 FNDC5

CJB10632_at CJB03518_at CJB02808_at

315.3 310.6 309.5

30.6 36.9 49.0

1.4 1.8 3.4

0.017 0.008 0.004

1.4 1.6 10.2

0.038 0.015 0.007

1.3 1.3 9.4

0.031 0.048 0.010

HIGD1A (PIP3-E)

CJB08229_at CJG00166_at CJB09144_at CJB00572_at CJB00139_at

307.7 307.2 301.6 300.1 296.5

60.7 22.0 68.0 23.4 58.3

2.1 1.7 2.4 1.4 2.1

0.032 0.002 0.027 0.023 0.023

2.3 2.2 3.5 2.3 2.3

0.025 0.005 0.015 0.002 0.022

2.9 1.8 2.6 2.2 1.8

0.019 0.003 0.026 0.001 0.046

IER5 STAG2 SPRY2

CJB06527_at

295.5

56.7

2.1

0.021

3.1

0.010

7.3

0.016

CACNA1A

CJB11933_at

295.2

22.1

2.3

0.001

2.1

0.002

2.1

0.007

C13orf37

CJB05717_at CJB11516_at

295.0 294.3

18.1 23.6

2.0 1.5

0.001 0.036

1.6 1.8

0.001 0.004

1.6 1.4

0.002 0.012

UNC84A RNF6

CJB02676_at CJB06932_at CJB02981_at

293.1 287.4 282.6

30.7 30.9 18.9

2.3 2.8 4.1

0.005 0.003 0.000

3.2 3.2 5.2

0.006 0.003 0.000

3.0 3.0 5.3

0.008 0.002 0.000

ZNF219 C20orf117

CJB07441_at CJB09775_at CJB10636_at CJB06468_at

278.4 277.8 277.1 276.9

78.2 19.5 20.6 21.0

6.7 3.1 1.5 2.9

0.028 0.000 0.004 0.002

12.3 1.5 1.4 2.5

0.028 0.008 0.009 0.012

8.1 1.5 1.5 2.3

0.032 0.005 0.008 0.003

RCAN3 WSCD2

CJB05182_at

276.2

23.2

1.6

0.019

1.5

0.007

1.5

0.006

CKAP5

CJB04334_at

274.2

4.4

1.4

0.012

1.3

0.004

1.7

0.003

CJB11794_at CJB07838_at

271.8 269.0

31.1 26.6

1.6 1.8

0.027 0.005

1.6 1.7

0.029 0.012

1.7 1.6

0.013 0.012

FAM156A/ FAM156B PRDX6 FBXL3

CJB00659_at CJB03493_at

262.7 261.5

61.4 39.6

2.5 2.8

0.046 0.010

2.3 3.3

0.041 0.008

2.6 3.1

0.034 0.009

PLCL2 NETO2

CJB06524_at

259.9

50.0

2.4

0.022

4.0

0.018

5.5

0.014

C20orf39

CJB10160_at

256.6

34.0

2.0

0.008

2.5

0.010

2.4

0.005

TNRC6A

CJB04821_at CJB04053_at CJB04325_at

255.2 253.7 246.9

29.8 33.8 54.4

1.7 2.1 1.9

0.018 0.017 0.044

3.7 1.8 3.4

0.001 0.017 0.016

3.0 1.5 3.3

0.002 0.026 0.014

CCNDBP1 C9orf75

CJB05624_at

245.7

48.7

2.2

0.027

1.9

0.035

1.7

0.044

COX11

CJB10831_at

245.5

21.8

1.7

0.006

1.4

0.017

1.4

0.032

SFRS3

CJB00125_at

245.1

22.7

1.8

0.008

1.6

0.006

1.5

0.011

PIGS

CJB00698_at

243.8

18.4

1.8

0.006

3.2

0.001

2.4

0.001

PSD2

CJB03732_at CJB06175_at

237.6 230.7

34.7 32.3

1.8 1.9

0.028 0.015

6.5 1.8

0.009 0.015

5.5 1.8

0.003 0.017

CTCF

CJB06363_at

230.0

6.3

1.3

0.037

1.4

0.001

1.6

0.000

NAP1L4

ST13

MAPK9

HIG1 domain family, member 1A Phosphoinositide-binding protein PIP3-E (EntrezGene) Immediate early response 5 Stromal antigen 2 Sprouty homolog 2 (Drosophila) Suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) Calcium channel, voltagedependent, P/Q type, alpha 1A subunit Chromosome 13 open reading frame 37 unc-84 homolog A (C. elegans) Ring finger protein (C3H2C3 type) 6 Zinc finger protein 219 Chromosome 20 open reading frame 117 RCAN family member 3 WSC domain containing 2 Mitogen-activated protein kinase 9 Cytoskeleton associated protein 5 Family with sequence similarity 156, member A/B Peroxiredoxin 6 F-box and leucine-rich repeat protein 3 Phospholipase C-like 2 Neuropilin (NRP) and tolloid (TLL)-like 2 Chromosome 20 open reading frame 39 Trinucleotide repeat containing 6A Cyclin D-type binding-protein 1 Chromosome 9 open reading frame 75 COX11 homolog, cytochrome c oxidase assembly protein (yeast) Splicing factor, arginine/ serine-rich 3 Phosphatidylinositol glycan anchor biosynthesis, class S Pleckstrin and Sec7 domain containing 2 CCCTC-binding factor (zinc finger protein) Nucleosome assembly protein 1-like 4

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

78 Table 5 (Continued ) Probe sets

Cbe_AVEb

Cbe_SDc

Fold change

p value

Fold change

p value

Fold change

p value

Cbe/FLa

Cbe/FLa

Cbe/Hid

Cbe/Hid

Cbe/ANf

Cbe/ANf

Symbol

Description

Retinaldehyde binding protein 1-like 1 Potassium inwardly rectifying channel, subfamily J, member 12 Solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6 Melanoma cell adhesion molecule Mitochondrial tumor suppressor 1 EP300 interacting inhibitor of differentiation 2B CDC42 binding protein kinase alpha (DMPK-like) Transmembrane and tetratricopeptide repeat containing 4

CJB10553_at

226.1

14.6

2.1

0.001

1.7

0.008

1.4

0.025

RLBP1L1

CJB07508_at

224.7

36.7

10.2

0.011

34.6

0.009

19.2

0.009

KCNJ12

CJB06064_at

224.2

41.7

16.3

0.012

2.9

0.018

4.3

0.016

SLC1A6

CJB04909_at CJB01669_at CJB03915_at

223.2 222.1 221.3

16.4 21.0 18.7

4.7 4.6 2.4

0.000 0.002 0.002

14.7 4.5 1.6

0.001 0.005 0.017

6.6 3.5 1.8

0.000 0.003 0.004

MCAM MTUS1 EID2B

CJB11898_at

221.3

35.0

1.9

0.035

1.6

0.045

1.9

0.018

CDC42BPA

CJB07647_at

218.2

37.2

3.6

0.011

5.9

0.011

5.6

0.007

TMTC4

CJB03884_at CJB06418_at

210.5 209.7

8.7 28.8

1.6 5.9

0.007 0.007

1.3 9.3

0.022 0.007

1.3 7.6

0.002 0.005

SLCO4A1

CJB11713_at

205.1

44.2

2.8

0.019

2.0

0.039

2.8

0.033

FHOD3

CJB04259_at CJB00607_at

203.1 200.3

9.9 23.1

1.4 1.9

0.035 0.007

1.7 1.5

0.001 0.038

1.6 1.5

0.006 0.023

CYTH2 C3orf39

CJB04836_at CJB00219_at CJB09329_at CJB02967_at CJB02745_at

197.2 193.6 191.2 191.1 188.9

10.2 14.4 33.9 43.6 10.9

1.4 1.2 4.0 2.2 1.4

0.003 0.034 0.014 0.039 0.025

1.2 1.5 3.6 1.9 1.4

0.015 0.033 0.009 0.049 0.017

1.3 1.6 5.1 2.1 1.5

0.009 0.003 0.005 0.041 0.002

RBM22 TK1 TRIM32 EZH1

CJB11709_at

188.4

14.8

2.0

0.001

1.5

0.042

1.5

0.019

CABC1

CJB08920_at CJB10031_at CJB06206_at

187.3 186.5 185.6

19.9 24.8 39.3

2.4 5.6 4.0

0.003 0.006 0.015

2.4 7.2 1.8

0.004 0.007 0.046

2.1 9.0 4.0

0.004 0.006 0.025

EED SHROOM1 DPF3

CJB10178_at CJB09313_at

176.7 176.0

31.7 12.4

1.7 2.1

0.040 0.002

1.7 1.6

0.043 0.004

1.8 1.6

0.039 0.007

USP24 IER3IP1

CJB08953_at CJB03812_at CJB09400_at

175.8 173.4 173.3

29.8 19.8 30.5

4.4 1.4 2.4

0.011 0.028 0.012

12.8 1.5 1.9

0.010 0.019 0.023

2.9 1.5 1.9

0.011 0.042 0.042

TMEM163 LTA4H PRPF38B

CJB11827_at

173.3

18.5

2.1

0.004

2.3

0.003

1.5

0.022

SSBP2

CJB06369_at

172.0

24.2

2.8

0.004

1.9

0.025

3.2

0.013

C3orf59

CJB03132_at CJB03787_at CJB07756_at CJB06536_at

170.9 170.7 170.3 168.2

3.7 5.8 17.9 18.9

2.5 1.4 1.5 6.1

0.000 0.004 0.017 0.004

2.0 1.7 1.6 14.4

0.007 0.000 0.015 0.004

1.6 1.8 1.6 4.9

0.017 0.001 0.011 0.004

HLTF GPR107 GPRC5C

CJG00109_at

167.3

37.0

1.9

0.047

2.5

0.029

2.2

0.034

MPP1

CJB00800_at

165.9

26.1

1.8

0.020

3.3

0.008

2.3

0.019

PACSIN2

CJB09146_at

165.0

10.2

1.8

0.006

3.0

0.002

1.6

0.002

SEMA6A

CJB05078_at

164.5

7.5

1.3

0.003

1.5

0.001

1.6

0.003

SART3

CJB10368_at

161.9

10.9

1.7

0.004

2.0

0.002

2.1

0.003

HNRPDL

CJB07945_at

161.2

33.2

2.5

0.028

2.2

0.026

2.0

0.032

UBE2G1

CJB11712_at

161.0

11.0

1.6

0.004

1.4

0.008

1.3

0.037

SLU7

CJB09422_at

160.3

16.1

2.1

0.003

2.0

0.004

2.3

0.004

DDX46

CJB04602_at

160.1

44.4

9.1

0.028

6.3

0.032

7.2

0.030

SHF

Solute carrier organic anion transporter family, member 4A1 Formin homology 2 domain containing 3 Cytohesin 2 Chromosome 3 open reading frame 39 RNA binding motif protein 22 Thymidine kinase 1, soluble Tripartite motif-containing 32 Enhancer of zeste homolog 1 (Drosophila) Chaperone, ABC1 activity of bc1 complex homolog (S. pombe) Embryonic ectoderm development Shroom family member 1 D4, zinc and double PHD fingers, family 3 Ubiquitin specific peptidase 24 Immediate early response 3 interacting protein 1 Transmembrane protein 163 Leukotriene A4 hydrolase PRP38 pre-mRNA processing factor 38 (yeast) domain containing B Single-stranded DNA binding protein 2 Chromosome 3 open reading frame 59 Helicase-like transcription factor G protein-coupled receptor 107 G protein-coupled receptor, family C, group 5, member C Membrane protein, palmitoylated 1, 55 kDa Protein kinase C and casein kinase substrate in neurons 2 Sema domain, transmembrane domain (TM), and Cytoplasmic domain (semaphorin) 6A Squamous cell carcinoma antigen recognized by T cells 3 Heterogeneous nuclear ribonucleoprotein D-like Ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, yeast) SLU7 splicing factor homolog (S. cerevisiae) DEAD (Asp-Glu-Ala-Asp) box polypeptide 46 Src homology 2 domain containing F

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

79

Table 5 (Continued ) Probe sets

Cbe_AVEb

Cbe_SDc

Fold change

p value

Fold change

p value

Fold change

p value

Cbe/FLa

Cbe/FLa

Cbe/Hid

Cbe/Hid

Cbe/ANf

Cbe/ANf

Symbol

Description

Neuropilin (NRP) and tolloid (TLL)-like 2 Methyl CpG binding protein 2 (Rett syndrome) Sestrin 1

CJB02064_at

155.0

10.3

3.2

0.000

3.2

0.000

3.1

0.000

NETO2

CJG00089_at

154.4

2.3

1.2

0.037

1.7

0.000

1.6

0.024

MECP2

CJB06854_at CJB03403_at CJB02759_at

153.9 152.5 149.5

27.3 18.1 26.0

3.1 1.4 1.9

0.008 0.033 0.023

3.6 1.5 1.9

0.007 0.019 0.033

3.3 1.6 1.6

0.012 0.032 0.047

SESN1

CJB04026_at CJB11155_at

147.4 146.9

4.8 27.4

1.5 8.4

0.008 0.014

1.9 8.6

0.004 0.012

1.6 7.8

CJB07957_at

146.2

11.2

2.2

0.001

1.5

0.006

CJB03940_at

145.8

27.7

2.0

0.037

2.2

CJB06833_at

145.8

14.3

2.2

0.004

CJB06002_at CJB04336_at

145.6 143.7

15.4 18.2

1.6 1.5

CJB06106_at CJB03922_at

142.6 142.2

22.2 39.6

CJB08607_at

142.1

CJB08954_at

AIFM1

Apoptosis-inducing factor, mitochondrion-associated, 1

0.017 0.010

CHD7

1.3

0.024

TLE4

0.030

2.6

0.025

MMP24

1.8

0.014

1.6

0.013

FAM122A

0.010 0.029

1.7 1.4

0.007 0.034

2.0 1.5

0.004 0.024

N4BP1 MARK3

1.9 9.3

0.025 0.027

2.3 27.5

0.023 0.026

1.7 12.2

0.025 0.027

EXTL2 LDLRAP1

15.2

4.6

0.001

6.4

0.001

7.2

0.001

GALNT13

140.4

8.0

1.6

0.003

1.5

0.006

1.5

0.002

SPOCK2

CJB04080_at CJA00025_at

138.4 137.6

24.6 32.5

2.5 3.0

0.019 0.030

2.2 2.6

0.020 0.031

2.7 2.0

0.013 0.046

UBTD2 PRPF38B

CJB11142_at

137.1

30.0

6.8

0.017

8.7

0.011

10.4

0.017

IL16

CJB01661_at

136.7

9.9

2.3

0.001

1.8

0.012

2.0

0.001

PXK

CJB01572_at CJB02868_at CJB02836_at CJB03397_at

136.5 135.6 133.6 133.4

11.6 16.8 19.4 19.3

1.6 2.8 1.8 28.4

0.014 0.006 0.014 0.006

1.3 6.9 3.1 58.0

0.017 0.004 0.004 0.007

1.7 4.6 2.1 31.3

0.012 0.008 0.010 0.006

EP400 ASTN2 FOXP4 EOMES

CJB11331_at CJB11426_at

132.1 131.6

15.1 25.9

1.5 2.6

0.026 0.016

1.4 3.7

0.037 0.015

1.6 3.6

0.015 0.021

ZNF248 RERG

CJB10428_at

129.9

14.6

1.7

0.009

2.0

0.004

2.1

0.007

RGL2

CJB07712_at

129.8

9.0

2.2

0.021

3.3

0.000

2.8

0.000

ATF7

CJB04416_at

129.3

18.3

5.0

0.007

3.9

0.003

3.4

0.007

PPM1D

CJB06667_at

125.2

21.0

3.0

0.013

2.3

0.015

2.0

0.018

GNB5

CJB12060_at

124.2

15.0

1.6

0.017

1.7

0.024

1.5

0.031

KBTBD4

CJB06439_at

123.3

14.6

1.8

0.020

1.9

0.010

1.8

0.020

DDX27

CJB11471_at

123.0

8.9

3.3

0.001

2.5

0.001

2.9

0.001

RGN

Chromodomain helicase DNA binding protein 7 Transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) Matrix metallopeptidase 24 (membrane-inserted) Family with sequence similarity 122A NEDD4 binding protein 1 MAP/microtubule affinityregulating kinase 3 Exostoses (multiple)-like 2 Low density lipoprotein receptor adaptor protein 1 UDP-N-acetyl-alpha-Dgalactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13) sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2 Ubiquitin domain containing 2 PRP38 pre-mRNA processing factor 38 (yeast) domain containing B Interleukin 16 (lymphocyte chemoattractant factor) PX domain containing serine/threonine kinase E1A binding protein p400 Astrotactin 2 Forkhead box P4 Eomesodermin homolog (Xenopus laevis) Zinc finger protein 248 RAS-like, estrogen-regulated, growth inhibitor ral guanine nucleotide dissociation stimulator-like 2 Activating transcription factor 7 Protein phosphatase 1D magnesium-dependent, delta isoform Guanine nucleotide binding protein (G protein), beta 5 kelch repeat and BTB (POZ) domain containing 4 DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 Regucalcin (senescence marker protein-30)

CJB04028_at CJB01098_at CJB07208_at

118.1 117.1 113.3

15.9 8.6 23.9

4.3 19.3 2.8

0.005 0.001 0.033

4.3 33.1 2.9

0.003 0.001 0.031

6.4 54.9 2.9

0.003 0.001 0.021

LBXCOR1 PAIP2B(d)

CJB01912_at CJB03465_at

113.2 112.0

5.5 3.8

2.6 1.7

0.002 0.007

2.8 2.9

0.000 0.001

2.9 1.7

0.000 0.016

TMPO ARFGAP3

CJB03644_at

111.5

14.7

3.4

0.003

3.2

0.003

2.4

0.006

CDC7

CJB09437_at

110.2

32.9

4.3

0.043

9.3

0.031

6.2

0.038

KLHL13

LBXCOR1 homolog (mouse) Poly(A) binding protein interacting protein 2B (downstream) Thymopoietin ADP-ribosylation factor GTPase activating protein 3 Cell division cycle 7 homolog (S. cerevisiae) kelch-like 13 (Drosophila)

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

80 Table 5 (Continued ) Probe sets

Cbe_AVEb

Cbe_SDc

Fold change

p value

Fold change

p value

Fold change

p value

Cbe/FLa

Cbe/FLa

Cbe/Hid

Cbe/Hid

Cbe/ANf

Cbe/ANf

Symbol

Description

Inositol polyphosphate-5phosphatase J Nucleoporin 188 kDa Sirtuin (silent mating type information regulation 2 homolog) 7 (S. cerevisiae) Membrane protein, palmitoylated 1, 55 kDa Similar to zinc finger protein 598 (EntrezGene) Cytochrome b5 reductase 4

CJB06529_at

109.5

8.1

5.5

0.000

7.0

0.000

4.1

0.000

INPP5J

CJB09469_at CJB02894_at

107.1 106.8

9.9 9.8

1.8 1.6

0.010 0.012

1.7 1.7

0.018 0.005

2.0 2.0

0.004 0.003

NUP188 SIRT7

CJB03793_s_at

106.5

10.5

1.8

0.022

2.0

0.024

1.9

0.013

MPP1

CJB07968_at

105.6

8.4

1.4

0.016

1.7

0.019

1.9

0.047

(LOC645937)

CJB02295_at CJB10398_at CJB00431_at

105.2 104.7 103.7

9.4 13.4 14.6

2.8 2.8 1.9

0.001 0.006 0.011

2.2 1.6 1.7

0.008 0.022 0.021

2.1 2.6 1.4

0.005 0.005 0.045

CYB5R4

CJB05115_at CJB00661_at

103.4 100.3

12.8 21.2

10.1 2.4

0.002 0.026

8.1 2.5

0.003 0.019

4.2 2.3

0.002 0.029

CA14 UCKL1

CJB01556_at

100.2

14.4

2.5

0.006

2.7

0.005

2.4

0.007

TBC1D8

CJB08512_at CJB07398_at

99.3 98.9

2.5 6.6

1.5 2.2

0.004 0.001

1.5 2.1

0.008 0.001

1.5 2.3

0.002 0.002

TARBP2

CJB06806_at

97.8

23.5

3.2

0.033

2.9

0.041

3.4

0.027

HBEGF

CJB09992_at CJB03676_at CJB07043_at

97.1 96.8 96.0

13.2 7.3 36.0

1.6 3.0 29.4

0.027 0.000 0.046

1.8 4.5 23.8

0.029 0.000 0.047

2.3 5.0 14.9

0.016 0.002 0.048

TBC1D2B MUTYH CDH15

CJB06288_at

94.9

15.9

1.7

0.033

3.4

0.013

2.0

0.035

PRDM2

CJB01237_at

94.0

12.0

4.4

0.003

6.9

0.003

7.5

0.002

CJB04872_at

93.8

19.6

2.9

0.021

3.7

0.019

2.5

0.021

(C22:CTA250D10.9) PIP5K1B

CJB09486_at

93.5

20.6

1.8

0.049

5.3

0.023

3.5

0.015

KCNAB3

CJB06214_at

92.6

22.0

6.6

0.021

6.4

0.017

6.3

0.024

GRIA4

CJB07060_at

92.5

22.7

3.1

0.024

6.0

0.021

4.0

0.027

PCSK6

CJB06368_at CJB01166_at CJB11490_at

90.2 89.1 88.9

7.2 0.9 5.9

1.5 1.6 1.7

0.009 0.004 0.002

1.5 1.8 2.0

0.020 0.002 0.019

1.8 2.4 1.6

0.026 0.000 0.018

NISCH(i) ZNF653 RGS20

CJB10678_at

87.8

21.6

2.8

0.036

3.7

0.035

2.9

0.041

DCXR

CJB08123_at

86.0

6.8

2.9

0.000

2.4

0.005

2.2

0.004

PLAU

CJB11848_at CJB03619_at

85.6 82.7

16.4 19.4

3.1 2.2

0.020 0.047

3.3 2.8

0.015 0.040

2.9 2.1

0.023 0.043

KCTD2

CJB08406_at

82.2

4.7

1.4

0.040

1.7

0.001

1.7

0.002

DNMT1

CJB08936_at

81.3

9.0

3.3

0.005

4.1

0.001

2.8

0.006

WWOX

CJB08919_at CJB04253_at

80.7 80.4

14.1 6.1

4.0 2.7

0.014 0.005

3.2 2.9

0.011 0.000

2.8 4.8

0.011 0.004

TMEM74 PAG1

CJB03284_at

79.9

22.1

5.5

0.032

22.6

0.025

7.1

0.031

PIP5KL1

CJB09348_at

78.8

13.7

1.9

0.034

2.5

0.020

2.9

0.021

ZFYVE28

CJB10623_at

78.7

4.0

1.7

0.001

1.4

0.046

1.6

0.001

GABPB1

CJG00076_at

78.0

13.6

1.9

0.028

1.8

0.040

1.7

0.035

PISD

CJB11414_at CJB03114_at CJB05396_at

77.1 76.0 75.9

1.5 9.9 2.8

1.4 21.5 1.8

0.006 0.003 0.024

1.6 14.1 1.5

0.004 0.006 0.001

1.7 9.5 1.8

0.030 0.005 0.021

ZNF385C

IVNS1ABP

Influenza virus NS1A binding protein Carbonic anhydrase XIV Uridine-cytidine kinase 1-like 1 TBC1 domain family, member 8 (with GRAM domain) TAR (HIV-1) RNA binding protein 2 Heparin-binding EGF-like growth factor TBC1 domain family, member 2B mutY homolog (E. coli) Cadherin 15, M-cadherin (myotubule) PR domain containing 2, with ZNF domain Transmembrane protein 46-like (EntrezGene) Phosphatidylinositol-4phosphate 5-kinase, type I, beta Potassium voltage-gated channel, shaker-related subfamily, beta member 3 Glutamate receptor, ionotrophic, AMPA 4 Proprotein convertase subtilisin/kexin type 6 Nischarin (intron) Zinc finger protein 653 Regulator of G-protein signaling 20 Dicarbonyl/L-xylulose reductase Plasminogen activator, urokinase Potassium channel tetramerisation domain containing 2 DNA (cytosine-5-)methyltransferase 1 WW domain containing oxidoreductase Transmembrane protein 74 Phosphoprotein associated with glycosphingolipid microdomains 1 Phosphatidylinositol-4phosphate 5-kinase-like 1 Zinc finger, FYVE domain containing 28 GA binding protein transcription factor, beta subunit 1 Phosphatidylserine decarboxylase Zinc finger protein 385C

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

81

Table 5 (Continued ) Probe sets

Cbe_AVEb

Cbe_SDc

Fold change

p value

Fold change

p value

Fold change

p value

Cbe/FLa

Cbe/FLa

Cbe/Hid

Cbe/Hid

Cbe/ANf

Cbe/ANf

Symbol

Description

CJB02570_at CJB03413_at CJB10744_at CJB05516_at

75.7 74.9 73.8 73.4

10.0 5.3 7.2 8.0

1.8 1.5 1.7 2.2

0.012 0.004 0.008 0.003

1.9 1.6 3.5 2.5

0.010 0.003 0.004 0.003

2.5 1.6 2.8 1.6

0.004 0.031 0.006 0.022

DOM3Z

dom-3 homolog Z (C. elegans)

ZDHHC5

CJB01439_at

73.1

11.0

2.1

0.011

2.3

0.010

3.0

0.012

(LOC100134137)

Zinc finger, DHHC-type containing 5 Similar to IQ motif and Sec7 domain 2 (EntrezGene)

CJB06580_at CJB06704_at CJB02357_at

70.3 69.6 69.4

5.6 5.4 17.0

2.1 2.6 2.8

0.002 0.004 0.034

1.7 2.6 2.9

0.003 0.002 0.030

1.8 2.4 2.7

0.029 0.003 0.046

CABLES2

Cdk5 and Abl enzyme substrate 2

CJB10452_at CJB08544_at

69.1 68.5

5.7 7.8

2.0 1.8

0.003 0.011

1.8 2.4

0.020 0.004

1.4 2.0

0.013 0.005

GADD45G

CJB07737_at

68.4

17.1

2.5

0.043

4.0

0.032

2.5

0.045

MOBKL2B

Growth arrest and DNAdamage-inducible, gamma MOB1, Mps One Binder kinase activator-like 2B (yeast)

CJB08401_at CJB01306_at

67.2 65.8

9.0 8.2

1.6 1.6

0.025 0.027

1.6 1.4

0.024 0.049

1.4 1.4

0.049 0.048

RBM12

CJB08649_at

65.4

3.3

1.5

0.016

1.3

0.003

1.3

0.018

SNRPD1

CJB06464_at

63.8

9.0

1.5

0.044

3.2

0.004

2.2

0.014

KCNH2

CJB08865_at

63.7

11.0

3.9

0.017

3.7

0.010

3.7

0.010

RDH12

CJB00816_at

63.0

13.4

1.9

0.040

2.1

0.037

2.8

0.019

CDC73

CJB11217_at

62.1

8.3

1.6

0.026

1.6

0.037

1.4

0.036

XPC

CJB01035_at

61.1

9.2

3.1

0.009

3.9

0.011

2.8

0.025

ABHD3

CJB09496_at

60.8

5.7

2.2

0.002

1.6

0.008

2.4

0.002

NFKBIZ(i)

CJB04975_at CJB05052_at

59.7 59.6

1.7 6.7

1.4 1.5

0.001 0.046

1.4 1.5

0.033 0.016

1.5 1.6

0.007 0.035

WDR74 GNPNAT1

CJB05297_at CJB06011_at CJG00067_at

59.3 59.3 59.3

5.7 4.6 3.8

2.7 2.7 3.4

0.003 0.002 0.000

4.2 3.7 2.4

0.005 0.000 0.000

4.6 2.4 2.2

0.004 0.007 0.001

TMEM38B HISPPD2A

CJB11096_at

57.9

4.8

1.3

0.017

1.9

0.013

2.0

0.037

MAP3K3

CJB03917_at

57.9

12.7

2.4

0.023

2.4

0.024

2.6

0.027

ABCG1

CJB03021_at CJB09124_at CJB01538_at

57.6 57.0 57.0

9.2 5.1 5.1

1.6 1.7 1.4

0.049 0.008 0.023

1.7 2.0 1.5

0.032 0.005 0.012

1.5 2.3 1.5

0.049 0.002 0.016

ZNF181

CJB11199_at CJB04650_at CJB10635_at

56.8 56.7 54.1

14.7 8.3 4.9

3.2 1.5 1.8

0.041 0.032 0.004

4.8 2.7 2.0

0.029 0.005 0.002

4.6 2.3 2.1

CJB08632_at

52.3

14.9

3.9

0.043

5.0

0.039

CJB05705_at CJB01766_at

51.0 51.0

8.2 5.2

2.8 2.0

0.009 0.005

1.9 1.7

CJB09942_at CJB03324_at CJB11985_at CJB10872_at

50.4 49.0 46.0 44.9

6.0 8.6 15.4 4.9

1.4 1.7 6.8 1.8

0.037 0.045 0.042 0.006

CJB09838_at

44.4

4.8

2.0

CJB10007_at

44.3

5.1

1.9

RNA binding motif protein 12 Small nuclear ribonucleoprotein D1 polypeptide 16 kDa Potassium voltage-gated channel, subfamily H (eag-related), member 2 Retinol dehydrogenase 12 (all-trans/9-cis/11-cis) Cell division cycle 73, Paf1/ RNA polymerase II complex component, homolog (S. cerevisiae) Xeroderma pigmentosum, complementation group C Abhydrolase domain containing 3 Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta (intron) WD repeat domain 74 Glucosamine-phosphate N-acetyltransferase 1 Transmembrane protein 38B Histidine acid phosphatase domain containing 2A Mitogen-activated protein kinase kinase kinase 3 ATP-binding cassette, sub-family G (WHITE), member 1 Zinc finger protein 181

C14orf21

Chromosome 14 open reading frame 21

0.033 0.007 0.002

SMARCD2

3.4

0.039

CCDC48

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 Coiled-coil domain containing 48

0.018 0.007

2.3 1.6

0.010 0.009

ATP6V1G1

2.5 1.9 22.3 2.2

0.031 0.039 0.037 0.010

1.4 2.1 38.3 2.0

0.038 0.029 0.037 0.005

LRRC38 DDX39

0.007

3.7

0.001

1.8

0.010

WIPI1

0.008

1.8

0.007

1.7

0.014

HAS1

ATPase, H+ transporting, lysosomal 13 kDa, V1 subunit G1 Hyaluronan synthase 1 Leucine-rich repeat containing 38 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 WD repeat domain, phosphoinositide interacting 1

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

82 Table 5 (Continued ) Probe sets

Cbe_AVEb

Cbe_SDc

Fold change

p value

Fold change

p value

Fold change

p value

Cbe/FLa

Cbe/FLa

Cbe/Hid

Cbe/Hid

Cbe/ANf

Cbe/ANf

Symbol

Description

CJB11248_at CJB02611_at CJB02499_at CJB03017_at

44.2 43.4 40.7 40.3

1.8 2.2 5.2 8.6

2.2 1.8 1.7 3.1

0.003 0.044 0.014 0.017

2.6 1.7 2.5 3.1

0.000 0.012 0.004 0.014

1.9 1.8 1.5 4.7

0.000 0.004 0.033 0.021

CDCA4 NIPBL

Cell division cycle associated 4 Nipped-B homolog (Drosophila)

C15orf27

CJB09268_at

40.2

5.5

2.1

0.010

3.4

0.005

2.7

0.004

ST8SIA5

Chromosome 15 open reading frame 27 ST8 alpha-N-acetylneuraminide alpha-2, 8-sialyltransferase 5

CJB10436_at CJB02146_at

39.7 39.1

3.1 6.8

2.2 2.8

0.001 0.017

3.6 2.9

0.001 0.011

2.3 2.0

0.007 0.021

DHRS13

Dehydrogenase/reductase (SDR family) member 13

CJB08020_at CJB07533_at

38.6 38.5

3.7 4.9

1.4 1.5

0.016 0.044

1.5 2.3

0.013 0.009

1.9 2.3

0.008 0.009

GCAT

CJB11291_at CJB11962_at CJB10830_at

36.0 35.6 34.3

5.4 6.3 3.1

1.8 3.1 2.6

0.020 0.008 0.002

2.3 3.6 2.4

0.010 0.012 0.007

2.2 2.2 1.9

0.011 0.021 0.007

ENDOGL1 TMEM90A CHAC2

CJB07557_at CJB10783_s_at CJB04462_at

34.0 33.4 32.4

5.9 7.5 4.8

2.2 4.0 1.5

0.017 0.013 0.038

2.4 6.5 1.8

0.012 0.008 0.029

2.0 3.2 1.8

0.029 0.029 0.017

PHF17 TUFT1 DBR1

Glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase) Endonuclease G-like 1 Transmembrane protein 90A ChaC, cation transport regulator homolog 2 (E. coli) PHD finger protein 17 Tuftelin 1 Debranching enzyme homolog 1 (S. cerevisiae)

CJB03856_at CJB04316_at CJB01514_at CJB02521_at

31.5 30.6 30.4 29.4

3.5 6.5 2.3 3.0

1.7 2.7 1.8 1.6

0.013 0.019 0.021 0.032

1.9 1.9 1.6 1.8

0.006 0.049 0.016 0.006

2.0 2.1 1.8 1.6

0.007 0.031 0.002 0.014

SETX CYB5D1

Senataxin Cytochrome b5 domain containing 1

CJB01383_at CJB04392_at

29.3 29.0

3.1 4.3

1.6 2.1

0.037 0.013

1.6 3.4

0.018 0.007

1.7 2.1

0.033 0.049

MTHFD2

Methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase

CJB10449_at CJB07349_at CJB06594_at CJB03228_at

28.2 28.0 26.9 25.1

1.2 0.7 1.7 0.7

1.3 1.5 2.8 1.6

0.021 0.013 0.002 0.000

4.7 1.9 2.2 3.4

0.006 0.000 0.001 0.022

2.9 1.6 2.6 2.2

0.002 0.005 0.000 0.012

FBXO5 SLC29A2

F-box protein 5 Solute carrier family 29 (nucleoside transporters), member 2

CJB07384_at CJB00408_at

24.3 24.1

3.5 3.7

4.2 2.5

0.005 0.015

23.5 2.0

0.006 0.021

12.2 8.3

0.001 0.006

PFKFB4

6-Phosphofructo-2-kinase/ fructose-2,6-biphosphatase 4

CJB00127_at CJB04261_at CJB07503_at

23.6 23.1 21.2

5.9 1.6 4.0

11.4 2.0 2.1

0.018 0.004 0.023

70.8 2.6 3.8

0.021 0.000 0.014

10.6 1.6 2.2

0.015 0.040 0.035

TTC7A

CJB01987_at CJB01838_at CJB09414_at CJB07296_at CJB01866_at

20.4 20.0 19.4 18.5 17.6

2.1 0.8 4.2 2.5 3.4

2.2 1.9 12.1 3.8 3.7

0.009 0.023 0.010 0.002 0.008

2.2 1.4 4.0 6.9 3.5

0.003 0.036 0.019 0.001 0.009

1.4 1.9 5.3 3.7 1.9

0.023 0.039 0.014 0.003 0.029

ZNF75D TBCD

Tetratricopeptide repeat domain 7A Zinc finger protein 75D Tubulin folding cofactor D

CJB11665_at CJG00106_at

16.0 14.6

2.7 3.2

2.0 2.4

0.022 0.043

1.8 2.2

0.046 0.029

2.0 2.5

0.022 0.025

CNTN2 (HYPK)

CJB07952_at CJB11550_at

14.6 11.6

2.3 3.5

2.4 4.2

0.014 0.030

2.3 8.1

0.014 0.021

2.0 5.9

0.015 0.027

ANf_SDc

Fold change

p value

Fold change

p value

Fold change

p value

ANf/FLa

ANf/FLa

ANf/Hid

ANf/Hid

ANf/Cbe

ANf/Cbe

33.0 164.2 150.9 47.2

1.2 142.2 3.1 3.7

0.024 0.013 0.028 0.000

1.3 6.7 4.0 1.5

0.034 0.008 0.014 0.006

1.1 449.4 2.2 2.8

Probe sets

ANf_AVEb

(D) Amygdaloid nucleus CJB08452_at 841.8 CJB09658_at 838.9 CJB03496_at 715.6 CJB05008_at 690.2

(PDP2)

Pyruvate dehydrogenase phosphatase isoenzyme 2 (EntrezGene) Contactin 2 (axonal) Huntingtin interacting protein K (EntrezGene)

Symbol

Description

0.044 0.013 0.006 0.000

TEGT CARTPT CALB2 ZCCHC12

Testis enhanced gene transcript CART prepropeptide Calbindin 2 Zinc finger, CCHC domain containing 12 Insulin-like growth factor binding protein 3 Peptidylprolyl cis/trans isomerase, NIMA-interacting 1 Adducin 3 (gamma)

CJB02264_at

636.6

68.5

2.2

0.003

2.0

0.011

6.8

0.002

IGFBP3

CJB02655_at

543.5

38.2

1.2

0.042

1.2

0.039

1.6

0.004

PIN1

CJB01618_at

406.9

50.9

1.6

0.030

1.4

0.035

1.8

0.022

ADD3

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

83

Table 5 (Continued ) Probe sets

a b c d e f

ANf_AVEb

ANf_SDc

Fold change

p value

Fold change

p value

Fold change

p value

ANf/FLa

ANf/FLa

ANf/Hid

ANf/Hid

ANf/Cbe

ANf/Cbe

Symbol

Description

G protein-coupled receptor 37 (endothelin receptor type B-like) Phytanoyl-CoA 2-hydroxylase interacting protein-like Angiotensinogen (serpin peptidase inhibitor, clade A, member 8) odz, odd Oz/ten-m homolog 3 (Drosophila) Synaptogyrin 3 Frizzled-related protein Retinal G protein coupled receptor Neural precursor cell expressed, developmentally down-regulated 9 Fumarylacetoacetate hydrolase (fumarylacetoacetase) FEZ family zinc finger 2 KIAA1191 LY6/PLAUR domain containing 1 Hairy and enhancer of split 1 (Drosophila) GDP-mannose pyrophosphorylase B

CJB02107_at

265.4

35.4

3.3

0.003

1.8

0.023

2.1

0.001

GPR37

CJB03052_at

259.1

19.7

1.8

0.017

1.6

0.040

1.1

0.038

PHYHIPL

CJB02360_at

242.9

32.1

1.9

0.011

2.1

0.008

17.8

0.001

AGT

CJB08461_at

237.8

37.4

2.2

0.016

2.2

0.011

3.4

0.002

ODZ3

CJB00003_at CJB00242_at CJB06887_at CJB09026_at

231.7 215.1 193.5 136.3

2.5 36.9 15.8 0.6

1.2 3.0 1.2 2.0

0.002 0.020 0.044 0.022

1.5 3.9 1.6 1.8

0.021 0.005 0.009 0.025

1.4 3.2 20.5 3.2

0.008 0.003 0.002 0.000

SYNGR3 FRZB RGR NEDD9

CJB11538_at

129.7

13.8

2.5

0.010

1.4

0.036

3.4

0.000

FAH

CJB01080_at CJA00033_at CJB07927_at CJB08095_at

128.6 103.1 70.1 60.9

16.4 13.1 20.4 3.3

8.7 1.7 4.5 1.4

0.006 0.013 0.043 0.003

1.4 1.6 2.7 1.8

0.039 0.020 0.043 0.000

46.5 1.8 25.0 2.1

0.000 0.002 0.028 0.001

FEZF2 KIAA1191 LYPD1 HES1

CJB01874_at

24.2

3.1

1.5

0.033

1.6

0.043

1.6

0.004

GMPPB

FL, frontal lobe. bAVE, average Signal values of three common marmosets. SD, standard deviation of Signal values of three common marmosets. Hi, hippocampus. Cb, cerebellum. AN, amygdaloid nucleus.

Fig. 2. Validation of DNA microarray data by real-time quantitative PCR. RNA was isolated from the frontal lobe (n = 1), hippocampus (n = 3), cerebellum (n = 2) and amygdaloid nucleus (n = 1) and reverse-transcribed as described in Section 2. Real-time quantitative PCR reactions were performed on cDNAs for the indicated transcripts with GAPDH applied as an internal control. Results are depicted as averages. FL, frontal lobe; Hi, hippocampus; Cb, cerebellum; AN, amygdaloid nucleus; ALDOC, aldolase C, fructosebisphosphate; GABRA6, gamma-aminobutyric acid (GABA) A receptor, alpha 6; NEUROD1, neurogenic differentiation 1; CALB1, calbindin 1; CA8, carbonic anhydrase 8.

84

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

Student’s t-test from the average Signal values of three replicates were generated to examine gene expression differences among structures. The numbers of structure-specific expressed probe sets were 114, 33, 340 and 21, in the frontal lobe, hippocampus, cerebellum, amygdaloid nucleus, respectively. 3.3. Validation of DNA microarray data by real-time quantitative PCR Of the cerebellum-specifically expressed 18 probe sets, 5 genes (ALDOC, aldolase C, fructose-bisphosphate; GABRA6, gammaaminobutyric acid (GABA) A receptor, alpha 6; NEUROD1, neurogenic differentiation 1; CALB1, calbindin 1; CA8, carbonic anhydrase 8) were selected and analyzed by real-time quantitative PCR to verify the DNA microarray results. Relative expression of each gene in the 4 structures is illustrated in Fig. 2. 4. Discussion Nonhuman primates are used as experimental models to study human brain diseases or disorders. Recently, DNA microarray has become a very useful tool to monitor the alteration of gene expression profile between normal brain and abnormal brain. However, there were not an appropriate DNA microarray for common marmoset brain and we could not carry out gene expression analysis. In order to identify the character of gene expression in common marmoset brain, we have planed to make a new DNA microarray and a newly developed common marmoset DNA microarray with 7557 probe sets was named Marmoa520295F. The present gene expression analysis demonstrated lists of the top 100 probe sets in the frontal lobe, hippocampus and amygdaloid nucleus to be very similar, sharing 68 probe sets were in common (Tables 1A–D and 3). Also the scattered plots of the normalized data clearly suggested that the gene expression profiles of the individual samples in the same structure were very similar (R2 = 0.9533–0.9759) and the gene expression profiles of the frontal lobe, hippocampus and amygdaloid nucleus were relatively similar (R2 = 0.9223–0.9537) while the gene expression profile of cerebellum was a little different (R2 = 0.8183–0.8443) (Fig. 1A and B). Categorization according to gene ontology showed the greatest number of the genes to be involved in transport in all for 4 structures (Table 2). However, while the second-most function was nervous system development in the cerebellum, it was metabolism in the other 3 structures. From the point of gene function, the character of gene expression in the cerebellum can thus be considered somewhat different from those of the frontal lobe, hippocampus and amygdaloid nucleus. Twelve probe sets, which were common among 3 structures except for cerebellum, and 18 probe sets, which were cerebellum-specific, were not categorized to a particular kind of function (Tables 2 and 4A and B). Lists of probe sets specifically expressed in each structure of brain were shown in Table 5A–D. The numbers of structurespecific expressed probe sets were 114, 33, 340 and 21, in frontal lobe, hippocampus, cerebellum, amygdaloid nucleus, respectively. These genes might play specific roles in each structure. Frontal lobe-specific probe sets were more than hippocampus- or amygdaloid nucleus-specific probe sets. The number of probe sets (340 probe sets), which were specifically expressed in cerebellum, was more than those of other 3 structures. The results are in line with earlier findings indicating the gene expression profile of the cerebellum to differ from those in other structures in human, the chimpanzee (Khaitovich et al., 2004) and inbred strains of mouse (Sandberg et al., 2000). We found 18 probe sets expressed only in cerebellum in top 100 genes, while 4 of these were not strictly cerebellum-specific but they were not listed in the top 100 probe sets for the other

structures (HPCAL1, hippocalcin-like 1; CALM1, calmodulin 1; DPYSL2, dihydropyrimidinase-like 2; EIF4H, eukaryotic translation initiation factor 4H). To confirm DNA microarray data, we selected 5 genes from the remaining 14 probe sets with very high average Signal values and we thought that they were easy to detect by real-time quantitative PCR. They are known as genes specifically expressed in cerebellum (ALDOC, aldolase C, fructose-bisphosphate; GABRA6, gamma-aminobutyric acid (GABA) A receptor, alpha 6; NEUROD1, neurogenic differentiation 1; CALB1, calbindin 1; CA8, carbonic anhydrase 8). It is reported that ALDOC is strongly expressed in cerebellar Purkinje cells but only weakly expressed in cerebral cortex and hippocampus in mouse and rat (Popovici et al., 1990). Studies with a monoclonal antibody against aldolase C suggested this to be a selective marker of human cerebellar Purkinje cells (Royds et al., 1987). GABRA6 is known to be specifically expressed in the cerebellum of rodents (Wisden et al., 1996; Kato, 1990) and has been applied as a molecular marker for this brain structure in man (Ernst et al., 2007). NEUROD1 is also reported to exhibit cerebellum-specific expression in human brain and to be a major player in development of the cerebellum in the mouse (Siu et al., 2001; Cho and Tsai, 2006). CALB1 is expressed in most human Purkinje cells and in almost all squirrel monkey Purkinje cells (Fournet et al., 1986; Fortin et al., 1998). In addition, CA8 was found to be exclusively expressed in Purkinje cells of mouse cerebellum (Hirota et al., 2003). The relative expression results for each gene in the 4 structures, as shown in Fig. 1A–E, confirmed all 5 to have markedly stronger expression in cerebellum than in the other 3 structures. Especially, GABRA6 and CA8 were essentially cerebellum-specific, the GABRA6 expression level in cerebellum being 731-fold, 2751-fold and 793-fold more than in the frontal lobe, hippocampus and amygdaloid nucleus, respectively, with figures of 90-fold, 53-fold and 55-fold for CA8. Furthermore, the results of ALDOC, NEUROD1 and CALB1 genes from real-time quantitative PCR were well consistent with those of the DNA microarray. The results suggest that the cerebellum of the common marmoset might have unique features. Analysis of the gene lists might also provide scientific explanations for differences in function of the other structures. Although we did not carry out confirmation by real-time quantitative PCR, the CART peptide is reported to be a neuropeptide expressed in several brain regions such as the hypothalamus, amygdala, and hippocampus and a peptide neurotransmitter which has a role in a number of physiological processes, including body weight homeostasis and energy balance, in a number of vertebrate species (Larsen and Hunter, 2006; Bjo¨rkqvist et al., 2007). We were afraid CART peptide was not amygdaloid nucleus-specific because it was expressed in hippocampus according to the report. However, our DNA microarray data showed the expression level of the CART peptide in the amygdaloid nucleus to 142fold, 7-fold and 449-fold greater than in the frontal lobe, hippocampus and cerebellum, respectively, well compatible with these reports. In the future, we intend to extend our gene expression profiling of other structures, like the anterior and middle temporal lobes, for example. It would be of particular interest to compare gene expression profiles among these and the frontal lobe, because the cortex is segmentalized. In conclusion, we were able to develop a useful tool for gene expression profiling of common marmoset brain. Evaluation of the performance of our newly developed DNA microarray by real-time quantitative PCR, demonstrated good compatibility of the data obtained with the two approaches. Furthermore, analysis of gene expression profiles of frontal lobe, hippocampus, cerebellum and amygdaloid nucleus, allowed generation of lists of probe sets specifically expressed in each of these brain structures. Thus our DNA microarray with good performance should be a useful tool for

T. Fukuoka et al. / Neuroscience Research 66 (2010) 62–85

common marmoset investigations in the biomedical field. We have now also established a second version of common marmoset DNA microarray, which contains about 23,000 probe sets, derived from not only brain but also other organs. Acknowledgments The authors are grateful to Izumi Furukawa, Mitsue Yoshioka and Chiharu Nakashima of the Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd. for their gene expression analysis in this work. References Abbott, D.H., Barnett, D.K., Colman, R.J., Yamamoto, M.E., Schultz-Darken, N.J., 2003. Aspects of common marmoset basic biology and life history important for biomedical research. Comp. Med. 53, 339–350. Baker, H.F., Ridley, R.M., Duchen, L.W., Crow, T.J., Bruton, C.J., 1993. Experimental induction of b-amyloid plaques and cerebral angiopathy in primates. Ann. N. Y. Acad. Sci. 695, 228–231. Bjo¨rkqvist, M., Leavitt, B.R., Nielsen, J.E., Landwehrmeyer, B., Ecker, D., Mulder, H., Brundin, P., Peterse´n, A., 2007. 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