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Table 1. Summary of cDNA libraries.
♣ Substantia Nigra (SN) Library Information.
Table 2. Genes showing significant difference (P > 0.9) in expression between normal and PD' SN.
| Unigene | Copies in normal(%) | Copies in PD(%) | Gene | Cyband | Title | GO id | GO Term | |
|---|---|---|---|---|---|---|---|---|
| Hs.356190 | 9 (4.71) | < | 28 (13.59) | UBB | 17p12-p11.2 | Ubiquitin B, mRNA (cDNA clone MGC:47606 IMAGE:4943285) | GO:0006464 | protein modification process |
| Hs.433670 | 0 (0.00) | < | 10 (4.85) | FTL | 19q13.3-q13.4|19q13.3 | Full length insert cDNA clone YB24D08 | GO:0006826 | iron ion transport |
| Hs.551713 | 144 (75.39) | < | 196 (95.15) | MBP | 18q23 | Golli-mbp gene | GO:0006955 | immune response |
| Hs.125898 | 0 (0.00) | < | 7 (3.40) | GNAS | 20q13.3 | Adenyl cyclase mRNA | GO:0007165 | signal transduction |
| Hs.356572 | 0 (0.00) | < | 5 (2.43) | RPS3A | 4q31.2-q31.3 | (clone 03) liver expessed ribosomal protein S3 homologue | GO:0006413 | translational initiation |
| Hs.2795 | 0 (0.00) | < | 5 (2.43) | LDHA | 11p15.4 | Lactate dehydrogenase-A (LDH-A, EC 1.1.1.27) | GO:0006100 | tricarboxylic acid cycle intermediate metabolic process |
| Hs.653181 | 1 (0.52) | < | 7 (3.40) | THY1 | 11q22.3-q23 | 5E10 antigen (Thy-1) | GO:0001525 | angiogenesis |
| Hs.526521 | 1 (0.52) | < | 7 (3.40) | MDH1 | 2p13.3 | CDNA FLJ52206 complete cds, highly similar to Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) | GO:0006096 | glycolysis |
| Hs.10842 | 0 (0.00) | < | 4 (1.94) | RAN | 12q24.3 | Androgen receptor associated protein 24 (ARA24) | GO:0006259 | DNA metabolic process |
| Hs.654848 | 0 (0.00) | < | 4 (1.94) | EIF6 | 20q12 | B4 integrin interactor | GO:0006412 | translation |
| Hs.628678 | 1 (0.52) | < | 6 (2.91) | VIM | 10p13 | Vimentin | GO:0006928 | cell motility |
| Hs.78771 | 2 (1.05) | < | 7 (3.40) | PGK1 | Xq13 | MRNA encoding phosphoglycerate kinase | GO:0006096 | glycolysis |
| Hs.505337 | 1 (0.52) | < | 5 (2.43) | CLDN5 | 22q11.21 | Transmembrane protein | GO:0016338 | calcium-independent cell-cell adhesion |
| Hs.525205 | 1 (0.52) | < | 5 (2.43) | NDRG2 | 14q11.2 | CDNA FLJ55190 complete cds, highly similar to Protein NDRG2 | GO:0007275 | multicellular organismal development |
| Hs.437403 | 1 (0.52) | < | 5 (2.43) | PPA1 | 10q11.1-q24 | Cytosolic inorganic pyrophosphatase | GO:0006796 | phosphate metabolic process |
| Hs.530479 | 0 (0.00) | < | 3 (1.46) | PMF1 | 1q12 | CDNA FLJ78329 complete cds, highly similar to Homo sapiens polyamine-modulated factor 1, mRNA | GO:0006350 | transcription |
| Hs.1701 | 0 (0.00) | < | 3 (1.46) | ELAVL3 | 19p13.2 | ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C), mRNA (cDNA clone MGC:20263 IMAGE:3161837) | GO:0007275 | multicellular organismal development |
| Hs.5120 | 0 (0.00) | < | 3 (1.46) | DYNLL1 | 12q24.23 | Cytoplasmic dynein light chain 1 (hdlc1) | GO:0007017 | microtubule-based process |
| Hs.185910 | 0 (0.00) | < | 3 (1.46) | HDHD1A | Xp22.32 | Haloacid dehalogenase-like hydrolase domain containing 1A (HDHD1A), transcript variant 1, mRNA | GO:0008152 | metabolic process |
| Hs.292156 | 0 (0.00) | < | 3 (1.46) | DKK3 | 11p15.2 | CDNA FLJ59893 complete cds, highly similar to Dickkopf-related protein 3 precursor | GO:0007275 | multicellular organismal development |
| Hs.118076 | 0 (0.00) | < | 3 (1.46) | RPS4X | Xq13.1 | CDNA FLJ40595 fis, clone THYMU2010705, highly similar to 40S RIBOSOMAL PROTEIN S4, X ISOFORM | GO:0006412 | translation |
| Hs.9857 | 0 (0.00) | < | 3 (1.46) | DCXR | 17q25.3 | Dicarbonyl/L-xylulose reductase (DCXR) | GO:0005975 | carbohydrate metabolic process |
| Hs.647117 | 0 (0.00) | < | 3 (1.46) | ACTR3B | 7q36.1 | CDNA FLJ58769 complete cds, highly similar to Homo sapiens ARP3 actin-related protein 3 homolog B (yeast) (ACTR3B), mRNA | GO:0030041 | actin filament polymerization |
| Hs.270428 | 0 (0.00) | < | 3 (1.46) | SUCLG1 | 2p11.2 | Succinyl CoA synthetase | GO:0006099 | tricarboxylic acid cycle |
| Hs.25597 | 0 (0.00) | < | 3 (1.46) | ELOVL1 | 1p34.2 | CDNA FLJ51720 complete cds, highly similar to Elongation of very long chain fatty acids protein 1 | GO:0006633 | fatty acid biosynthetic process |
| Hs.355927 | 0 (0.00) | < | 3 (1.46) | VDAC2 | 10q22 | Porin (por) mRNA, complete cds and truncated cds | GO:0006820 | anion transport |
| Hs.494875 | 0 (0.00) | < | 3 (1.46) | RGS3 | 9q32 | RGS3 mRNA, 5' UTR | GO:0000188 | inactivation of MAPK activity |
| Hs.410683 | 0 (0.00) | < | 3 (1.46) | HOMER3 | 19p13.11 | Homer homolog 3 (Drosophila), mRNA (cDNA clone MGC:20122 IMAGE:4555641) | GO:0006605 | protein targeting |
| Hs.471785 | 0 (0.00) | < | 3 (1.46) | UBE2F | 2q37.3 | CDNA clone IMAGE:5303613 | GO:0006512 | ubiquitin cycle |
| Hs.76152 | 0 (0.00) | < | 3 (1.46) | AQP1 | 7p14 | Uterine water channel=28 kda erythrocyte integral membrane protein homolog [human, uterus, mRNA, 1340 nt] | GO:0006810 | transport |
| Hs.2780 | 0 (0.00) | < | 3 (1.46) | JUND | 19p13.2 | Jun-D mRNA for JUN-D protein | GO:0006357 | regulation of transcription from RNA polymerase II promoter |
| Hs.655179 | 0 (0.00) | < | 3 (1.46) | THTPA | 14q11.2 | CDNA FLJ33428 fis, clone BRACE2020742 | GO:0006091 | generation of precursor metabolites and energy |
| Hs.637017 | 0 (0.00) | < | 3 (1.46) | MAP1B | 5q13 | Homo sapiens, clone IMAGE:5550730, mRNA | GO:0001578 | microtubule bundle formation |
| Hs.654865 | 0 (0.00) | < | 3 (1.46) | FDX1L | 19p13.2 | Ferredoxin 1-like (FDX1L), mRNA | GO:0006118 | electron transport |
| Hs.212838 | 0 (0.00) | < | 3 (1.46) | A2M | 12p13.3-p12.3 | Alpha-2-macroglobulin, mRNA (cDNA clone MGC:47683 IMAGE:6056126) | GO:0006886 | intracellular protein transport |
| Hs.707171 | 0 (0.00) | < | 3 (1.46) | HLA-B | 6p21.3 | MRNA fragment for the histocompatibility antigen (HLA-B) | GO:0002474 | antigen processing and presentation of peptide antigen via MHC class I |
| Hs.119598 | 7 (3.66) | < | 14 (6.80) | RPL3 | 22q13 | Ribosomal protein L3, mRNA (cDNA clone IMAGE:4510463) | GO:0006412 | translation |
| Hs.374596 | 10 (5.24) | < | 18 (8.74) | TPT1 | 13q12-q14 | Tumor protein, translationally-controlled 1, mRNA (cDNA clone IMAGE:5219529) | GO:0006816 | calcium ion transport |
| Hs.209983 | 5 (2.62) | < | 11 (5.34) | STMN1 | 1p36.1-p35 | Stathmin | GO:0007019 | microtubule depolymerization |
| Hs.446149 | 6 (3.14) | < | 12 (5.83) | LDHB | 12p12.2-p12.1 | Lactate dehydrogenase B (LDH-B) | GO:0006100 | tricarboxylic acid cycle intermediate metabolic process |
| Hs.518475 | 4 (2.09) | < | 9 (4.37) | EIF4A2 | 3q28 | EIF4A2=protein synthesis initiation factor 4A-II homolog [human, fetal lung tissue, mRNA Partial, 1881 nt] | GO:0006412 | translation |
| Hs.350927 | 2 (1.05) | < | 6 (2.91) | SLC25A6 | Xp22.32 and Yp11.3 | ADP/ATP translocase mRNA, 3'UTR | GO:0006810 | transport |
| Hs.483635 | 2 (1.05) | < | 6 (2.91) | FGF1 | 5q31 | Beta-endothelial cell growth factor (ECGF-beta) | GO:0001525 | angiogenesis |
| Hs.522555 | 2 (1.05) | < | 6 (2.91) | APOD | 3q26.2-qter | Apolipoprotein D {3' region} [human, lacrimal gland, mRNA Partial, 315 nt] | GO:0006629 | lipid metabolic process |
| Hs.534293 | 16 (8.38) | > | 2 (0.97) | SERPINA3 | 14q32.1 | Serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3, mRNA (cDNA clone MGC:18107 IMAGE:4152390) | GO:0006953 | acute-phase response |
| Hs.524390 | 54 (28.27) | > | 27 (13.11) | TUBA1B | 12q13.12 | Alpha-tubulin {EST} [human, mRNA Partial, 337 nt] | GO:0007018 | microtubule-based movement |
| Hs.534322 | 7 (3.66) | > | 1 (0.49) | HLA-DRB1 | 6p21.3 | MHC class II HLA-DRB3 mRNA (HLA-DRB3*01012 allele) | GO:0002504 | antigen processing and presentation of peptide or polysaccharide antigen via MHC class II |
| Hs.586423 | 26 (13.61) | > | 13 (6.31) | EEF1A1 | 6q14.1 | MRNA fragment for elongation factor TU (N-terminus) | GO:0006414 | translational elongation |
| Hs.313 | 34 (17.80) | > | 19 (9.22) | SPP1 | 4q21-q25 | OPN-a | GO:0001503 | ossification |
| Hs.436568 | 29 (15.18) | > | 16 (7.77) | CD74 | 5q32 | (clone pcDG-79) MHC HLA-DG protein 41 | GO:0001516 | prostaglandin biosynthetic process |
| Hs.90073 | 4 (2.09) | > | 0 (0.00) | CSE1L | 20q13 | CDNA FLJ54022 complete cds, highly similar to Exportin-2 | GO:0000059 | protein import into nucleus, docking |
| Hs.656471 | 4 (2.09) | > | 0 (0.00) | AP1S2 | Xp22.2 | CDNA FLJ52741 complete cds, highly similar to Mus musculus adaptor-related protein complex 1, sigma 2 subunit (Ap1s2), mRNA | GO:0006461 | protein complex assembly |
| Hs.504877 | 4 (2.09) | > | 0 (0.00) | ARHGDIB | 12p12.3 | MRNA sequence with homology to GDP-dissociation inhibitor | GO:0006928 | cell motility |
| Hs.474005 | 4 (2.09) | > | 0 (0.00) | SUMO3 | 21q22.3 | SMT3A protein | GO:0006464 | protein modification process |
| Hs.435052 | 4 (2.09) | > | 0 (0.00) | ATP8A1 | 4p14-p12 | Clone 23664 and 23905 mRNA sequence | GO:0006810 | transport |
| Hs.712735 | 4 (2.09) | > | 0 (0.00) | TUBA1B | 12q13.12 | (xs31) mRNA, 835bp | GO:0007018 | microtubule-based movement |
| Hs.523185 | 4 (2.09) | > | 0 (0.00) | RPL13A | 19q13.3 | RPL13a mRNA for ribosomal protein L13a | GO:0006412 | translation |
| Hs.50425 | 8 (4.19) | > | 2 (0.97) | PTGES3 | 12q13.3|12 | (p23) | GO:0000723 | telomere maintenance |
| Hs.357637 | 3 (1.57) | > | 0 (0.00) | EXTL2 | 1p21 | EXT-like protein 2 (EXTL2) | GO:0006044 | N-acetylglucosamine metabolic process |
| Hs.444472 | 3 (1.57) | > | 0 (0.00) | SDHC | 1q23.3 | Cytochrome b large subunit of complex II | GO:0006099 | tricarboxylic acid cycle |
| Hs.487933 | 3 (1.57) | > | 0 (0.00) | NT5C3 | 7p14.3 | CDNA FLJ76348 complete cds | GO:0006213 | pyrimidine nucleoside metabolic process |
| Hs.647774 | 3 (1.57) | > | 0 (0.00) | RHOU | 1q42.11-q42.3 | Ras homolog gene family, member U, mRNA (cDNA clone MGC:47524 IMAGE:5768957) | GO:0007264 | small GTPase mediated signal transduction |
| Hs.97858 | 3 (1.57) | > | 0 (0.00) | KIF1B | 1p36.2 | KIAA0591 protein | GO:0007018 | microtubule-based movement |
| Hs.75256 | 3 (1.57) | > | 0 (0.00) | RGS1 | 1q31 | CDNA FLJ57687 complete cds, highly similar to Regulator of G-protein signaling 1 | GO:0006955 | immune response |
| Hs.632249 | 3 (1.57) | > | 0 (0.00) | MPDU1 | 17p13.1-p12 | CDNA FLJ90818 fis, clone Y79AA1001212, highly similar to Mannose-P-dolichol utilization defect 1 protein | GO:0006457 | protein folding |
| Hs.647078 | 3 (1.57) | > | 0 (0.00) | CDK5 | 7q36 | Gene sequence | GO:0006468 | protein amino acid phosphorylation |
| Hs.212102 | 3 (1.57) | > | 0 (0.00) | PDIA6 | 2p25.1 | Protein disulfide isomerase-related protein P5 | GO:0006457 | protein folding |
| Hs.632345 | 3 (1.57) | > | 0 (0.00) | FNTB | 14q23-q24 | CDNA clone IMAGE:5264828 | GO:0008285 | negative regulation of cell proliferation |
| Hs.469473 | 3 (1.57) | > | 0 (0.00) | RPL31 | 2q11.2 | Ribosomal protein L31 | GO:0006412 | translation |
| Hs.483564 | 3 (1.57) | > | 0 (0.00) | PFDN1 | 5q31 | CDNA FLJ36239 fis, clone THYMU2001443 | GO:0006457 | protein folding |
| Hs.503787 | 3 (1.57) | > | 0 (0.00) | DARS | 2q21.3 | Aspartyl-tRNA synthetase alpha-2 subunit | GO:0006422 | aspartyl-tRNA aminoacylation |
| Hs.487296 | 3 (1.57) | > | 0 (0.00) | PHGDH | 1p12 | CDNA FLJ35987 fis, clone TESTI2014269, highly similar to D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | GO:0006564 | L-serine biosynthetic process |
| Hs.716493 | 3 (1.57) | > | 0 (0.00) | ARL6IP5 | 3p14 | CDNA FLJ90131 fis, clone HEMBB1000447, highly similar to PRA1 family protein 3 | GO:0015813 | L-glutamate transport |
| Hs.654600 | 3 (1.57) | > | 0 (0.00) | HIF1A | 14q21-q24 | Hypoxia-inducible factor 1 alpha (HIF-1 alpha) | GO:0001666 | response to hypoxia |
| Hs.300701 | 3 (1.57) | > | 0 (0.00) | TUBB2B | 6p25 | Clone 23678 | GO:0007018 | microtubule-based movement |
| Hs.438219 | 3 (1.57) | > | 0 (0.00) | GPS2 | 17p13 | Gps2 (GPS2) | GO:0000188 | inactivation of MAPK activity |
| Hs.143261 | 3 (1.57) | > | 0 (0.00) | CAPN3 | 15q15.1-q21.1 | Glucosidase | GO:0006508 | proteolysis |
| Hs.362728 | 3 (1.57) | > | 0 (0.00) | 15-Sep | 1p31 | 15 kDa selenoprotein, mRNA (cDNA clone MGC:24367 IMAGE:4051151) | GO:0051084 | 'de novo' posttranslational protein folding |
| Hs.180877 | 3 (1.57) | > | 0 (0.00) | H3F3B | 17q25 | CDNA FLJ52843 complete cds, highly similar to Histone H3.3 | GO:0006334 | nucleosome assembly |
| Hs.141308 | 3 (1.57) | > | 0 (0.00) | MOG | 6p22.1 | Myelin/oligodendrocyte glycoprotein MOG beta 2 isoform (MOG) | GO:0007268 | synaptic transmission |
| Hs.516155 | 3 (1.57) | > | 0 (0.00) | CAPG | 2p11.2 | CDNA FLJ51488 complete cds, highly similar to Macrophage capping protein | GO:0006461 | protein complex assembly |
| Hs.410817 | 5 (2.62) | > | 1 (0.49) | RPL13 | 16q24.3|17p11.2 | CDNA: FLJ21752 fis, clone COLF6324, highly similar to HSBBC1 Homo sapiens BBC1 mRNA | GO:0006412 | translation |
| Hs.591996 | 5 (2.62) | > | 1 (0.49) | BBOX1 | 11p14.2 | CDNA FLJ78172 complete cds, highly similar to Homo sapiens butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1 (BBOX1), mRNA | GO:0006118 | electron transport |
| Hs.74137 | 5 (2.62) | > | 1 (0.49) | TMED10 | 14q24.3 | (clone S31i125) mRNA, 3' end of cds | GO:0015031 | protein transport |
| Hs.517338 | 11 (5.76) | > | 5 (2.43) | ATP6V1E1 | 22pter-q11.2|22q11.1 | Vacuolar proton ATPase, subunit E | GO:0006811 | ion transport |
| Hs.654404 | 11 (5.76) | > | 5 (2.43) | HLA-B | 6p21.3 | MHC class I human leukocyte antigen, allele HLA-Cw*12042 | GO:0002474 | antigen processing and presentation of peptide antigen via MHC class I |
| Hs.527105 | 6 (3.14) | > | 2 (0.97) | HNRPDL | 4q13-q21 | HnRNP JKTBP | GO:0006350 | transcription |
Table 3. Alternative Splicing Events Statistics.
