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. 2008 May 7;19(1):91–107. doi: 10.1111/j.1750-3639.2008.00171.x

Table 2.

Overview of the most significant expression changes in the PD SN, caudate nucleus and putamen, as determined by microarray analysis. For the SN, only the 50 most significant genes are given (the full list of significantly changed genes in the SN can be found in Supplementary Table S3). Abbreviations: DE = differential expression, as fraction of control levels; P‐value = Bonferroni‐adjusted P‐value; PD = Parkinson's disease; SN = substantia nigra pars compacta.

Substantia nigra
Systematic name Gene name Description DE P‐value
Downregulated genes
 NM_000158 GBE1 Glucan (1,4‐alpha‐), branching enzyme 1 (glycogen branching enzyme, Andersen disease, glycogen storage disease type IV) 0.18 0.00002
 NM_033495 KLHL13 Kelch‐like 13 (Drosophila) 0.24 0.00003
 AL117636 MRNA; cDNA DKFZp434H205 (from clone DKFZp434H205) 0.34 0.00004
 NM_004411 DYNC1I1 Dynein, cytoplasmic 1, intermediate chain 1 0.26 0.00005
 NM_002863 PYGL Phosphorylase, glycogen; liver (Hers disease, glycogen storage disease type VI) 0.26 0.00005
 AB002376 CAST1 CAZ‐associated structural protein 0.28 0.00011
 NM_000345 SNCA Synuclein, alpha (non A4 component of amyloid precursor) 0.27 0.00016
 NM_002928 RGS16 Regulator of G‐protein signalling 16 0.22 0.00017
 AB014731 DENR Density‐regulated protein 0.41 0.00025
 NM_018092 NETO2 Neuropilin (NRP) and tolloid (TLL)‐like 2 0.46 0.00029
 NM_014332 SMPX Small muscle protein, X‐linked 0.31 0.00031
 NM_006670 TPBG Trophoblast glycoprotein 0.18 0.00035
 NM_017999 RNF31 Ring finger protein 31 0.32 0.00037
 NM_006350 FST Follistatin 0.17 0.00037
 BF035258 AKAP12 A kinase (PRKA) anchor protein (gravin) 12 0.39 0.00043
 AW974789 TTMA Two transmembrane domain family member A 0.47 0.00047
 AF428101 DACH2 Dachshund homolog 2 (Drosophila) 0.35 0.00053
 NM_018700 TRIM36 Tripartite motif‐containing 36 0.30 0.00054
 AK024251 SLITRK5 SLIT and NTRK‐like family, member 5 0.46 0.00056
 NM_005639 SYT1 Synaptotagmin I 0.23 0.00062
 AB020710 EHBP1 EH domain binding protein 1 0.49 0.00063
 H06068 yl72g10.s1 Soares infant brain 1NIB Homo sapiens cDNA clone IMAGE:43489 3‐, mRNA sequence 0.46 0.00064
 AF225987 SCN3A Sodium channel, voltage‐gated, type III, alpha 0.47 0.00067
 AL390172 Homo sapiens genomic DNA; cDNA DKFZp547I204 (from clone DKFZp547I204) 0.35 0.00068
 AK055427 DGKH Diacylglycerol kinase, eta 0.31 0.00075
 NM_022726 ELOVL4 Elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)‐like 4 0.46 0.00086
 NM_006186 NR4A2 Nuclear receptor subfamily 4, group A, member 2 0.20 0.00089
 NM_031850 AGTR1 Angiotensin II receptor, type 1 0.07 0.00095
 NM_014309 RPL41 Ribosomal protein L41 0.38 0.00101
 R42166 yf99d08.s1 Soares infant brain 1NIB Homo sapiens cDNA clone IMAGE:30780 3‐, mRNA sequence 0.25 0.00103
 NM_012189 CABYR Calcium binding tyrosine‐(Y)‐phosphorylation regulated (fibrousheathin 2) 0.49 0.00112
 NM_006113 VAV3 Vav 3 oncogene 0.34 0.00113
 NM_014905 GLS Glutaminase 0.43 0.00141
 J04621 SDC2 Syndecan 2 (heparan sulfate proteoglycan 1, cell surface‐associated, fibroglycan) 0.37 0.00142
 AF070623 LOC138046 Hypothetical protein LOC138046 0.38 0.00144
 NM_004796 NRXN3 Neurexin 3 0.49 0.00148
 AK025615 BCAT1 Branched chain aminotransferase 1, cytosolic 0.31 0.00153
 NM_003979 GPRC5A G protein‐coupled receptor, family C, group 5, member A 0.30 0.00170
 AF339796 HS6ST3 Heparan sulfate 6‐O‐sulfotransferase 3 0.48 0.00172
 AL137498 SCN2A2 Sodium channel, voltage‐gated, type II, alpha 2 0.45 0.00174
 NM_000809 GABRA4 Gamma‐aminobutyric acid (GABA) A receptor, alpha 4 0.29 0.00182
 AW294729 Transcribed locus, moderately similar to NP_509344.1 HIStone family member (his‐71) [Caenorhabditis elegans] 0.55 0.00185
 NM_003138 SRPK2 Homo sapiens SFRS protein kinase 2 (SRPK2), transcript variant 2, mRNA 0.53 0.00186
 AF397397 OLFM3 Olfactomedin 3 0.31 0.00197
 NM_005100 AKAP12 A kinase (PRKA) anchor protein (gravin) 12 0.43 0.00220
 AB046788 ROBO2 Roundabout, axon guidance receptor, homolog 2 (Drosophila) 0.32 0.00232
 AV707343 V707343 ADB Homo sapiens cDNA clone ADBBSH02 5‐, mRNA sequence 0.25 0.00238
Upregulated genes
 NM_018276 SSH3 Slingshot homolog 3 (Drosophila) 1.66 0.00222
 BC013923 SOX2 SRY (sex determining region Y)‐box 2 1.86 0.00117
 BI823317 603041226F1 NIH_MGC_115 Homo sapiens cDNA clone IMAGE:5182015 5‐, mRNA sequence 2.18 0.00136
Caudate nucleus
Downregulated genes
 NM_001888 CRYM Crystallin, mu 0.43 0.02542
 NM_006211 PENK Proenkephalin 0.45 0.03796
 NM_030615 KIF25 Kinesin family member 25 0.56 0.01649
 NM_016454 TMEM85 Transmembrane protein 85 0.61 0.00577
 NM_006680 ME3 Malic enzyme 3, NADP(+)‐dependent, mitochondrial 0.62 0.02043
 NM_000783 CYP26A1 Cytochrome P450, family 26, subfamily A, polypeptide 1 0.64 0.02402
 AL538117 CXADR Coxsackie virus and adenovirus receptor 0.65 0.02382
 NM_015417 C20orf28 Chromosome 20 open reading frame 28 0.68 0.03102
 NM_004087 DLG1 Discs, large homolog 1 (Drosophila) 0.70 0.04833
 NM_021252 RAB18 RAB18, member RAS oncogene family 0.71 0.03775
Upregulated genes
 AL136693 CYBRD1 Cytochrome b reductase 1 1.39 0.03087
 NM_003243 TGFBR3 Transforming growth factor, beta receptor III (betaglycan, 300kDa) 1.47 0.01079
 NM_005413 SIX3 Sine oculis homeobox homolog 3 (Drosophila) 1.52 0.01266
 NM_005859 PURA Purine‐rich element binding protein A 1.54 0.04095
 AK026152 CTSH Cathepsin H 1.64 0.00460
 NM_002343 LTF Lactotransferrin 2.57 0.00004
Putamen
Downregulated genes
 BF381899 GNPDA2 Glucosamine‐6‐phosphate deaminase 2 0.52 0.00000
 AC016696 Homo sapiens BAC clone RP11‐130P22 from 2, complete sequence. 0.71 0.00313
Upregulated genes
 NM_015556 SIPA1L1 Signal‐induced proliferation‐associated 1 like 1 1.28 0.00944
 NM_001124 ADM Adrenomedullin 1.80 0.02671