Table 3.
Altered gene groups in the PD SN and putamen. Gene groups identified by functional class scoring as significantly different (False Discovery Rate‐corrected P‐value < 0.05) between PD and control, based on the microarray data. Class size: the number of genes with a particular GO or KEGG annotation on the array. Fold change: the mean fold change of all group members, as fraction of control levels. Abbreviations: PUT = putamen; PD = Parkinson's disease; SN = substantia nigra pars compacta; GO = Gene Ontology database; KEGG = Kyoto Encyclopedia of Genes and Genomes.
| Identifier | Description | P‐value | Class size | Fold change | Brain area |
|---|---|---|---|---|---|
| Synaptic transmission | |||||
| hsa04540 | Gap junction | 0.0002 | 71 | 0.92 | SN |
| GO:0019717 | Synaptosome | 0.0002 | 17 | 0.66 | SN |
| GO:0007264 | Small GTPase mediated signal transduction | 0.0004 | 149 | 0.94 | SN |
| GO:0045211 | Postsynaptic membrane | 0.0007 | 60 | 0.83 | SN |
| GO:0007268 | Synaptic transmission | 0.0016 | 146 | 0.92 | SN |
| GO:00052161 | Ion channel activity | 0.0016 | 96 | 0.94 | SN |
| GO:0045202 | Synapse | 0.0019 | 34 | 0.80 | SN |
| hsa04530 | Tight junction | 0.0027 | 75 | 1.00 | SN |
| GO:0008021 | Synaptic vesicle | 0.0146 | 33 | 0.79 | SN |
| hsa04540 | Gap junction | 0.0179 | 70 | 0.99 | PUT |
| GO:0006887 | Exocytosis | 0.0247 | 31 | 0.81 | SN |
| GO:0001518 | Voltage‐gated sodium channel complex | 0.0247 | 9 | 0.85 | SN |
| GO:0015075 | Ion transporter activity | 0.0293 | 9 | 1.01 | SN |
| GO:0004890 | GABA‐A receptor activity | 0.0304 | 16 | 0.76 | SN |
| GO:0009966 | Regulation of signal transduction | 0.0304 | 12 | 0.87 | SN |
| GO:0005248 | Voltage‐gated sodium channel activity | 0.0304 | 12 | 0.95 | SN |
| GO:0030426 | Growth cone | 0.0320 | 8 | 0.73 | SN |
| GO:0006814 | Sodium ion transport | 0.0325 | 70 | 0.92 | SN |
| GO:0008503 | Benzodiazepine receptor activity | 0.0331 | 6 | 0.59 | SN |
| GO:0005234 | Glutamate‐gated ion channel activity | 0.0341 | 22 | 0.89 | SN |
| GO:0030424 | Axon | 0.0349 | 8 | 0.76 | SN |
| GO:0006904 | Vesicle docking during exocytosis | 0.0367 | 16 | 0.84 | SN |
| GO:0030594 | Neurotransmitter receptor activity | 0.0393 | 19 | 0.77 | SN |
| GO:0008308 | Voltage‐gated ion‐selective channel activity | 0.0440 | 7 | 0.73 | SN |
| GO:0006836 | Neurotransmitter transport | 0.0440 | 28 | 0.80 | SN |
| hsa04070 | Phosphatidylinositol signaling system | 0.0459 | 71 | 0.95 | SN |
| GO:0017137 | Rab interactor activity | 0.0492 | 15 | 0.86 | SN |
| Energy synthesis | |||||
| hsa00193 | ATP synthesis | 0.0002 | 26 | 0.70 | SN |
| hsa00190 | Oxidative phosphorylation | 0.0002 | 79 | 0.75 | SN |
| GO:0046961 | Hydrogen‐transporting atpase activity, rotational mechanism | 0.0002 | 30 | 0.74 | SN |
| GO:0046933 | Hydrogen‐transporting ATP synthase activity, rotational mechanism | 0.0002 | 29 | 0.75 | SN |
| GO:0015986 | ATP synthesis coupled proton transport | 0.0002 | 31 | 0.75 | SN |
| GO:0016469 | Proton‐transporting two‐sector atpase complex | 0.0002 | 29 | 0.75 | SN |
| hsa00190 | Oxidative phosphorylation | 0.0004 | 79 | 0.91 | PUT |
| GO:0015992 | Proton transport | 0.0007 | 37 | 0.79 | SN |
| GO:0003954 | NADH dehydrogenase activity | 0.0037 | 30 | 0.79 | SN |
| GO:0008137 | NADH dehydrogenase (ubiquinone) activity | 0.0040 | 30 | 0.79 | SN |
| GO:0005743 | Mitochondrial inner membrane | 0.0043 | 58 | 0.86 | SN |
| GO:0005753 | Proton‐transporting ATP synthase complex (sensu Eukaryota) | 0.0095 | 7 | 0.68 | SN |
| GO:0019866 | Inner membrane | 0.0157 | 27 | 0.80 | SN |
| GO:0042623 | Atpase activity, coupled | 0.0247 | 16 | 0.90 | SN |
| GO:0004129 | Cytochrome‐c oxidase activity | 0.0304 | 17 | 0.79 | SN |
| hsa00193 | ATP synthesis | 0.0336 | 26 | 0.90 | PUT |
| GO:0006120 | Mitochondrial electron transport, NADH to ubiquinone | 0.0492 | 19 | 0.81 | SN |
| Cytoskeleton | |||||
| GO:0005874 | Microtubule | 0.0002 | 117 | 0.91 | SN |
| hsa04810 | Regulation of actin cytoskeleton | 0.0026 | 144 | 1.02 | SN |
| GO:0007018 | Microtubule‐based movement | 0.0182 | 52 | 0.86 | SN |
| GO:0003774 | Motor activity | 0.0304 | 64 | 0.99 | SN |
| GO:0000776 | Kinetochore | 0.0319 | 15 | 0.79 | SN |
| GO:0008092 | Cytoskeletal protein binding | 0.0320 | 35 | 1.08 | SN |
| GO:0005875 | Microtubule associated complex | 0.0407 | 46 | 0.93 | SN |
| GO:0000146 | Microfilament motor activity | 0.0444 | 11 | 1.03 | SN |
| GO:0030048 | Actin filament‐based movement | 0.0492 | 13 | 0.96 | SN |
| Metabolism | |||||
| GO:0006096 | Glycolysis | 0.0002 | 35 | 0.82 | SN |
| hsa00710 | Carbon fixation | 0.0086 | 18 | 0.74 | SN |
| hsa00020 | Citrate cycle (TCA cycle) | 0.0086 | 14 | 0.90 | SN |
| hsa00260 | Glycine, serine and threonine metabolism | 0.0106 | 33 | 1.05 | SN |
| hsa00564 | Glycerophospholipid metabolism | 0.0153 | 56 | 0.95 | SN |
| hsa00740 | Riboflavin metabolism | 0.0176 | 11 | 0.88 | SN |
| hsa00330 | Arginine and proline metabolism | 0.0226 | 40 | 1.01 | PUT |
| hsa00220 | Urea cycle and metabolism of amino groups | 0.0336 | 15 | 1.01 | PUT |
| hsa00620 | Pyruvate metabolism | 0.0385 | 35 | 0.86 | SN |
| hsa00720 | Reductive carboxylate cycle (CO2 fixation) | 0.0385 | 7 | 0.89 | SN |
| hsa00910 | Nitrogen metabolism | 0.0409 | 18 | 0.99 | PUT |
| hsa00340 | Histidine metabolism | 0.0417 | 35 | 0.94 | SN |
| hsa00480 | Glutathione metabolism | 0.0417 | 18 | 0.97 | SN |
| hsa00410 | Beta‐Alanine metabolism | 0.0431 | 20 | 0.98 | SN |
| hsa00650 | Butanoate metabolism | 0.0459 | 39 | 0.96 | SN |
| hsa00271 | Methionine metabolism | 0.0459 | 14 | 1.02 | SN |
| hsa00251 | Glutamate metabolism | 0.0476 | 24 | 0.91 | SN |
| Extracellular matrix | |||||
| hsa04512 | ECM‐receptor interaction | 0.0013 | 59 | 1.19 | SN |
| hsa04510 | Focal adhesion | 0.0027 | 143 | 1.09 | SN |
| GO:0005518 | Collagen binding | 0.0060 | 11 | 1.16 | SN |
| hsa04514 | Cell adhesion molecules (cams) | 0.0122 | 84 | 1.10 | SN |
| hsa04510 | Focal adhesion | 0.0179 | 137 | 1.01 | PUT |
| GO:0007160 | Cell‐matrix adhesion | 0.0182 | 48 | 1.12 | SN |
| GO:0005201 | Extracellular matrix structural constituent | 0.0222 | 52 | 1.07 | PUT |
| Neurodegeneration | |||||
| hsa05010 | Alzheimer's disease | 0.0086 | 15 | 0.93 | SN |
| hsa01510 | Neurodegenerative disorders | 0.0102 | 26 | 0.89 | SN |
| hsa05020 | Parkinson's disease | 0.0191 | 14 | 0.77 | SN |
| hsa05040 | Huntington's disease | 0.0459 | 18 | 1.06 | SN |
| Ubiquitin‐proteasome system | |||||
| hsa03050 | Proteasome | 0.0002 | 20 | 0.73 | SN |
| GO:0051082 | Unfolded protein binding | 0.0058 | 114 | 0.90 | SN |
| GO:0005839 | Proteasome core complex (sensu Eukaryota) | 0.0146 | 13 | 0.84 | SN |
| GO:0005838 | Proteasome regulatory particle (sensu Eukaryota) | 0.0325 | 7 | 0.78 | SN |
| GO:0006511 | Ubiquitin‐dependent protein catabolism | 0.0393 | 98 | 0.96 | SN |
| Other | |||||
| GO:0005829 | Cytosol | 0.0002 | 134 | 0.89 | SN |
| GO:0043234 | Protein complex | 0.0002 | 30 | 0.74 | SN |
| GO:0007417 | Central nervous system development | 0.0002 | 68 | 0.95 | SN |
| GO:0005516 | Calmodulin binding | 0.0002 | 110 | 1.00 | SN |
| GO:0003924 | Gtpase activity | 0.0002 | 124 | 0.89 | SN |
| hsa04020 | Calcium signaling pathway | 0.0013 | 129 | 0.97 | SN |
| hsa05110 | Cholera—infection | 0.0016 | 35 | 0.85 | SN |
| GO:0007517 | Muscle development | 0.0020 | 96 | 1.05 | SN |
| GO:0004618 | Phosphoglycerate kinase activity | 0.0022 | 6 | 0.89 | SN |
| GO:0051301 | Cell division | 0.0058 | 115 | 1.01 | SN |
| GO:0005386 | Carrier activity | 0.0070 | 9 | 0.84 | SN |
| GO:0004721 | Phosphoprotein phosphatase activity | 0.0093 | 37 | 0.99 | SN |
| GO:0004298 | Threonine endopeptidase activity | 0.0094 | 14 | 0.82 | SN |
| GO:0030145 | Manganese ion binding | 0.0094 | 84 | 0.99 | SN |
| GO:0045786 | Negative regulation of cell cycle | 0.0157 | 65 | 1.07 | SN |
| GO:0004252 | Serine‐type endopeptidase activity | 0.0157 | 12 | 1.00 | SN |
| GO:0051258 | Protein polymerization | 0.0173 | 16 | 0.68 | SN |
| hsa04110 | Cell cycle | 0.0176 | 82 | 1.01 | SN |
| GO:0004553 | Hydrolase activity, hydrolyzing O‐glycosyl compounds | 0.0247 | 8 | 0.72 | SN |
| GO:0030529 | Ribonucleoprotein complex | 0.0247 | 64 | 1.02 | SN |
| GO:0007420 | Brain development | 0.0269 | 31 | 0.96 | SN |
| GO:0016310 | Phosphorylation | 0.0304 | 10 | 0.84 | SN |
| GO:0003705 | RNA polymerase II transcription factor activity, enhancer binding | 0.0333 | 11 | 1.05 | PUT |
| hsa00280 | Valine, leucine and isoleucine degradation | 0.0336 | 36 | 0.99 | PUT |
| hsa00970 | Aminoacyl‐trna synthetases | 0.0385 | 27 | 0.84 | SN |
| GO:0008020 | G‐protein coupled photoreceptor activity | 0.0444 | 6 | 0.80 | SN |
| GO:0006821 | Chloride transport | 0.0444 | 32 | 0.93 | SN |
| GO:0004176 | ATP‐dependent peptidase activity | 0.0451 | 7 | 0.71 | SN |
| hsa00770 | Pantothenate and coa biosynthesis | 0.0457 | 17 | 0.95 | SN |
| hsa00290 | Valine, leucine and isoleucine biosynthesis | 0.0459 | 9 | 0.90 | SN |
| hsa04910 | Insulin signaling pathway | 0.0459 | 97 | 0.94 | SN |
| hsa00960 | Alkaloid biosynthesis II | 0.0496 | 14 | 1.06 | SN |