Table 1.
Cellular functions with genes changed in primary neurons relative to neural stem cells
| GO Type | GO Name | Number Changed | Number Measured | Number in GO | Adjusted P Value |
|---|---|---|---|---|---|
| Downregulated | |||||
| C | Intracellular part | 1188 | 7905 | 8617 | <0.0001 |
| C | Organelle | 1011 | 6576 | 7174 | <0.0001 |
| P | Cell cycle | 156 | 593 | 633 | <0.0001 |
| P | DNA replication | 55 | 134 | 138 | <0.0001 |
| P | Cell division | 72 | 239 | 249 | <0.0001 |
| F | Catalytic activity | 657 | 4431 | 4851 | <0.0001 |
| P | Organelle organization and biogenesis | 179 | 955 | 1028 | <0.0001 |
| P | Ribonucleoprotein complex biogenesis and assembly | 39 | 134 | 143 | <0.0001 |
| P | Apoptosis | 124 | 639 | 691 | <0.0001 |
| C | Protein/DNA complex | 30 | 94 | 108 | <0.0001 |
| P | Chromosome segregation | 18 | 45 | 50 | <0.0001 |
| C | Basement membrane | 19 | 49 | 54 | <0.0001 |
| P | Hexose metabolic process | 31 | 110 | 123 | <0.0001 |
| P | Angiogenesis | 33 | 125 | 136 | <0.0001 |
| P | DNA geometric change | 5 | 7 | 7 | <0.0001 |
| P | Ribonucleoside metabolic process | 5 | 7 | 9 | <0.0001 |
| P | Nucleoside monophosphate biosynthetic process | 8 | 16 | 17 | <0.0001 |
| P | IMP metabolic process | 3 | 3 | 3 | 0.0195 |
| P | 4-Hydroxyproline metabolic process | 3 | 3 | 3 | 0.0465 |
| P | SMAD protein nuclear translocation | 3 | 3 | 3 | 0.0195 |
| P | Translation | 59 | 285 | 351 | <0.0001 |
| F | Structural constituent of ribosome | 29 | 111 | 134 | <0.0001 |
| P | Embryonic development ending in birth or egg Hatching | 61 | 300 | 325 | <0.0001 |
| F | Adenyl nucleotide binding | 192 | 1212 | 1314 | 0.0195 |
| F | L-ascorbic acid binding | 8 | 17 | 19 | 0.0195 |
| P | Tube morphogenesis | 34 | 142 | 155 | <0.0001 |
| C | MHC class I protein complex | 7 | 14 | 17 | <0.0001 |
| P | Response to DNA damage stimulus | 48 | 226 | 241 | <0.0001 |
| P | Immune system process | 166 | 1031 | 1133 | <0.0001 |
| P | rRNA metabolic process | 18 | 61 | 64 | <0.0001 |
| P | Cell proliferation | 90 | 507 | 553 | <0.0001 |
| P | Peptidyl-histidine modification | 4 | 6 | 6 | 0.0465 |
| P | Folic acid and derivative biosynthetic process | 4 | 6 | 7 | 0.034 |
| P | Transcription factor import into nucleus | 6 | 12 | 14 | <0.0001 |
| F | Calcium-dependent phospholipid binding | 8 | 19 | 20 | <0.0001 |
| C | Integrin complex | 9 | 23 | 25 | 0.0195 |
| P | Liver development | 10 | 28 | 31 | 0.0195 |
| P | Positive regulation of NF-κB transcription factor activity | 6 | 13 | 16 | <0.0001 |
| P | Endoplasmic reticulum unfolded protein response | 5 | 10 | 12 | 0.034 |
| P | Homeostasis of number of cells | 56 | 301 | 327 | 0.0195 |
| P | Oxidation reduction | 149 | 961 | 1040 | 0.0465 |
| P | Nonapoptotic programmed cell death | 72 | 412 | 444 | 0.0195 |
| P | Protein folding | 24 | 105 | 117 | 0.034 |
| P | Regulation of angiogenesis | 9 | 27 | 30 | 0.034 |
| P | Cytokine production | 26 | 118 | 127 | <0.0001 |
| P | Regulation of cell size | 25 | 113 | 119 | <0.0001 |
| P | Extracellular matrix organization and biogenesis | 14 | 53 | 59 | 0.034 |
| C | Intracellular part | 1188 | 7905 | 8617 | <0.0001 |
| Upregulated | |||||
| P | Neurite development | 95 | 201 | 222 | <0.0001 |
| C | Synapse | 102 | 231 | 255 | <0.0001 |
| C | Neuron projection | 66 | 131 | 141 | <0.0001 |
| F | Protein binding | 916 | 4602 | 5018 | <0.0001 |
| P | Synaptic transmission | 82 | 188 | 205 | <0.0001 |
| P | Localization | 546 | 2607 | 2814 | <0.0001 |
| P | Small GTPase mediated signal transduction | 122 | 398 | 423 | <0.0001 |
| C | Cell junction | 121 | 401 | 432 | <0.0001 |
| C | Synaptic vesicle | 30 | 52 | 55 | <0.0001 |
| P | Telencephalon development | 25 | 51 | 55 | <0.0001 |
| P | Periplasmic space organization and biogenesis | 63 | 196 | 223 | <0.0001 |
| P | Neuron recognition | 10 | 12 | 12 | <0.0001 |
| P | Microtubule-based process | 61 | 197 | 211 | <0.0001 |
| P | Biological adhesion | 131 | 537 | 589 | <0.0001 |
| F | Kinase activity | 172 | 760 | 836 | <0.0001 |
| F | Ion transmembrane transporter activity | 138 | 585 | 643 | <0.0001 |
| P | Learning and/or memory | 28 | 69 | 76 | <0.0001 |
| C | Golgi apparatus | 134 | 570 | 607 | <0.0001 |
| C | Synaptosome | 24 | 56 | 59 | <0.0001 |
| F | Gated channel activity | 69 | 246 | 267 | <0.0001 |
| F | Calcium ion binding | 167 | 753 | 810 | <0.0001 |
| P | Neurite regeneration | 17 | 34 | 39 | <0.0001 |
| P | Negative regulation of neurogenesis | 16 | 31 | 33 | <0.0001 |
| C | Microtubule cytoskeleton | 73 | 268 | 294 | <0.0001 |
| F | GTPase regulator activity | 78 | 293 | 317 | <0.0001 |
| P | Neuromuscular process | 32 | 88 | 105 | <0.0001 |
| P | Regulation of adenylate cyclase activity | 9 | 13 | 14 | <0.0001 |
| F | α-N-acetylneuraminate α-2,8-Sialyltransferase activity | 5 | 5 | 5 | <0.0001 |
| P | Posttranslational protein modification | 188 | 899 | 972 | <0.0001 |
| C | Cell soma | 25 | 68 | 73 | <0.0001 |
| C | Ionotropic glutamate receptor complex | 8 | 12 | 13 | <0.0001 |
| F | GTP binding | 75 | 298 | 314 | <0.0001 |
| F | Glutamate receptor activity | 12 | 23 | 30 | <0.0001 |
| P | Membrane depolarization | 13 | 27 | 30 | <0.0001 |
| P | Central nervous system neuron differentiation | 15 | 34 | 36 | <0.0001 |
| P | Cerebellar granular layer development | 4 | 4 | 5 | <0.0001 |
| F | Calcium channel regulator activity | 6 | 8 | 9 | <0.0001 |
| C | Heterotrimeric G protein complex | 14 | 31 | 34 | <0.0001 |
| C | Coated pit | 13 | 28 | 29 | <0.0001 |
| C | Site of polarized growth | 10 | 19 | 21 | <0.0001 |
| P | Positive regulation of lyase activity | 7 | 11 | 12 | <0.0001 |
| P | Positive regulation of cyclase activity | 7 | 11 | 12 | <0.0001 |
| P | Synapse organization and biogenesis | 19 | 51 | 56 | <0.0001 |
| F | AMP binding | 8 | 14 | 16 | <0.0001 |
| F | l-Amino acid transmembrane transporter activity | 11 | 23 | 26 | 0.0135 |
| P | Sensory organ development | 60 | 244 | 276 | <0.0001 |
| C | cAMP-dependent protein kinase complex | 5 | 7 | 8 | 0.0135 |
| F | Kinase regulator activity | 19 | 54 | 58 | <0.0001 |
| P | Action potential propagation | 8 | 15 | 18 | <0.0001 |
| P | Enzyme-linked receptor protein signaling pathway | 66 | 280 | 299 | <0.0001 |
| C | Coated membrane | 16 | 43 | 51 | <0.0001 |
| F | UDP-galactose:β-N-Acetylglucosamine β-1,3-Galactosyltransferase activity | 4 | 5 | 5 | 0.025 |
| P | Regulation of neuron differentiation | 15 | 40 | 42 | <0.0001 |
| P | Regulation of cellular component size | 16 | 44 | 45 | <0.0001 |
| P | Membrane organization and biogenesis | 66 | 284 | 311 | <0.0001 |
| P | Cerebral cortex neuron differentiation | 7 | 13 | 13 | 0.025 |
| P | Response to organic substance | 17 | 49 | 55 | <0.0001 |
| P | Regulation of GTPase activity | 21 | 66 | 72 | <0.0001 |
| P | Wnt receptor signaling pathway | 43 | 170 | 182 | <0.0001 |
| P | Multicellular organismal response to stress | 11 | 27 | 31 | 0.0135 |
| F | Adenylate cyclase activity | 6 | 11 | 11 | 0.044 |
| P | Protein polymerization | 16 | 47 | 51 | <0.0001 |
| P | Notch signaling pathway | 27 | 96 | 104 | <0.0001 |
| P | Adult behavior | 23 | 78 | 88 | <0.0001 |
| P | Sensory perception of pain | 10 | 25 | 26 | 0.025 |
| P | Regulation of protein polymerization | 8 | 18 | 20 | <0.0001 |
| P | Sterol biosynthetic process | 11 | 29 | 34 | <0.0001 |
| F | Potassium ion binding | 28 | 104 | 111 | <0.0001 |
| P | Metabotropic glutamate receptor Signaling pathway | 13 | 38 | 44 | <0.0001 |
| P | Peptidyl-serine modification | 16 | 51 | 55 | <0.0001 |
| F | Microtubule motor activity | 16 | 51 | 54 | 0.0135 |
| C | Voltage-gated potassium channel complex | 17 | 56 | 60 | 0.0135 |
| P | Photoreceptor cell differentiation | 29 | 113 | 121 | 0.044 |
| F | Receptor signaling protein activity | 22 | 81 | 86 | 0.025 |
| C | Perinuclear region of cytoplasm | 12 | 37 | 39 | 0.044 |
| C | Leading edge | 19 | 69 | 77 | 0.0135 |
| P | Calcium-mediated signaling | 18 | 65 | 73 | 0.044 |
| P | Regulation of action potential | 12 | 38 | 45 | 0.044 |
| P | Neuropeptide signaling pathway | 19 | 70 | 77 | 0.0345 |
| P | Dopamine receptor signaling pathway | 10 | 30 | 33 | 0.044 |
GO, Gene Ontology; P, biological process; C, cellular component; F, molecular function.