Table 4.
Biological process categories significantly overrepresented in Cognitive Differences Hypothesis (non-demented vs. AD)
| A. up regulated in AD | |||
|---|---|---|---|
| Category | # genes DEa | # genes on chipb |
FDRc |
| regulation of cellular physiological process | 208 | 2252 | 3.21E-05 |
| regulation of biological process | 231 | 2578 | 3.21E-05 |
| regulation of cellular process | 215 | 2365 | 3.21E-05 |
| regulation of physiological process | 214 | 2376 | 6.34E-05 |
| regulation of transcription, DNA dependent | 149 | 1533 | 6.35E-05 |
| regulation of transcription | 154 | 1598 | 6.35E-05 |
| regulation of nucleic acid metabolism | 155 | 1620 | 8.39E-05 |
| regulation of cellular metabolism | 157 | 1650 | 8.94E-05 |
| transcription | 159 | 1684 | 0.000115 |
| transcription, DNA-dependent | 151 | 1587 | 0.000137 |
| regulation of metabolism | 159 | 1733 | 0.000752 |
| negative regulation of cellular physiological process | 48 | 384 | 0.0011 |
| actin filament-based process | 17 | 88 | 0.00146 |
| negative regulation of physiological process | 49 | 412 | 0.00451 |
| negative regulation of cellular process | 49 | 416 | 0.0059 |
| chromatin modification | 16 | 87 | 0.00717 |
| actin cytoskeleton organization and biogenesis | 16 | 77 | 0.0114 |
| negative regulation of biological process | 51 | 456 | 0.0189 |
| phosphate transport | 14 | 78 | 0.0363 |
| nucleic acid metabolism | 205 | 2502 | 0.0418 |
| B. Down regulated in AD | |||
|---|---|---|---|
| Category | # genes | # genes on chip |
FDR |
| coenzyme metabolism | 65 | 124 | 1.69E-32 |
| cofactor metabolism | 70 | 145 | 1.42E-30 |
| oxidative phosphorylation | 41 | 65 | 2.47E-27 |
| coenzyme biosynthesis | 41 | 81 | 1.25E-18 |
| cofactor biosynthesis | 45 | 96 | 6.15E-18 |
| biosynthesis | 217 | 919 | 3.27E-17 |
| ribonucleotide biosynthesis | 34 | 69 | 1.76E-14 |
| nucleoside phosphate metabolism | 25 | 42 | 1.76E-14 |
| ATP biosynthesis | 25 | 42 | 1.76E-14 |
| ATP coupled proton transport | 23 | 38 | 1.30E-13 |
| energy coupled proton transport, down electrochemical gradient |
23 | 38 | 1.30E-13 |
| ribonucleotide metabolism | 34 | 72 | 1.58E-13 |
| ATP metabolism | 25 | 44 | 1.76E-13 |
| group transfer coenzyme metabolism | 28 | 54 | 4.57E-13 |
| ribonucleotide triphosphate biosynthesis | 27 | 51 | 4.57E-13 |
| purine ribonucleotide triphosphate biosynthesis | 27 | 51 | 4.57E-13 |
| purine nucleoside triphosphate biosynthesis | 27 | 51 | 4.57E-13 |
| nucleoside triphosphate metabolism | 27 | 52 | 1.27E-12 |
| generation of precursor metabolites and energy | 128 | 504 | 1.33E-12 |
| intracellular transport | 114 | 433 | 1.63E-12 |
| cellular biosynthesis | 183 | 807 | 2.29E-12 |
| ribonucleoside triphosphate metabolism | 27 | 53 | 2.55E-12 |
| purine ribonucleoside triphosphate metabolism | 27 | 53 | 2.55E-12 |
| purine nucleoside triphosphate metabolism | 27 | 53 | 2.55E-12 |
| purine ribonucleotide biosynthesis | 30 | 64 | 7.52E-12 |
| purine nucleotide biosynthesis | 31 | 68 | 1.18E-11 |
| nucleoside triphosphate metabolism | 27 | 55 | 1.59E-11 |
| establishment of protein localization | 108 | 417 | 2.77E-11 |
| purine ribonucleotide metabolism | 30 | 66 | 3.22E-11 |
| purine nucleotide metabolism | 31 | 70 | 4.56E-11 |
| purine nucleotide metabolism | 107 | 415 | 4.80E-11 |
| protein transport | 42 | 113 | 1.10E-10 |
| nucleotide biosynthesis | 108 | 425 | 1.23E-10 |
| hydrogen transport | 29 | 65 | 1.86E-10 |
| proton transport | 28 | 64 | 1.19E-09 |
| nucleotide metabolism | 51 | 159 | 2.90E-09 |
| intracellular protein transport | 74 | 271 | 7.39E-09 |
| aerobic respiration | 18 | 27 | 5.76E-08 |
| cellular respiration | 18 | 29 | 3.12E-07 |
| ATP synthesis coupled electron transport | 16 | 25 | 1.28E-06 |
| metabolism | 933 | 6083 | 1.75E-06 |
| translation | 42 | 138 | 1.75E-06 |
| RNA metabolism | 82 | 340 | 1.75E-06 |
| ATP synthesis coupled electron transport | 15 | 23 | 2.41E-06 |
| acety-CoA metabolism | 15 | 24 | 5.36E-06 |
| main pathways of carbohydrate metabolism | 29 | 84 | 5.82E-06 |
| energy derivation by oxidation of organic compounds | 38 | 127 | 1.61E-05 |
| tricarboxylic acid cycle | 13 | 20 | 2.10E-05 |
| acety-CoA catabolism | 13 | 20 | 2.10E-05 |
| coenzyme catabolism | 13 | 20 | 2.10E-05 |
| cofactor catabolism | 14 | 23 | 2.23E-05 |
| secretory pathway | 35 | 116 | 3.75E-05 |
| cellular metabolism | 869 | 5712 | 6.16E-05 |
| macromolecule metabolism | 462 | 2830 | 9.62E-05 |
| RNA processing | 63 | 266 | 0.000178 |
| secretion | 40 | 146 | 0.000178 |
| protein folding | 49 | 192 | 0.000189 |
| mitochondrial electron transport, NADH to ubiquinone |
12 | 20 | 0.000191 |
| mRNA metabolism | 44 | 167 | 0.000211 |
| cellular macromolecule metabolism | 436 | 2674 | 0.000251 |
| cellular physiological process | 1164 | 7955 | 0.000273 |
| protein biosynthesis | 95 | 455 | 0.000434 |
| RNA splicing, via transesterif | 26 | 83 | 0.000452 |
| nuclear mRNA splicing, via spliceosome | 26 | 83 | 0.000452 |
| RNA splicing, via transesterif | 26 | 83 | 0.000452 |
| electron transport | 70 | 312 | 0.000476 |
| establishment of localization | 305 | 1803 | 0.000597 |
| mRNA processing | 39 | 147 | 0.000626 |
| transport | 304 | 1801 | 0.000739 |
| localization | 305 | 1810 | 0.000823 |
| RNA splicing | 31 | 111 | 0.00151 |
| protein targeting | 31 | 111 | 0.00151 |
| biopolymer metabolism | 235 | 1361 | 0.00199 |
| macromolecule biosynthesis | 102 | 513 | 0.00205 |
| Golgi vesicle transport | 16 | 44 | 0.00229 |
| protein-mitochondrial targeting | 10 | 18 | 0.00292 |
| sterol biosynthesis | 12 | 25 | 0.00316 |
| primary metabolism | 815 | 5466 | 0.00606 |
| protein metabolism | 400 | 2514 | 0.00833 |
| mitochondrial organization and biogenesis | 8 | 14 | 0.0141 |
| translational initiation | 16 | 49 | 0.0175 |
| cellular protein metabolism | 394 | 2496 | 0.0193 |
| inner mitochondrial membrane organization and biogenesis |
5 | 6 | 0.0206 |
| mitochondrial inner membrane protein import | 5 | 6 | 0.0206 |
| regulated secretory pathway | 8 | 15 | 0.0248 |
| quinone cofactor metabolism | 4 | 4 | 0.0275 |
| quinone cofactor biosynthesis | 4 | 4 | 0.0275 |
| ubiquinone biosynthesis | 4 | 4 | 0.0275 |
| ubiquinone metabolism | 4 | 4 | 0.0275 |
| lipid biosynthesis | 39 | 170 | 0.036 |
a
the number of differentially expressed genes (q< 0.1 by ANOVA) that are members of the category
b
the number of genes on the Affymetrix GeneChip that are members of the category
c
the FDR values are from χ2 analysis corrected for multiple testing (see methods)