Table 2. Biological process categories overrepresented by overall correlations (ADGs)
Up-regulated (Total: 1,572/6,265; 25.1%) ease N/M/B Down-regulated (Total: 1,126/6,265; 18.0%) ease N/M/B
Regulation of transcription (269/792; 34%) 0.0000 21/38/41 Energy pathways (57/151; 37.7%) 0.0000 15/15/69
Cell proliferation (210/666; 31.5%) 0.0001 23/43/35 ATP biosynthesis (16/23; 69.6%) 0.0000 18/9/73
Oncogenesis (24/47; 51.1%) 0.0003 21/39/39 Synaptic transmission (49/143; 34.3%) 0.0000 9/30/61
Protein amino acid phosphorylation (104/310; 33.5%) 0.0006 23/30/47 Coenzyme biosynthesis (20/40; 50%) 0.0000 15/15/69
Transition metal ion homeostasis (10/16; 62.5%) 0.0076 18/45/36 Cation transport (60/197; 30.5%) 0.0000 13/18/69
Positive regulation cell proliferation (25/62; 40.3%) 0.0119 18/68/14 Protein folding (30/86; 34.9%) 0.0003 32/11/57
Chromatin architecture (34/94; 36.2%) 0.0186 25/43/33 Tricarboxylic acid cycle (12/22; 54.5%) 0.0006 27/27/47
Nucleosome assembly (13/27; 48.1%) 0.0219 11/56/33 Glycolysis (14/29; 48.3%) 0.0007 6/18/76
Histogenesis and organogenesis (22/57; 38.6%) 0.0319 22/17/61 Neurogenesis (64/244; 26.2%) 0.0011 19/27/53
Cell adhesion (94/314; 29.9%) 0.0346 19/46/35 Amino acid catabolism (13/30; 43.3%) 0.0038 33/0/67
Development (235/850; 27.6%) 0.0425 21/42/37 Ubiquitin-dependent protein catabolism (27/87; 31%) 0.0043 48/13/39
Complement activation, classical (9/18; 50%) 0.0576 10/40/50 Secretion (14/37; 37.8%) 0.0095 0/35/65
Negative regulation cell proliferation (28/83; 33.7%) 0.0762 09/50/41 Protein transport (66/288; 22.9%) 0.0245 26/25/49
Isoprenoid metabolism (6/10; 60%) 0.0789 00/83/17 Neurotransmitter metabolism (6/11; 54.5%) 0.0329 17/17/67
Apoptosis (72/255; 29.5%) 0.0818 13/32/55 Axon guidance (8/19; 42.1%) 0.0404 27/9/64
Defense response (102/360; 28.3%) 0.1010 15/57/28 Calcium ion transport (11/32; 34.4%) 0.0482 7/7/87
Lipid metabolism (82/288; 28.5%) 0.1250 15/47/38 Microtubule-based process (20/73; 27.4%) 0.0538 11/21/68
  • Biological process categories significantly overrepresented by ADGs (P ≤ 0.05; ease score) and a few other selected categories are shown. Numerous other similar significant categories are not included to reduce redundancy. Significant functional categories are those with a higher ratio of identified genes to all genes tested on the array for associations with that category, relative to the ratio of total identified genes in the study to all genes tested on the array for associations with all categories. Association numbers approximate but are not exactly equal to gene numbers in a category. After each category description (in parentheses) is the ratio of associations for that category and the percentage represented by that ratio. The analogous ratios for total identified up-regulated and down-regulated genes are shown in the headings (Total). ease, modified Fisher's exact test P value; N/M/B, percentage of genes included in category because they were significant by NFT correlation (N), MMSE correlation (M), or both (B). (The complete list of ADGs is given alphabetically in Table 5).