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).