Table II.
Results of NEA based on 281 DC gene pairs.
| Path_name | No. of links |
|---|---|
| Metabolic pathways | 1,282 |
| Phagosome | 848 |
| Chemokine signaling pathway | 800 |
| Cell adhesion molecules (CAMs) | 701 |
| Natural killer cell-mediated cytotoxicity | 653 |
| Osteoclast differentiation | 609 |
| Cytokine-cytokine receptor interaction | 603 |
| Leishmaniasis | 578 |
| Toxoplasmosis | 563 |
| Regulation of actin cytoskeleton | 554 |
| Fc γ R-mediated phagocytosis | 529 |
| Leukocyte transendothelial migration | 529 |
| Staphylococcus aureus infection | 502 |
| Rheumatoid arthritis | 501 |
| Neuroactive ligand-receptor interaction | 489 |
| Pathways in cancer | 480 |
| Viral myocarditis | 479 |
| Antigen processing and presentation | 438 |
| T-cell receptor signaling pathway | 438 |
| Systemic lupus erythematosus | 411 |
| Hematopoietic cell lineage | 406 |
| Fc ε RI signaling pathway | 388 |
| B cell receptor signaling pathway | 382 |
| Endocytosis | 373 |
| Autoimmune thyroid disease | 356 |
| Graft-vs.-host disease | 354 |
| Type I diabetes mellitus | 351 |
| Allograft rejection | 347 |
| Intestinal immune network for IgA production | 344 |
| Focal adhesion | 327 |
| Jak-STAT signaling pathway | 318 |
| Toll-like receptor signaling pathway | 311 |
| Chagas disease (American trypanosomiasis) | 289 |
| Calcium signaling pathway | 263 |
| Asthma | 254 |
| Amoebiasis | 253 |
| Olfactory transduction | 251 |
| Neurotrophin signaling pathway | 251 |
| Lysosome | 248 |
| Cell cycle | 247 |
| Bacterial invasion of epithelial cells | 237 |
| VEGF signaling pathway | 231 |
| Purine metabolism | 225 |
| Primary immunodeficiency | 222 |
| Hepatitis C | 221 |
| RNA transport | 219 |
| Pathogenic Escherichia coli infection | 216 |
| Oocyte meiosis | 204 |
| Epithelial cell signaling in Helicobacter pylori infection | 203 |
| Drug metabolism-cytochrome P450 | 194 |
| Shigellosis | 190 |
| Pyrimidine metabolism | 188 |
| Spliceosome | 185 |
| Protein processing in endoplasmic reticulum | 184 |
| Axon guidance | 184 |
| Pancreatic cancer | 180 |
| Metabolism of xenobiotics by cytochrome P450 | 177 |
| Cytosolic DNA-sensing pathway | 173 |
| Adherens junction | 168 |
| Huntington’s disease | 160 |
| Retinol metabolism | 158 |
| Drug metabolism - other enzymes | 157 |
| Apoptosis | 157 |
| Complement and coagulation cascades | 156 |
| Pancreatic secretion | 156 |
| Colorectal cancer | 155 |
| Wnt signaling pathway | 154 |
| Vibrio cholerae infection | 154 |
| Arachidonic acid metabolism | 147 |
| Alzheimer’s disease | 146 |
| Malaria | 146 |
| Small cell lung cancer | 144 |
| Long-term depression | 143 |
| Oxidative phosphorylation | 142 |
| Phosphatidylinositol signaling system | 141 |
| NOD-like receptor signaling pathway | 138 |
| Acute myeloid leukemia | 133 |
| Non-small cell lung cancer | 133 |
| DNA replication | 130 |
| Salivary secretion | 125 |
| Steroid hormone biosynthesis | 118 |
| Starch and sucrose metabolism | 118 |
| Dilated cardiomyopathy | 117 |
| Ubiquitin-mediated proteolysis | 114 |
| Amyotrophic lateral sclerosis (ALS) | 114 |
| mRNA surveillance pathway | 110 |
| Melanogenesis | 109 |
| Hypertrophic cardiomyopathy (HCM) | 106 |
| Glycerophospholipid metabolism | 105 |
| Type II diabetes mellitus | 104 |
| Carbohydrate digestion and absorption | 103 |
| Porphyrin and chlorophyll metabolism | 102 |
| Glutathione metabolism | 100 |
| Linoleic acid metabolism | 97 |
| Ribosome biogenesis in eukaryotes | 97 |
| Other types of O-glycan biosynthesis | 96 |
| Adipocytokine signaling pathway | 96 |
| Aldosterone-regulated sodium reabsorption | 95 |
| Long-term potentiation | 94 |
| p53 signaling pathway | 93 |
| Pentose and glucuronate interconversions | 92 |
| RNA degradation | 91 |
| Inositol phosphate metabolism | 88 |
| Bile secretion | 88 |
| Ascorbate and aldarate metabolism | 86 |
| Prion diseases | 86 |
| eCM-receptor interaction | 82 |
| Collecting duct acid secretion | 82 |
| Arginine and proline metabolism | 79 |
| Proteasome | 78 |
| Parkinson’s disease | 78 |
| Nucleotide excision repair | 75 |
| TGF-β signaling pathway | 74 |
| Fat digestion and absorption | 74 |
| Ether lipid metabolism | 70 |
| Ribosome | 69 |
| Protein digestion and absorption | 68 |
| Mismatch repair | 67 |
| PPAR signaling pathway | 66 |
| African trypanosomiasis | 65 |
| Alanine, aspartate and glutamate metabolism | 59 |
| Base excision repair | 58 |
| Aminoacyl-tRNA biosynthesis | 53 |
| Citrate cycle (TCA cycle) | 52 |
| RNA polymerase | 51 |
| α-linolenic acid metabolism | 49 |
| Glycerolipid metabolism | 47 |
| Tryptophan metabolism | 45 |
| Glycine, serine and threonine metabolism | 44 |
| Proximal tubule bicarbonate reclamation | 43 |
| Tyrosine metabolism | 41 |
| Homologous recombination | 40 |
| Notch signaling pathway | 40 |
| N-Glycan biosynthesis | 37 |
| Protein export | 37 |
| Bladder cancer | 36 |
| Histidine metabolism | 33 |
| Phenylalanine metabolism | 31 |
| Cardiac muscle contraction | 30 |
| Hedgehog signaling pathway | 30 |
| Other glycan degradation | 29 |
| Pantothenate and CoA biosynthesis | 27 |
| Nitrogen metabolism | 25 |
| Thyroid cancer | 24 |
| β-alanine metabolism | 22 |
| Renin-angiotensin system | 22 |
| Vitamin digestion and absorption | 19 |
| Valine, leucine and isoleucine biosynthesis | 17 |
| Glyoxylate and dicarboxylate metabolism | 17 |
| Non-homologous end-joining | 17 |
| Phenylalanine, tyrosine and tryptophan biosynthesis | 16 |
| Taurine and hypotaurine metabolism | 16 |
| Circadian rhythm-mammal | 16 |
| Basal cell carcinoma | 15 |
| Butanoate metabolism | 13 |
| Folate biosynthesis | 13 |
| Caffeine metabolism | 12 |
| Terpenoid backbone biosynthesis | 11 |
| Biosynthesis of unsaturated fatty acids | 9 |
| Basal transcription factors | 8 |
| Riboflavin metabolism | 7 |
| Fatty acid elongation in mitochondria | 2 |
| Glycosylphosphatidylinositol (GPI)-anchor biosynthesis | 2 |
| Mucin type O-glycan biosynthesis | 1 |
NEA, network enrichment analysis; DC, differentially co-expressed.