Table 1. Modules detected in the network of cofactor-interacting proteins and their first-degree neighbors.
| Module | Number of Proteins | Number of cofactor-protein (%) | Cofactor | Main Biological Functions and/or Pathways |
|---|---|---|---|---|
| 1 | 10 | 1 (10.0%) | Mg | (ribosomal)RNA processing and ribosome biogenesis |
| 2 | 19 | 2 (10.5%) | Mg, Vit B6 (PP) | Positive regulation of transcription and RNA metabolic process. |
| HIV infection. | ||||
| 3 | 83 | 19 (22.9%) | Ca, Mg, Zn, SAM, B5 (CoA) | Regulation of transcription, cell proliferation and apoptosis. |
| Cell surface signal transduction. Response to hormone (insulin) stimulus | ||||
| Erb and PDGF signaling. | ||||
| 4 | 31 | 2 (6.5%) | Mn, Zn | Cell surface signal transduction, Phosphate metabolic process, Regulation of apoptosis. |
| B and T cell receptor signaling | ||||
| 5 | 109 | 26 (23.9%) | Ca, Cu, Mg, Mn, SAM, Vit B5 (CoA), Zn, metal | Regulation of macronutrient metabolism, cell differentiation, apoptosis, angiogenesis and TGFß signaling. |
| Pathway in colorectal and pancreatic cancer. | ||||
| 6 | 110 | 26 (23.6%) | Ca, Mg, SAM, Vit A, Vit B2 (FAD), Vit B9 (THF), Zn | Regulation of apoptosis, RNA metabolism, transcription factor activity, and protein kinase activity. Response to stress. NOD/Toll receptors signaling. |
| 7 | 110 | 15 (13.6%) | Ca, Fe, Mg, Mn, SAM, Zn, metal, metal cation | Regulation of transcription, immune response, phosphorylation, and apoptosis. |
| 8 | 46 | 10 (21.7%) | Fe-S complex, Mg, Zn, GSH, Vit B2 (FAD) | Regulation of transcription, phosphorylation, JNK and MAPK activity. Insulin signaling pathway |
| 9 | 12 | 5 (41.7%) | Mg, Mn | Regulation of apoptosis, JNK and MAPKKK activity |
| 10 | 85 | 15 (17.6%) | Ca, Mg, Mn, Zn, SAM, metal | Phosphate metabolic process. |
| Regulation of apoptosis. | ||||
| 11 | 12 | 4 (33.3%) | Ca, Mg, Zn, metal | – |
| 12 | 25 | 9 (36.0%) | Mg, Zn, metal, Vit B3 (NAD) | Regulation of phosphate metabolism, protein kinase activity, cell proliferation and differentiation. |
| TGFß signaling, TCA cycle, signaling by BMP and diabetes pathways. |
Details of number of proteins, number (percentage) of cofactor-interacting proteins, cofactor interactions and main biological functions (GO) and pathways (KEGG hsa, Reactome and Biocarta) annotation per module.