Table S1.
The enriched KEGG pathways for each module
| Module | KEGG pathways | Input number | False discovery rate | Top genes |
|---|---|---|---|---|
| Red module | Cytokine–cytokine receptor interaction | 21 | 1.50E-19 | IL12B, CXCL9, CCR8, CCR7, IFNB1 |
| Chemokine signaling pathway | 11 | 1.03E-08 | CXCL9, CCR7, CCR8, CCL7, CXCL10 | |
| Type I diabetes mellitus | 5 | 4.33E-05 | IL12B, IFNG, GZMB, RBPJL, CD80 | |
| Jak-STAT signaling pathway | 7 | 8.04E-05 | IL12B, IL21, IFNB1, IFNG, GHR | |
| Toll-like receptor signaling pathway | 6 | 9.21E-05 | IL12B, CXCL9, IFNB1, CXCL10, CD80 | |
| Allograft rejection | 4 | 0.00031 | IL12B, IFNG, GZMB, CD80 | |
| Tryptophan metabolism | 4 | 0.00031 | IDO2, IDO1, IL4I1, ALDH2 | |
| RIG-I-like receptor signaling pathway | 4 | 0.00215 | IL12B, IFNB1, ISG15, CXCL10 | |
| PI3K-Akt signaling pathway | 7 | 0.00347 | TCL1A, IFNB1, EFNA2, FGF21, CD19, GHR | |
| Primary immunodeficiency | 3 | 0.00455 | TAP1, ICOS, CD19 | |
| Transcriptional misregulation in cancer | 5 | 0.00525 | ETV7, PAX5, CCR7, BCL2A1, GZMB | |
| TNF signaling pathway | 4 | 0.00622 | CREB3L3, RBPJL, CXCL10, CCL20 | |
| Intestinal immune network for IgA production | 3 | 0.00715 | CCL25, ICOS, CD80 | |
| Cytosolic DNA-sensing pathway | 3 | 0.01276 | ZBP1, IFNB1, CXCL10 | |
| CAMs | 4 | 0.01403 | ICOS, TIGIT, PDCD1, CD80 | |
| Blue module | Cell cycle | 29 | 1.26E-23 | CCNA2, MAD2L1, BUB1B, E2F1, ORC6 |
| Oocyte meiosis | 18 | 1.74E-11 | CDC25C, CCNB1, PLK1, CDC20, MAD2L1 | |
| Progesterone-mediated oocyte maturation | 13 | 7.85E-08 | CDC25C, CCNB1, PLK1, MAD2L1, CDC25A | |
| Fanconi anemia pathway | 10 | 3.27E-07 | RMI2, BRCA2, FANCI, BLM, UBE2T | |
| Homologous recombination | 7 | 9.22E-06 | RAD51, RAD54L, BLM, XRCC2, BRCA2 | |
| p53 signaling pathway | 9 | 1.59E-05 | CCNB2, CCNB1, CCNE2, CCNE1, CDKN2A | |
| HTLV-I infection | 13 | 0.00101 | CCNB2, MYBL2, CDC20, MAD2L1, CDKN2A | |
| DNA replication | 5 | 0.00309 | RNASEH2A, DNA2, MCM2, FEN1, MCM4 | |
| MicroRNAs in cancer | 13 | 0.00309 | CDC25C, DNMT3B, CDC25A, CCNE2, CCNE1 | |
| Protein digestion and absorption | 7 | 0.00371 | COL10A1, COL11A1, COL11A2, SLC15A1, SLC6A19 | |
| Pancreatic cancer | 6 | 0.00441 | BRCA2, CDKN2A, E2F2, MAPK10, E2F1 | |
| Neuroactive ligand-receptor interaction | 11 | 0.01537 | CHRNB4, CHRNA5, GABRA5, CHRM3, HTR6 | |
| Glycine, serine and threonine metabolism | 4 | 0.0293 | AGXT, PSAT1, CBS, CBSL | |
| Hepatitis B | 7 | 0.03896 | CCNA2, CCNE2, CCNE1, BIRC5, E2F2 | |
| Cholinergic synapse | 6 | 0.04077 | CHRNB4, CACNA1B, GNG4, KCNQ3, KCNJ4 | |
| Yellow module | Neuroactive ligand-receptor interaction | 9 | 0.00038 | NTSR1, ADRB3, GABRD, GRIA1, ADRA1A |
| Focal adhesion | 7 | 0.00166 | ITGA8, CAV1, FN1, FLNC, COL1A1 | |
| Calcium signaling pathway | 6 | 0.003759 | NTSR1, ADRB3, ADRA1A, AGTR1, ITPKA | |
| CAMs | 5 | 0.008612 | ITGA8, CLDN6, CLDN14, CLDN5, CDH15 | |
| ECM-receptor interaction | 4 | 0.008612 | ITGA8, TNN, FN1, COL1A1 | |
| Proteoglycans in cancer | 5 | 0.021599 | MMP9, CAV1, FN1, FLNC, PLAUR | |
| Renin secretion | 3 | 0.029087 | ADCYAP1R1, ADRB3, AGTR1 | |
| PI3K-Akt signaling pathway | 6 | 0.030187 | ITGA8, FN1, COL1A1, TNN, CSF3, SGK2 | |
| Drug metabolism – cytochrome P450 | 3 | 0.030187 | GSTM2, ADH7, UGT2B4 | |
| PPAR signaling pathway | 3 | 0.030471 | PPARG, FABP4, MMP1 | |
| Metabolism of xenobiotics by cytochrome P450 | 3 | 0.030471 | GSTM2, ADH7, UGT2B4 | |
| Chemical carcinogenesis | 3 | 0.038852 | GSTM2, ADH7, UGT2B4 | |
| cGMP-PKG signaling pathway | 4 | 0.038852 | ADRB3, MYLK2, ADRA1A, AGTR1 | |
| Pathways in cancer | 6 | 0.043731 | MMP1, FN1, MMP9, KLK3, AGTR1, PPARG | |
| Green module | Neuroactive ligand-receptor interaction | 28 | 4.01E-10 | ADRA2A, CCKBR, ADRB2, AVPR2, GRPR, P2RY6 |
| cAMP signaling pathway | 20 | 2.07E-07 | CALML5, GRIN2D, RAPGEF3, PLN, OXTR, NPR1 | |
| Regulation of lipolysis in adipocytes | 11 | 1.46E-06 | PLIN1, PLA2G16, ADRB2, NPR1, PNPLA2 | |
| Metabolic pathways | 52 | 2.04E-06 | MGLL, ALDH1A1, CKMT2, AK5, KL, AOX1 | |
| Tyrosine metabolism | 9 | 2.51E-06 | MAOA, TPO, AOC3, AOX1, PNMT | |
| Adipocytokine signaling pathway | 11 | 6.3E-06 | RXRG, CD36, LEPR, LEP, SLC2A1 | |
| Retinol metabolism | 10 | 2.37E-05 | ALDH1A1, CYP1A1, RDH5, AOX1, CYP2A6 | |
| AMPK signaling pathway | 13 | 2.92E-05 | PFKFB1, CD36E, F4EBP1, LEPR, IGF1 | |
| Drug metabolism – cytochrome P450 | 10 | 3.09E-05 | MAOA, AOX1, CYP2A6, UGT2B15, ADH1B | |
| Focal adhesion | 16 | 4.09E-05 | VEGFD, TNXB, COL2A1, VWF, CHAD | |
| Metabolism of xenobiotics by cytochrome P450 | 10 | 4.09E-05 | AKR1C1, CYP1A1, CYP2A6, ADH1B, GSTM5 | |
| PI3K-Akt signaling pathway | 21 | 4.51E-05 | VEGFD, FGF2, TNXB, COL2A1, IL6, IGF1 | |
| ECM-receptor interaction | 10 | 9.01E-05 | CHAD, TNXB, COL2A1, CD36, SDC1 | |
| Calcium signaling pathway | 14 | 0.00016 | CALML5, CCKBR, GRIN2D, PLN, OXTR, GRPR | |
| Protein digestion and absorption | 10 | 0.000167 | COL2A1, COL14A1, CPA1, COL17A1, COL4A6 | |
| Brown module | Transcriptional misregulation in cancer | 3 | 9.86E-12 | HIST1H3J, HMGA2, IBSP |
| PI3K-Akt signaling pathway | 6 | 0.040831 | IBSP, IGF2BP1, LAMA2, GNG13, ITGA7, FGF10 | |
| ECM-receptor interaction | 3 | 0.042262 | ITGA7, LAMA2, IBSP | |
| GABAergic synapse | 3 | 0.044141 | GNG13, KCNJ6, GABRA2 | |
| Morphine addiction | 3 | 0.045198 | GNG13, KCNJ6, GABRA2 |
Abbreviations: AMPK, AMP-activated protein kinase; CAM, cell adhesion molecule; ECM, extracellular matrix; GABA, gamma-aminobutyric acid; HTLV, human T-lymphotropic virus; IgA, immunoglobulin A; JAK, Janus kinase; KEGG, Kyoto Encyclopedia of Genes and Genomes; PPAR, peroxisome proliferator-activated receptors; STAT, signal transducers and activators of transcription; TNF, tumor necrosis factor.