Table 3.
Gene modules regulated by YY1, RFX2, and IRF1 motifs.
| Motif | Module No. | # of genes in the Module | Enriched GO/Pathway | GO/Pathway Enrichment pValue | Selected Genes with the enriched GO term |
|---|---|---|---|---|---|
| YY1 | 1 | 47 | cellular respiration | 1.97E-28 | SDHB/NDUFS4/NDUFS3 |
| YY1 | 4 | 31 | mitotic cell cycle | 5.62E-14 | RRM1/NDC80/RACGAP1 |
| YY1 | 7 | 27 | RNA processing | 2.41E-10 | RBM8A/RBM4/CNOT3 |
| YY1 | 10 | 25 | translational elongation | 3.34E-27 | RPSA/RPS3/RPL13A |
| YY1 | 12 | 22 | fatty acid beta-oxidation | 1.13E-06 | HADHA/ACADVL/HADHB |
| YY1 | 17 | 17 | ribosome biogenesis | 3.81E-06 | NOLC1/NIP7/CIRH1A |
| YY1 | 18 | 17 | histone modification | 2.60E-11 | EP300/CREBBP/CTCF |
| YY1 | 37 | 11 | RNA metabolic process | 5.15E-06 | PER1/POLR2A/PHF8 |
| YY1 | 42 | 10 | RNA splicing | 6.86E-11 | TARDBP/SRSF1/DDX39 |
| YY1 | 43 | 10 | type I interferon signaling pathway | 8.29E-06 | IRF1/ADAR/XAF1 |
| YY1 | 46 | 9 | regulation of mRNA processing | 4.14E-06 | CWC22/IWS1/CCDC55 |
| RFX2 | 1 | 73 | cilium morphogenesis | 9.10E-10 | ZMYND10/FOXJ1/AK7 |
| RFX2 | 2 | 48 | cilium assembly | 4.00E-19 | AHI1/CBY1/BBS1 |
| RFX2 | 4 | 20 | protein folding | 1.03E-11 | HSP90AA1/HSP90B1/HSPA1L |
| RFX2 | 5 | 14 | microtubule-based movement | 1.32E-06 | KIF14/KIF23/KIF18A |
| RFX2 | 10 | 12 | respiratory electron transport chain | 4.77E-09 | NDUFS3/CYC1/NDUFA5 |
| RFX2 | 21 | 8 | synaptic transmission | 5.03E-08 | CAMK2A/KCNIP2/SLC17A7 |
| RFX2 | 33 | 6 | regulation of striated muscle cell differentiation | 1.13E-06 | AKAP6/SMYD1/KBTBD10 |
| RFX2 | 42 | 5 | mitotic cell cycle | 5.34E-07 | PRKDC/MCM7/CENPH |
| IRF1 | 1 | 79 | Interferon alpha/beta signaling | 2.92E-30 | STAT1/MX1/ADAR |
| IRF1 | 2 | 60 | antigen processing and presentation of peptide antigen via MHC class I | 3.98E-23 | HLA-B/HLA-A/HLA-C |
| IRF1 | 3 | 35 | Interferon gamma signaling | 9.26E-07 | JAK2/CXCL10/IL12RB1 |
| IRF1 | 4 | 34 | response to virus | 3.44E-09 | CCL5/IFNB1/IL12A |
| IRF1 | 5 | 33 | synaptic transmission | 1.00E-06 | HTR2C/SNAP25/GABRG2 |
| IRF1 | 6 | 33 | hair follicle development | 8.11E-06 | NGFR/TFAP2C/SOSTDC1 |
| IRF1 | 7 | 31 | leukocyte activation | 3.80E-10 | TLR1/ICOS/CD247 |
| IRF1 | 12 | 12 | IFN alpha signaling | 3.12E-27 | IFNA17/IFNA5/IFNW1 |
| IRF1 | 13 | 10 | NOD-like receptor signaling pathway | 6.88E-06 | TLR2/NOD2/CASP1 |
| IRF1 | 18 | 7 | regulation of transposition | 4.35E-13 | APOBEC3G/APOBEC3F/APOBEC3C |
| IRF1 | 20 | 6 | neuronal action potential | 3.00E-06 | PLP1/ASPA/SCN7A |