Table 1. Functional modules recapitulate known transcription factor biology.
| Rank | Transcription Factor (name) | Functional Module ID | Number of genes in module bound by TF | Number of genes in module | Odds Ratio | Adjusted P Value |
| 1 | SREBP2 (Sterol regulatory element-binding protein) | 158 | 30 | 119 | 45.2 | 1E-31 |
| Module Enriched GO Terms (P<0.05) | ||||||
| lipid biosynthetic process, sterol biosynthetic process, sterol metabolic process, cholesterol metabolic process, steroid biosynthetic process, cholesterol biosynthetic process, steroid metabolic process, isoprenoid biosynthetic process, isoprenoid metabolic process, oxidation reduction, endoplasmic reticulum, endoplasmic reticulum membrane, nuclear envelope-endoplasmic reticulum network, endoplasmic reticulum part, organelle membrane, endomembrane system, microbody, peroxisome | ||||||
| Module Enriched KEGG Pathways (P<0.05) | ||||||
| Steroid biosynthesis, Terpenoid backbone biosynthesis | ||||||
| 2 | GCN5 (Histone acetyltransferase) | 104 | 8 | 69 | 33 | 5.13E-08 |
| Module Enriched GO Terms (P<0.05) | ||||||
| nucleosome assembly, chromatin assembly, protein-DNA complex assembly, nucleosome organization, DNA packaging, chromatin assembly or disassembly, cellular macromolecular complex assembly, cellular macromolecular complex subunit organization, chromatin organization, chromosome organization, macromolecular complex assembly, macromolecular complex subunit organization, nucleosome, protein-DNA complex, chromatin, chromosomal part, chromosome, intracellular non-membrane-bounded organelle, non-membrane-bounded organelle, DNA binding | ||||||
| Module Enriched KEGG Pathways (P<0.05) | ||||||
| Systemic lupus erythematosus | ||||||
| 3 | GCN5 (Histone acetyltransferase) | 62 | 13 | 183 | 20.5 | 2E-10 |
| Module Enriched GO Terms (P<0.05) | ||||||
| translational elongation, translation, cytosolic ribosome, ribosome, ribosomal subunit, cytosolic part, ribonucleoprotein complex, cytosol, cytosolic small ribosomal subunit, cytosolic large ribosomal subunit, large ribosomal subunit, small ribosomal subunit, intracellular non-membrane-bounded organelle, non-membrane-bounded organelle, structural constituent of ribosome, structural molecule activity, RNA binding | ||||||
| Module Enriched KEGG Pathways (P<0.05) | ||||||
| Ribosome | ||||||
| 4 | NELFe (Negative elongation factor E) | 104 | 19 | 69 | 19.5 | 2.85E-14 |
| See annotations for #2 | ||||||
| 5 | ZNF274 (zinc finger protein 274) | 111 | 71 | 196 | 18.6 | 7.2E-50 |
| Module Enriched GO Terms (P<0.05) | ||||||
| transcription, regulation of transcription, DNA-dependent, regulation of transcription, regulation of RNA metabolic process, zinc ion binding, DNA binding, transition metal ion binding, metal ion binding, cation binding, ion binding | ||||||
| Module Enriched Interpro Terms (P<0.05) | ||||||
| Zinc finger, C2H2-type/integrase, DNA-binding, Krueppel-associated box, Zinc finger, C2H2-type, Zinc finger, C2H2-like | ||||||
| 71 | NFKB | 8 | 217 | 257 | 4.6 | 1.8E-21 |
| Module Enriched GO Terms (P<0.05) | ||||||
| cell activation, leukocyte activation, lymphocyte activation, T cell activation, leukocyte differentiation, hemopoietic or lymphoid organ development, hemopoiesis, immune system development, lymphocyte differentiation, positive regulation of lymphocyte activation, positive regulation of T cell activation, T cell differentiation | ||||||
| Various | Module significantly associated with 121 Factors | 57 | Various | 159 | Various | Various |
| Module Enriched GO Terms (P<0.05) | ||||||
| regulation of RNA metabolic process, regulation of transcription, regulation of transcription from RNA polymerase II promoter, regulation of transcription, DNA-dependent, transcription, DNA binding, sequence-specific DNA binding, transcription factor activity, transcription regulator activity | ||||||
Top 5 TF-module associations, as well as NFκB and a general transcription module (associated with 141 different TFs) are shown.