Table 4 Complete target gene-based annotations for two example transcription factors (TFs) (A) NFKB1 and (B) SUZ12. Three types of information are provided (1) the top TF neighbors obtained by TF distance (target-gene overlap measured by Pearson’s phi coefficient) < 0.8, (2) the target functions in six categories, and (3) the functional diversities in six categories and total diversity. See Additional file 1: Figure S9 for a visualization of the regulator and target function networks surrounding NFKB1
From: Systematic target function annotation of human transcription factors
A | ||
Annotation of NFKB1 | Similar TFs: REL, BCL11A | |
| Â | Significant target functions (log 10 P value) | Functional diversity |
GWAS phenotype | Arthritis, rheumatoid (8.4) Psoriasis (6.95) Colitis, ulcerative (6.29) | 2.0 |
Mendelian disease | Disease of cellular proliferation (7) Organ system cancer (6.84) Cancer (6.64) + 10 more | 2.5 |
PD/PK pathway | EGFR inhibitor pathway (PD) (6.13) Doxorubicin pathway (cancer cell) (PD) (5.47) | 1.2 |
Signaling/metabolic pathway | Immune system (17.11) Cytokine signaling in immune system (14.62) Interferon gamma signaling (10.89) + 46 more | 13.2 |
Biological process (GO) | Adaptive immune response (5.86) Regulation of protein metabolic process (5.81) Regulation of cytokine production (5.72) + 71 more | 10.2 |
Molecular function (GO) | Cytokine activity (14.33) Receptor binding (8.3) Chemokine activity (7.22) + 4 more | 3.2 |
| Â | Total Diversity: | 23.7 |
B | ||
Annotation of SUZ12 | Similar TFs: CTBP2 | |
| Â | Significant Target Functions (log 10 P value) | Functional diversity |
GWAS phenotype | – | 0 |
Mendelian disease | Heart septal defect (8.13) Congenital heart disease (7.57) Disease (7.14) + 6 more | 1.8 |
PD/PK pathway | – | 0 |
Signaling/metabolic pathway | Regulation of beta cell development (12.19) Regulation of gene expression in beta cells (6.26) Class b 2 secretin family receptors (4.08) | 1.2 |
Biological process (GO) | Anatomical structure development (40.03) Multicellular organismal development (33.22) System development (32.56) + 29 more | 5.8 |
Molecular function (GO) | Transcription factor activity (36.68) DNA binding (33.55) RNA polymerase II transcription factor activity (11.83) + 1 more | 2.2 |
| Â | Total Diversity: | 8.3 |