Table 2.
The transcription factors identified by RegEnrich in interferon stimulation studies*.
| Type | Interferon | Time | Concentration | Cell type/line | Families of transcription factors | GEO accession | ||
|---|---|---|---|---|---|---|---|---|
| STAT | IRF | ETS | ||||||
| Type I | IFNa | 6 h and 12 h | 500U/ml | HT1080 | STAT1 (1), STAT2 (6), STAT5B (22) | ELF1 (14) | GSE3101966 | |
| 6 h | 500U/ml | SKOV3 | STAT1 (2), STAT2 (11) | IRF7 (5), IRF1 (13), IRF2 (18) | ETV6 (20), ELF1 (30) | GSE3101966 | ||
| 6 h | 10 U/mL | Primary Hepatocytes | STAT2 (12), STAT1 (24) | IRF7 (4), IRF9 (7), IRF1 (17), IRF6 (29) | ETV7 (1), ETV6 (27), ELK4 (28) | GSE3119367 | ||
| 24 h | 10 U/mL | Primary Hepatocytes | STAT2 (1), STAT4 (7), STAT1 (9) | IRF7 (3), IRF9 (11) | ETV7 (4), ELK4 (17) | GSE3119367 | ||
| 10 h | 1000 U/ml | Fibroblast | STAT1 (8), STAT2 (24) | IRF9 (7) | ELF1 (32) | GSE6773768 | ||
| IFNa2 | 6 h | 1000 U/ml | Keratinocyte | STAT1 (6), STAT2 (9), STAT5A (32) | IRF7 (20), IRF1 (21), IRF6 (25), IRF2 (28) | ETV7 (11), ELF1 (26) | GSE12493969 | |
| 18 h | 1000 U/ml | Primary macrophage | STAT3 (9), STAT1 (13) | IRF1 (26), IRF7 (27) | GSE3053670 | |||
| IFNa2b | 2 h | 1000 U/ml | EBV-transformed B lymphoblastoid cell lines | ELF1 (2) | GSE11763771 | |||
| 2 h | 1000 U/ml | Fibroblast | IRF2 (6) | FLI1 (29) | GSE11763771 | |||
| IFNa6 | 6 h | 1000 U/ml | Keratinocyte | STAT1 (14), STAT2 (17) | IRF7 (11), IRF1 (28), IRF6 (30) | ETV7 (9), ELF1 (32) | GSE12493969 | |
| IFNb | 6 h | 1000 U/ml | Keratinocyte | STAT1 (8), STAT2 (15) | IRF1 (5), IRF7 (6), IRF2 (19), IRF6 (20) | ETV7 (1), ELF1 (18) | GSE12493969 | |
| 10 h | 1000 U/ml | Fibroblast | STAT1 (10), STAT2 (30) | IRF9 (8) | ETV7 (34), ELF1 (35) | GSE6773768 | ||
| Type II | IFNg | 6 h | 5 ng/ml | Keratinocyte | STAT3 (13), STAT1 (23), STAT2 (24) | IRF2 (1), IRF1 (5) | ETV7 (8) | GSE12493969 |
| 20 h | 10 ng/ml | Monocyte-derived macrophages | STAT1 (2), STAT2 (25) | IRF1 (1), IRF9 (31) | ETV7 (3) | GSE7907772 | ||
| 6 h | 20 ng/mL | Monocytes | STAT2 (9), STAT1 (11) | IRF1 (3), IRF9 (15), IRF7 (22) | ETV7 (1) | GSE3653773 | ||
| 18 h | 20 ng/mL | Monocytes | GSE3653773 | |||||
| 18 h | 20 ng/mL | Monocyte-derived macrophages | STAT1 (17), STAT2 (34) | IRF1 (2), IRF7 (35) | ETV7 (1) | GSE3653773 | ||
| 24 h | 20 ng/mL | keratinocytes | STAT3 (3) | IRF1 (1), IRF2 (10), IRF7 (14) | ETV7 (2) | GSE1210974 | ||
| 24 h | 100 U/ml | Peripheral blood derived macrophages | STAT3 (4) | IRF7 (3), IRF1 (8), IRF9 (26) | ETV7 (2), ELF4 (27) | GSE1188675 | ||
| 10 h | 1000 U/ml | dermal fibroblast | STAT1 (8), STAT3 (23) | IRF1 (4), IRF9 (10) | ETV7 (11) | GSE6773768 | ||
| 3 h | n.a. | Monocyte-derived macrophages | STAT2 (12), STAT6 (30) | ETS2 (5), ELK1 (24) | GSE13056776 | |||
*Three families of transcription factors were assessed for 21 datasets, where cells were stimulated by different interferons. Only TFs in STAT, IRF, and ETS family ranked in top 35 were shown in “Families of transcription factors” columns as a format of “Regulator (ranking)”. The best combination of parameters (i.e., COEN network and GSEA enrichment method) identified in Table 1 was used in the analysis.