Skip to main content

Table 1 TFs showing significant changes in interaction strength between wild-type and knock-out mice

From: TIGERi: modeling and visualizing the responses to perturbation of a transcription factor network

Trans name TF group Cis name Regul-ation type GO analy-sis Known biological functions Ref.
OLF1 1.Dev EBF1 Down Imm NF-κB → EBF1 → B-cell development [52]
GATA-X 1. Dev GATA1 ~6 Down - p38 → HSp27 → GATA1 → Differentiation
GATA1 → IL9 → Asthma
[53, 54]
HNF3 1. Dev FOXM1 Down - p38 → FOXM1 → Apoptosis [45]
RSRFC4 5. Res MEF2 Down Apo, Dev Imm p38 → MEF2 → Development
→ Differentiation
[46, 55]
NF-κB 6. Lat NF-κB Down Imm p38 → NF-κB → IFNγ → STAT1 → Development
→ ZEB1 → Immune
[56,57,58]
SOX9 7. Unk SOX9 Down Apop, Dev p38 → SOX9 → Apoptosis [59,60,61,62]
PITX2 1. Dev PITX2 Up Apo p38 → PITX2 → Development → Apoptosis [63, 64]
HFH4 1. Dev FOXJ1 Up - FOXJ1 NF-κB [65]
FXR 3. Ste FXR Up Apo, Dev p38 → FXR → Apoptosis [66, 67]
AP1 5. Res c-JUN Up - p38 ─JNK → c-JUN → Proliferation → Apoptosis [37]
MYC 5. Res MYC Up Apo, Dev p38 ─MYC → Apoptosis [68]
  1. The TFs predicted to have significantly different behaviors between the wild-type and knock-out mice. “Trans Name”—the official gene symbol of the TF. “Cis Name”—the name given to the binding site of the TF. TFs were characterized into different functional groupings (see Fig. 3c for details: Dev—cell-type specific developmental TFs, Res—signal dependent resident nuclear factors, Lat—signal dependent latent cytoplasmic factors, Ste—signal dependent steroid receptor group, Unk—unknown). “Regulation Type”, the way in which the TF regulates its target genes in the absence of p38α. “GO Analysis”, provides more functional classification for the identified TFs (see Methods and Additional file 1: Figure S1 to S3 for details). The abbreviations of the GO terms are: Apo, Apoptosis; Dev, Developmental Process; Imm, Immune System Development. “Known Biological Functions” summarizes the findings from the recent biological literature as shown in the “References”
  2. The boldface ones are the main node in Fig. 5