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

BMC Bioinformatics

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

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]

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”
The boldface ones are the main node in Fig. 5

ISSN: 1471-2105