Functional genomic delineation of TLR-induced transcriptional networks

BMC Genomics

Table 7 Predicted NF-κB target genes in the universal TLR response network.

Symbol	NFkB BS (location)		LPS maximum induction (log₂)				LPS	Validated
	Human	Mouse	MmBMM	MmRAW	HsM1	HsM2	kinetics	BS
CXCL10	GGGAAATTCC (-176)	GGGAAATTCC (-233)	10.42	5.47	7.98	6.9	ED	[41]
RELB	GGGGTTTTCC (-107)	GGGGTTTTCC (-96)	4.3	1.27	0.77	1.46	ED/EE*	[42]
NFKBIA	TGGAAATTCC (-84)	GGGAAACCCC (-81)	4.1	4.25	3.35	2.58	ED	[43]
NFKB2	GGGAATTCCC (-101,-73)	CGGGAATTCC (-102,-74)	3.56	3.82	1.17	1.72	ED	[44]
SDC4	N/F	GGGGAATTCC (-81)	1.53	2.78	1.01	2.02	DD/ED*	[45]
CD69	GGGAAAATCC (-222)	GGGAAAATCC (-220,-155)	8.3	1.82	0.88	3.11	ED/DD*	[46]
BIRC3	GGAAATCCCC (-177)	GGAAATCCCC (-60)	2.97	0.75	3.19	4.03	ED	[47]
MAP3K8	GGAAAACCCC (-724)	CGGAATTTCC (-490)	3.42	0.46	0.65	2.98	ED	---
BATF	N/F	GGGATTTTCC (-233)	4.51	3.07	3.31	1.04	DD	---
IRG1	N/F	TGGAAATTCC (-50)	10.8	7.69	x	x	ED	---
RIPK2	GGGGCTTTCC (-310)	GGGATTTTCC (-521)	2.51	x	x	3.23	ED	---
GCH1	CGGGCTTTCC (-11)	N/F	3.19	0.82	6.19	3.64	ED/DD**	---
TNIP1	GGGGACTTTC (-68)	N/F	3.51	-0.64	3.01	2.46	ED/DD**	---

Promoter sequences matching the PWMs of NF-κB and ISRE were identified by the PRIMA software; mapping between human and mouse orthologous genes was downloaded from the Ensembl web-site; sequences are shown on the coding strand; in cases of multiple matches, the sequence of the first listed match is shown; "N/F" means no putative BS was found. For each gene, the tables indicate (the log₂ of) its maximum fold-induction (over all time-points) in response to LPS in all four datasets, as well as its kinetic pattern (in case of conflicting patterns in different datasets, the default pattern is in MmBMM, * is in MmRAW, and ** is in HsM1). References for validated BSs are given in the last column.

ISSN: 1471-2164