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

From: Functional genomic delineation of TLR-induced transcriptional networks

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** ---
  1. 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.