Curation Information

Publication
ChIP-seq and transcriptome analysis of the OmpR regulon of Salmonella enterica serovars Typhi and Typhimurium reveals accessory genes implicated in host colonization.;Perkins TT, Davies MR, Klemm EJ, Rowley G, Wileman T, James K, Keane T, Maskell D, Hinton JC, Dougan G, Kingsley RA;Molecular microbiology 2013 Feb; 87(3):526-38 [23190111]
TF
OmpR [P0AA16, view regulon]
Reported TF sp.
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Reported site sp.
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Created by
Elliot White
Curation notes
-
External databases
NCBI GEO (GSE35938) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35938.

Experimental Process

Researchers used CHiP-seq to discover OmpR binding sites; binding sequences were determined from enriched sequences using the motif finding algorithm YMF. Regulation was assayed in a previous paper (19609351) with both a microarray and RNA-seq.

Transcription Factor Binding Sites


AGTTAGT
AGTTAGT
ACGGCCT
TTGTAAC
TGTAACA
AGTTAGT
AGTTAGT
ACGGCCT
TTGTAAC
TGTAACA

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
AGTTAGT mglB,
... ... mglB galS yeiB folE mglA mglC yeiA t0669
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details RNA-Seq (ECO:0005664) - activator not specified
AGTTAGT dppA,
... ... dppA t3884 t3883 t3882 t3881 t3880 yhjW
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details RNA-Seq (ECO:0005664) - activator not specified
ACGGCCT dppA,
... ... dppA t3884 t3883 t3882 t3881 t3880 yhjW
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details RNA-Seq (ECO:0005664) - activator not specified
TTGTAAC dppA,
... ... dppA t3884 t3883 t3882 t3881 t3880 yhjW
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details RNA-Seq (ECO:0005664) - activator not specified
TGTAACA dppA,
... ... dppA t3884 t3883 t3882 t3881 t3880 yhjW
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details RNA-Seq (ECO:0005664) - activator not specified