The Library
Extracting regulator activity profiles by integration of de novo motifs and expression data : characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor
Tools
Iqbal, Mudassar, Mast, Yvonne, Amin, Rafat, Hodgson, D. A., Wohlleben, W. and Burroughs, Nigel John (2012) Extracting regulator activity profiles by integration of de novo motifs and expression data : characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor. Nucleic Acids Research, Vol.40 (No.12). pp. 5227-5239. doi:10.1093/nar/gks205 ISSN 0305-1048.
|
Text
WRAP_Burroughs_Nucl. Acids Res.-2012-Iqbal-nar_gks205.pdf - Published Version Download (1534Kb) | Preview |
Official URL: http://dx.doi.org/10.1093/nar/gks205
Abstract
Determining transcriptional regulator activities is a major focus of systems biology, providing key insight into regulatory mechanisms and co-regulators. For organisms such as Escherichia coli, transcriptional regulator binding site data can be integrated with expression data to infer transcriptional regulator activities. However, for most organisms there is only sparse data on their transcriptional regulators, while their associated binding motifs are largely unknown. Here, we address the challenge of inferring activities of unknown regulators by generating de novo (binding) motifs and integrating with expression data. We identify a number of key regulators active in the metabolic switch, including PhoP with its associated directed repeat PHO box, candidate motifs for two SARPs, a CRP family regulator, an iron response regulator and that for LexA. Experimental validation for some of our predictions was obtained using gel-shift assays. Our analysis is applicable to any organism for which there is a reasonable amount of complementary expression data and for which motifs (either over represented or evolutionary conserved) can be identified in the genome.
Item Type: | Journal Article | ||||
---|---|---|---|---|---|
Subjects: | Q Science > QH Natural history > QH426 Genetics | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Research Centres > Warwick Systems Biology Centre |
||||
Library of Congress Subject Headings (LCSH): | Genetic transcription -- Regulation, Gene expression, Streptomyces coelicolor -- Genetics | ||||
Journal or Publication Title: | Nucleic Acids Research | ||||
Publisher: | Oxford University Press | ||||
ISSN: | 0305-1048 | ||||
Official Date: | 2012 | ||||
Dates: |
|
||||
Volume: | Vol.40 | ||||
Number: | No.12 | ||||
Page Range: | pp. 5227-5239 | ||||
DOI: | 10.1093/nar/gks205 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Open Access (Creative Commons) | ||||
Date of first compliant deposit: | 22 December 2015 | ||||
Date of first compliant Open Access: | 22 December 2015 | ||||
Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Pakistan. Higher Education Commission, Dow University of Health Sciences, Sixth Framework Programme (European Commission) (FP6) | ||||
Grant number: | BB/FF003498/1 (BBSRC), 0315931 (FP6) |
Request changes or add full text files to a record
Repository staff actions (login required)
View Item |
Downloads
Downloads per month over past year