ArticleNucleic acids research2012
Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- LexA, an SOS response repressor, activates TGase synthesis inFrontiers in microbiology · 2024Article
- Small molecule inducers of actinobacteria natural product biosynthesis.Journal of industrial microbiology & biotechnology · 2023Review
- A Regulator Based "Semi-Targeted" Approach to Activate Silent Biosynthetic Gene Clusters.International journal of molecular sciences · 2021Article
- Disclosing the Potential of the SARP-Type Regulator PapR2 for the Activation of Antibiotic Gene Clusters in Streptomycetes.Frontiers in microbiology · 2020Article
- Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator.Frontiers in microbiology · 2020Article
- LmbU, a Cluster-Situated Regulator for Lincomycin, Consists of a DNA-Binding Domain, an Auto-Inhibitory Domain, and Forms Homodimer.Frontiers in microbiology · 2019Article
- The metabolic switch can be activated in a recombinant strain of Streptomyces lividans by a low oxygen transfer rate in shake flasks.Microbial cell factories · 2018Article
- Efficient inference for sparse latent variable models of transcriptional regulation.Bioinformatics (Oxford, England) · 2017Article
- Antibiotics and the art of bacterial war.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities.BMC genomics · 2014Article
- Triggers and cues that activate antibiotic production by actinomycetes.Journal of industrial microbiology & biotechnology · 2014Review
- Molecular regulation of antibiotic biosynthesis in streptomyces.Microbiology and molecular biology reviews : MMBR · 2013Review
- Interspecies modulation of bacterial development through iron competition and siderophore piracy.Molecular microbiology · 2012Article
Corrections and comments
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Authors and funding
7 authors.
Funding
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.
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