ArticleEvolutionary bioinformatics online2012
Inference of self-regulated transcriptional networks by comparative genomics.
Article in Evolutionary bioinformatics online, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 9 citations in OpenAlex.
- Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes.Nucleic acids research · 2021Article
- Flexible comparative genomics of prokaryotic transcriptional regulatory networks.BMC genomics · 2020Article
- Assessment of transfer methods for comparative genomics of regulatory networks in bacteria.BMC bioinformatics · 2016Article
- The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response.Frontiers in molecular biosciences · 2016Article
- An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria.Journal of bacteriology · 2015Article
- Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton.BMC genomics · 2014Article
- Characterization of the SOS meta-regulon in the human gut microbiome.Bioinformatics (Oxford, England) · 2014Article
- The LexA regulated genes of the Clostridium difficile.BMC microbiology · 2014Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The assumption of basic properties, like self-regulation, in simple transcriptional regulatory networks can be exploited to infer regulatory motifs from the growing amounts of genomic and meta-genomic data. These motifs can in principle be used to elucidate the nature and scope of transcriptional networks through comparative genomics. Here we assess the feasibility of this approach using the SOS regulatory network of Gram-positive bacteria as a test case. Using experimentally validated data, we show that the known regulatory motif can be inferred through the assumption of self-regulation. Furthermore, the inferred motif provides a more robust search pattern for comparative genomics than the experimental motifs defined in reference organisms. We take advantage of this robustness to generate a functional map of the SOS response in Gram-positive bacteria. Our results reveal definite differences in the composition of the LexA regulon between Firmicutes and Actinobacteria, and confirm that regulation of cell-division inhibition is a widespread characteristic of this network among Gram-positive bacteria.
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