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Inference of Self-Regulated Transcriptional Networks by Comparative Genomics
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 ne...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Libertas Academica
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422134/ https://www.ncbi.nlm.nih.gov/pubmed/23032607 http://dx.doi.org/10.4137/EBO.S9205 |
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author | Cornish, Joseph P. Matthews, Fialelei Thomas, Julien R. Erill, Ivan |
author_facet | Cornish, Joseph P. Matthews, Fialelei Thomas, Julien R. Erill, Ivan |
author_sort | Cornish, Joseph P. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3422134 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Libertas Academica |
record_format | MEDLINE/PubMed |
spelling | pubmed-34221342012-10-02 Inference of Self-Regulated Transcriptional Networks by Comparative Genomics Cornish, Joseph P. Matthews, Fialelei Thomas, Julien R. Erill, Ivan Evol Bioinform Online Original Research 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. Libertas Academica 2012-08-06 /pmc/articles/PMC3422134/ /pubmed/23032607 http://dx.doi.org/10.4137/EBO.S9205 Text en © the author(s), publisher and licensee Libertas Academica Ltd. This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. |
spellingShingle | Original Research Cornish, Joseph P. Matthews, Fialelei Thomas, Julien R. Erill, Ivan Inference of Self-Regulated Transcriptional Networks by Comparative Genomics |
title | Inference of Self-Regulated Transcriptional Networks by Comparative Genomics |
title_full | Inference of Self-Regulated Transcriptional Networks by Comparative Genomics |
title_fullStr | Inference of Self-Regulated Transcriptional Networks by Comparative Genomics |
title_full_unstemmed | Inference of Self-Regulated Transcriptional Networks by Comparative Genomics |
title_short | Inference of Self-Regulated Transcriptional Networks by Comparative Genomics |
title_sort | inference of self-regulated transcriptional networks by comparative genomics |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422134/ https://www.ncbi.nlm.nih.gov/pubmed/23032607 http://dx.doi.org/10.4137/EBO.S9205 |
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