Towards a unified resource for transcriptional regulation inEscherichia coliK-12: Incorporating high throughput-generated binding data within the classic framework of regulation of initiation of transcription in RegulonDB
| Autor: | David A. Velázquez-Ramírez, Socorro Gama-Castro, Mishael Sánchez-Pérez, Steve Busby, Xin Fang, Bernhard O. Palsson, Heladia Salgado, Alberto Santos-Zavaleta, Víctor H. Tierrafría, Julio Collado-Vides, James E. Galagan |
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| Rok vydání: | 2017 |
| Předmět: |
Regulation of gene expression
0303 health sciences 030306 microbiology Systems biology Computational biology Biology computer.software_genre medicine.disease_cause Genome 03 medical and health sciences Transcription (biology) Controlled vocabulary Transcriptional regulation medicine Data mining Transcription factor computer Escherichia coli 030304 developmental biology |
| Popis: | Our understanding of the regulation of gene expression has been strongly benefited by the availability of high throughput technologies that enable questioning the whole genome for the binding of specific transcription factors and expression profiles. In the case of genome models, such asEscherichia coliK-12, this knowledge needs to be integrated with the legacy of accumulated genetics and molecular biology pre-genomic knowledge in order to attain deeper levels in the understanding of their biology. In spite of the several repositories and curated databases, there is no effort, nor electronic site yet, to comprehensively integrate the available knowledge from all these different sources around the regulation of gene expression ofE. coliK-12. In this paper, we describe a first effort to expand RegulonDB, the database containing the rich legacy of decades of classic molecular biology experiments supporting what we know about gene regulation and operon organization inE. coliK-12, to include the genome-wide data set collections from 25 ChIP and 18 gSELEX publications, respectively, in addition to around 60 expression profiles used in their curation. Three essential features for the integration of this information coming from different methodological approaches are; first, a controlled vocabulary within an ontology for precisely defining growth conditions, second, the criteria to separate elements with enough evidence to consider them involved in gene regulation from isolated sites, and third, an expanded computational model supporting this knowledge. Altogether, this constitutes the basis for adequately gathering and enabling the comparisons and integration strongly needed to manage and access such wealth of knowledge. This version of RegulonBD is a first step toward what should become the unifying access point for current and future knowledge on gene regulation inE. coliK-12. Furthermore, this model platform and associated methodologies and criteria, can well be emulated for gathering knowledge on other microbial organisms. |
| Databáze: | OpenAIRE |
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