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RegulonDB 11.0: comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12

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dc.contributor.author Tierrafría, Víctor H.
dc.contributor.author Collado Vides, Pedro Julio
dc.date.accessioned 2022-06-21T09:38:55Z
dc.date.available 2022-06-21T09:38:55Z
dc.date.issued 2022
dc.identifier.citation Tierrafría VH, Rioualen C, Salgado H, Lara P, Gama-Castro S, Lally P, Gómez-Romero L et al. RegulonDB 11.0: comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12. Microb Genom. 2022 May;8(5). DOI:10.1099/mgen.0.000833
dc.identifier.issn 2057-5858
dc.identifier.uri http://hdl.handle.net/10230/53556
dc.description.abstract Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. However, accessing and navigating such a wealth of data is not straightforward. No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. RegulonDB (https://regulondb.ccg.unam.mx) began gathering high-throughput dataset collections in 2009, starting with transcription start sites, then adding ChIP-seq and gSELEX in 2012, with up to 99 different experimental high-throughput datasets available in 2019. In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. For ChIP-seq experiments we offer both the data as presented by the authors, as well as data uniformly processed in-house, enhancing their comparability, as well as the traceability of the methods and reproducibility of the results. Furthermore, we have expanded the tools available for browsing and visualization across and within datasets. We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. We provide summaries with the total number of interactions found in each experiment, as well as tools to identify common results among different experiments. This is a long-awaited resource to make use of such wealth of knowledge and advance our understanding of the biology of the model bacterium E. coli K-12.
dc.description.sponsorship We acknowledge funding from Universidad Nacional Autónoma de México (UNAM), as well as funding by NIGMS-NIH grant number 5RO1GM131643, and by UNAM-PAPIIT IA203420. CR is a doctoral student from the Programa de Doctorado en Ciencias Biomédicas, UNAM, and has received fellowship 929687 from CONACyT. PL acknowledges a postdoctoral fellow-ship from DGAPA-UNAM. EGN thanks DGAPA-UNAM for the scholarships 181821, 369220
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Microbiology Society
dc.rights © 2022 Víctor H. Tierrafría et al. This is an open-access article distributed under the terms of a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/deed.ast)
dc.rights.uri https://creativecommons.org/licenses/by/4.0/deed.ast
dc.subject.other Genòmica
dc.subject.other Regulació genètica
dc.subject.other Escheríchia coli
dc.subject.other Conjunts de dades
dc.title RegulonDB 11.0: comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1099/mgen.0.000833
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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