CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria

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dc.contributor.authorKılıç, Sefa
dc.contributor.authorWhite, Elliot R.
dc.contributor.authorSagitova, Dinara M.
dc.contributor.authorCornish, Joseph P.
dc.contributor.authorErill, Ivan
dc.date.accessioned2021-03-08T19:32:33Z
dc.date.available2021-03-08T19:32:33Z
dc.date.issued2013-11-14
dc.description.abstractThe influx of high-throughput data and the need for complex models to describe the interaction of prokaryotic transcription factors (TF) with their target sites pose new challenges for TF-binding site databases. CollecTF (http://collectf.umbc.edu) compiles data on experimentally validated, naturally occurring TF-binding sites across the Bacteria domain, placing a strong emphasis on the transparency of the curation process, the quality and availability of the stored data and fully customizable access to its records. CollecTF integrates multiple sources of data automatically and openly, allowing users to dynamically redefine binding motifs and their experimental support base. Data quality and currency are fostered in CollecTF by adopting a sustainable model that encourages direct author submissions in combination with in-house validation and curation of published literature. CollecTF entries are periodically submitted to NCBI for integration into RefSeq complete genome records as link-out features, maximizing the visibility of the data and enriching the annotation of RefSeq files with regulatory information. Seeking to facilitate comparative genomics and machine-learning analyses of regulatory interactions, in its initial release CollecTF provides domain-wide coverage of two TF families (LexA and Fur), as well as extensive representation for a clinically important bacterial family, the Vibrionaceae.en_US
dc.description.sponsorshipThe authors are indebted to Dr Stacy Ciufo and Dr Tatiana Tatusova from the National Center for Biotechnology Information RefSeq team, for their kind assistance in setting up and coordinating an automated submission system to integrate CollecTF data into RefSeq records. The authors would like to thank Patrick K. O’Neill, Chad Elkins, Zachary Margulies and Kathryn Cronise for significant contributions, and all other CollecTF curators for their dedicated work. The US National Sciences Foundation [MCB-1158056]; The UMBC Office of Research through a Special Research Assistantship/Initiative Support (SRAIS) award. Funding for open access charge: US National Sciences Foundation [MCB-1158056].en_US
dc.description.urihttps://academic.oup.com/nar/article/42/D1/D156/1051934en_US
dc.format.extent5 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/m2rz6m-zg8i
dc.identifier.citationSefa Kılıç, Elliot R. White, Dinara M. Sagitova, Joseph P. Cornish, Ivan Erill, CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria, Nucleic Acids Research, Volume 42, Issue D1, 1 January 2014, Pages D156–D160, https://doi.org/10.1093/nar/gkt1123en_US
dc.identifier.urihttps://doi.org/10.1093/nar/gkt1123
dc.identifier.urihttp://hdl.handle.net/11603/21100
dc.language.isoen_USen_US
dc.publisherOxford Academicen_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Biological Sciences Department Collection
dc.relation.ispartofUMBC Faculty Collection
dc.relation.ispartofUMBC Student Collection
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.
dc.rightsAttribution 3.0 Unported*
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/*
dc.titleCollecTF: a database of experimentally validated transcription factor-binding sites in Bacteriaen_US
dc.typeTexten_US

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