TFutils: Data structures for transcription factor bioinformatics

DNA transcription is intrinsically complex. Bioinformatic work with transcription factors (TFs) is complicated by a multiplicity of data resources and annotations. The Bioconductor package TFutils includes data structures and functions to enhance the precision and utility of integrative analyses tha...

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Autores principales: Stubbs, Benjamin J., Gopaulakrishnan, Shweta, Glass, Kimberly, Pochet, Nathalie, Everaert, Celine, Raby, Benjamin, Carey, Vincent
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2019
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6600865/
https://www.ncbi.nlm.nih.gov/pubmed/31297189
http://dx.doi.org/10.12688/f1000research.17976.2
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author Stubbs, Benjamin J.
Gopaulakrishnan, Shweta
Glass, Kimberly
Pochet, Nathalie
Everaert, Celine
Raby, Benjamin
Carey, Vincent
author_facet Stubbs, Benjamin J.
Gopaulakrishnan, Shweta
Glass, Kimberly
Pochet, Nathalie
Everaert, Celine
Raby, Benjamin
Carey, Vincent
author_sort Stubbs, Benjamin J.
collection PubMed
description DNA transcription is intrinsically complex. Bioinformatic work with transcription factors (TFs) is complicated by a multiplicity of data resources and annotations. The Bioconductor package TFutils includes data structures and functions to enhance the precision and utility of integrative analyses that have components involving TFs. TFutils provides catalogs of human TFs from three reference sources (CISBP, HOCOMOCO, and GO), a catalog of TF targets derived from MSigDb, and multiple approaches to enumerating TF binding sites, including an interface to results of 690 ENCODE experiments. Aspects of integration of TF binding patterns and genome-wide association study results are explored in examples.
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spelling pubmed-66008652019-07-10 TFutils: Data structures for transcription factor bioinformatics Stubbs, Benjamin J. Gopaulakrishnan, Shweta Glass, Kimberly Pochet, Nathalie Everaert, Celine Raby, Benjamin Carey, Vincent F1000Res Software Tool Article DNA transcription is intrinsically complex. Bioinformatic work with transcription factors (TFs) is complicated by a multiplicity of data resources and annotations. The Bioconductor package TFutils includes data structures and functions to enhance the precision and utility of integrative analyses that have components involving TFs. TFutils provides catalogs of human TFs from three reference sources (CISBP, HOCOMOCO, and GO), a catalog of TF targets derived from MSigDb, and multiple approaches to enumerating TF binding sites, including an interface to results of 690 ENCODE experiments. Aspects of integration of TF binding patterns and genome-wide association study results are explored in examples. F1000 Research Limited 2019-05-17 /pmc/articles/PMC6600865/ /pubmed/31297189 http://dx.doi.org/10.12688/f1000research.17976.2 Text en Copyright: © 2019 Stubbs BJ et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Stubbs, Benjamin J.
Gopaulakrishnan, Shweta
Glass, Kimberly
Pochet, Nathalie
Everaert, Celine
Raby, Benjamin
Carey, Vincent
TFutils: Data structures for transcription factor bioinformatics
title TFutils: Data structures for transcription factor bioinformatics
title_full TFutils: Data structures for transcription factor bioinformatics
title_fullStr TFutils: Data structures for transcription factor bioinformatics
title_full_unstemmed TFutils: Data structures for transcription factor bioinformatics
title_short TFutils: Data structures for transcription factor bioinformatics
title_sort tfutils: data structures for transcription factor bioinformatics
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6600865/
https://www.ncbi.nlm.nih.gov/pubmed/31297189
http://dx.doi.org/10.12688/f1000research.17976.2
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