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TFutils: Data structures for transcription factor bioinformatics.

ABSTRACT: 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.

SUBMITTER: Stubbs BJ

PROVIDER: S-EPMC6600865 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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TFutils: Data structures for transcription factor bioinformatics.

Stubbs Benjamin J BJ Gopaulakrishnan Shweta S Glass Kimberly K Pochet Nathalie N Everaert Celine C Raby Benjamin B Carey Vincent V

F1000Research 20190205

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 ...[more]

PMID: 31297189

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