CiiiDER: A tool for predicting and analysing transcription factor binding sites.

Autor: Gearing LJ; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.; Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia., Cumming HE; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.; Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia., Chapman R; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.; Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia., Finkel AM; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.; Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia., Woodhouse IB; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.; Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia., Luu K; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.; Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia., Gould JA; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.; Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia., Forster SC; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.; Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia., Hertzog PJ; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.; Department of Molecular Translational Science, Monash University, Clayton, Victoria, Australia.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2019 Sep 04; Vol. 14 (9), pp. e0215495. Date of Electronic Publication: 2019 Sep 04 (Print Publication: 2019).
DOI: 10.1371/journal.pone.0215495
Abstrakt: The availability of large amounts of high-throughput genomic, transcriptomic and epigenomic data has provided opportunity to understand regulation of the cellular transcriptome with an unprecedented level of detail. As a result, research has advanced from identifying gene expression patterns associated with particular conditions to elucidating signalling pathways that regulate expression. There are over 1,000 transcription factors (TFs) in vertebrates that play a role in this regulation. Determining which of these are likely to be controlling a set of genes can be assisted by computational prediction, utilising experimentally verified binding site motifs. Here we present CiiiDER, an integrated computational toolkit for transcription factor binding analysis, written in the Java programming language, to make it independent of computer operating system. It is operated through an intuitive graphical user interface with interactive, high-quality visual outputs, making it accessible to all researchers. CiiiDER predicts transcription factor binding sites (TFBSs) across regulatory regions of interest, such as promoters and enhancers derived from any species. It can perform an enrichment analysis to identify TFs that are significantly over- or under-represented in comparison to a bespoke background set and thereby elucidate pathways regulating sets of genes of pathophysiological importance.
Competing Interests: The authors have declared that no competing interests exist.
Databáze: MEDLINE
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