TFregulomeR

TFregulomeR, an R package, provides a comprehensive toolkit for analyzing transcription factor (TF) binding sites (TFBSs) in a cell-specific context. It is connected to a regularly updated ChIP-seq and DNA methylation datasets database, enabling users to perform integrative analyses of TF binding landscapes across various cell types. The package offers functionalities to identify TF binding partners and cell-specific TFBSs and study the impact of different partnerships and DNA methylation levels on TF functions. By re-analyzing well-known TFs, TFregulomeR revealed that many leucine zipper TFBSs in current databases were incorrectly characterized due to the use of mixed homodimer and heterodimer binding sites in constructing position weight matrices. TFregulomeR facilitates a better understanding of context-specific transcriptional regulation and the role of regulatory networks in shaping TF functions.

Topic

Transcription factors and regulatory sites;Epigenomics;ChIP-seq;Methylated DNA immunoprecipitation;Gene transcripts

Detail

  • Operation: Protein super-secondary structure prediction;Peak calling;DNA-binding protein prediction;Transcription factor binding site prediction;DNA binding site prediction

  • Software interface: Command-line user interface

  • Language: R

  • License: GNU General Public License v3.0

  • Cost: Free of charge with restrictions

  • Version name: 2.1.1

  • Credit: National Research Foundation, the Singapore Ministry of Education under its Centres of Excellence initiative, National Medical Research Council of Singapore, Canada Research Chairs Program, Institut Français à Singapour, RNA Biology Center at the Cancer Science Institute of Singapore, NUS, as part of funding under the Singapore Ministry of Education's AcRF Tier 3 grants, Cancer Science Institute of Singapore Doctoral Scholarship, Ministry of Education Academic Research Fund.

  • Input: -

  • Output: -

  • Contact: Touati Benoukraf tbenoukraf@mun.ca

  • Collection: -

  • Maturity: Stable

Publications

  • TFregulomeR reveals transcription factors' context-specific features and functions.
  • Lin QXX, et al. TFregulomeR reveals transcription factors' context-specific features and functions. TFregulomeR reveals transcription factors' context-specific features and functions. 2020; 48:e10. doi: 10.1093/nar/gkz1088
  • https://doi.org/10.1093/NAR/GKZ1088
  • PMID: 31754708
  • PMC: PMC6954419

Download and documentation

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