ChIPanalyser

"ChIPanalyser" is an R package designed to predict and model the binding of transcription factors (TFs) to DNA. This user-friendly tool is versatile and powerful, providing insights into TF binding mechanisms. The software has been evaluated on three Drosophila cell lines, focusing on TFs CTCF, BEAF-32, and su(Hw). The analysis reveals diverse binding mechanisms, with CTCF binding preferentially to high-affinity sites in open chromatin, BEAF-32 binding to most high-affinity sites in open chromatin, and su(Hw) binding to open and partially closed chromatin. The tool highlights the impact of DNA accessibility on TF binding profiles across cell lines. Additionally, the software is applied to investigate the binding of Hox TFs in Drosophila, revealing distinct binding behaviors for Ubx, Abd-B, and Dfd. The model provides an explainable approach to understanding TF-DNA interactions.

Topic

ChIP-seq;ChIP-on-chip;Sequencing;Gene expression

Detail

  • Operation: Alignment

  • Software interface: Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.24.0

  • Credit: University of Essex and by the Wellcome Trust.

  • Input: -

  • Output: -

  • Contact: Patrick C.N. Martin pcnmartin@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.
  • Martin PCN and Zabet NR. Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. 2020; 18:3590-3605. doi: 10.1016/j.csbj.2020.11.006
  • https://doi.org/10.1016/J.CSBJ.2020.11.006
  • PMID: 33304457
  • PMC: PMC7708957

Download and documentation

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