CRUP

CRUP (Condition-specific Regulatory Units Prediction) is a software tool designed to identify regulatory units, which consist of dynamically changing enhancers and their target genes, using epigenetic data. The main features of CRUP are:

1. Novel pre-trained enhancer predictor: CRUP includes a new enhancer predictor that can be applied across various cell types and species, using only histone modification ChIP-seq data.

2. Condition-specific enhancer assignment: The software assigns enhancers to different conditions based on the epigenetic data.

3. Enhancer-gene correlation: CRUP correlates the condition-specific enhancers with gene expression data to identify regulatory units.

4. Thorough testing and application: The tool has been extensively tested and applied to a rheumatoid arthritis model, successfully identifying enhancer-gene pairs that include known disease genes and novel candidate genes.

Topic

Epigenetics;ChIP-seq;Gene regulation;Transcription factors and regulatory sites;Pathology

Detail

  • Operation: Pathway or network prediction;Expression correlation analysis;Transcriptional regulatory element prediction

  • Software interface: Command-line interface

  • Language: R

  • License: Not stated

  • Cost: Free of charge

  • Version name: 1.0

  • Credit: Bundesministerium für Bildung und Forschung.

  • Input: -

  • Output: -

  • Contact: Martin Vingron vingron@molgen.mpg.de

  • Collection: -

  • Maturity: -

Publications

  • CRUP: a comprehensive framework to predict condition-specific regulatory units.
  • Ramisch A, et al. CRUP: a comprehensive framework to predict condition-specific regulatory units. CRUP: a comprehensive framework to predict condition-specific regulatory units. 2019; 20:227. doi: 10.1186/s13059-019-1860-7
  • https://doi.org/10.1186/S13059-019-1860-7
  • PMID: 31699133
  • PMC: PMC6839171

Download and documentation

< Back to DB search