Cistrome: An Integrative Platform for Transcriptional Regulation Studies

Genome Biol. 2011 Aug 22;12(8):R83. doi: 10.1186/gb-2011-12-8-r83.

Abstract

The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms. We developed a web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. Cistrome is available at http://cistrome.org/ap/.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin Immunoprecipitation / methods*
  • Computational Biology / methods
  • Databases, Genetic
  • Gene Expression Regulation*
  • Humans
  • Internet
  • Oligonucleotide Array Sequence Analysis / methods
  • Software*
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism

Substances

  • Transcription Factors