F1000Research (Jan 2018)

A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression [version 2; referees: 2 approved]

  • Daniel Carlin,
  • Kassi Kosnicki,
  • Sara Garamszegi,
  • Trey Ideker,
  • Helga Thorvaldsdóttir,
  • Michael Reich,
  • Jill Mesirov

DOI
https://doi.org/10.12688/f1000research.11616.2
Journal volume & issue
Vol. 6

Abstract

Read online

One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor. However, until now, this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or “recipe”, and a user interface with inter-operating software tools to identify protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from a RNA-Seq experiment. By integrating RNA-Seq and ChIP-seq analyses, a user is easily able to associate differing expression phenotypes with changing epigenetic landscapes.

Keywords