A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression

F1000Research
Daniel CarlinJill Mesirov

Abstract

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 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 identifying protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from an 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.

Software Mentioned

Gene Pattern
Filter subtool
MACS2
EdgeR
Bigwig
GenomeSpace
Integrative Genomics Viewer ( IGV )
Galaxy
bedGraph
IGV

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