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

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.

 Workflow diagram

rna-seq

Availability – The recipe providing all the detailed steps and corresponding videos associated with this process is accessible at: http://recipes.genomespace.org/view/69.

Carlin D, Kosnicki K, Garamszegi S, Ideker T, Thorvaldsdóttir H, Reich M, Mesirov J. (2018) A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res 6:784. [article].

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