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 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.

References

Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
Apr 28, 2006·Nature Genetics·Michael ReichJill P Mesirov
Jun 2, 2007·Science·David S JohnsonBarbara Wold
May 3, 2008·Science·Ugrappa NagalakshmiMichael Snyder
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Apr 21, 2012·Briefings in Bioinformatics·Helga ThorvaldsdóttirJill P Mesirov
Sep 1, 2012·Nature Protocols·Jianxing FengXiaole Shirley Liu
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva
Dec 12, 2012·Nature Biotechnology·Cole TrapnellLior Pachter
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders

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Datasets Mentioned

BETA
GSE63282

Methods Mentioned

BETA
ChIP-Seq
RNA-seq

Software Mentioned

IGV
Filter subtool
MACS2
bedGraph
GenePattern
MACS2 callpeak
Integrative Genomics Viewer ( IGV )
Gene Pattern
EdgeR
GenomeSpace

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