Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators

BMC Bioinformatics

Software

Joanna Ficek¹  Andrzej Tomski¹  Ryszard Przewlocki¹  Marcin Piechota¹  Michal Korostynski¹ 

[1] Department of Molecular Neuropharmacology, Institute of Pharmacology Polish Academy of Sciences, 31-344, Krakow, Poland;

关键词: ChIP-seq;    RNA-seq;    Microarray;    Gene expression;    Promoter analysis;    Transcription factor;   

DOI  :  10.1186/s12859-016-0938-4

 received in 2015-03-25, accepted in 2016-02-05,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe regulation of gene expression in eukaryotic cells is a complex process that involves epigenetic modifications and the interaction of DNA with multiple transcription factors. This process can be studied with unprecedented sensitivity using a combination of chromatin immunoprecipitation and next-generation DNA sequencing (ChIP-seq). Available ChIP-seq data can be further utilized to interpret new gene expression profiling experiments.ResultsHere, we describe seqinspector, a tool that accepts any set of genomic coordinates from ChIP-seq or RNA-seq studies to identify shared transcriptional regulators. The presented web resource includes a large collection of publicly available ChIP-seq and RNA-seq experiments (>1300 tracks) performed on transcription factors, histone modifications, RNA polymerases, enhancers and insulators in humans and mice. Over-representation is calculated based on the coverage computed directly from indexed files storing ChIP-seq data (bigwig). Therefore, seqinspector is not limited to pre-computed sets of gene promoters.ConclusionThe tool can be used to identify common gene expression regulators for sets of co-expressed transcripts (including miRNAs, lncRNAs or any novel unannotated RNAs) or for sets of ChIP-seq peaks to identify putative protein-protein interactions or transcriptional co-factors. The tool is available at http://seqinspector.cremag.org.

【 授权许可】

CC BY   
© Piechota et al. 2016