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

BMC Bioinformatics. 2016 Feb 12;17:85. doi: 10.1186/s12859-016-0938-4.


Background: The 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.

Results: Here, 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.

Conclusion: The 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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin Immunoprecipitation / methods*
  • DNA-Directed RNA Polymerases / metabolism*
  • Epigenesis, Genetic / genetics
  • Gene Expression Regulation*
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Mice
  • MicroRNAs / genetics
  • RNA, Long Noncoding / genetics
  • Sequence Analysis, DNA / methods*
  • Software*
  • Transcription Factors / metabolism
  • Transcriptome*


  • MicroRNAs
  • RNA, Long Noncoding
  • Transcription Factors
  • DNA-Directed RNA Polymerases