title: Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators.
abstract: 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.
  
  
  CONCLUSIONS
  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 http://seqinspector.cremag.org.
authors: Department of Molecular Neuropharmacology, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-344, Poland. marpiech@if-pan.krakow.pl.
authors: Marcin
authors: M
authors: Piechota
authors: Department of Molecular Neuropharmacology, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-344, Poland.
authors: Michal
authors: M
authors: Korostynski
authors: Department of Molecular Neuropharmacology, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-344, Poland.
authors: Joanna
authors: J
authors: Ficek
authors: Department of Molecular Neuropharmacology, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-344, Poland.
authors: Andrzej
authors: A
authors: Tomski
authors: Department of Molecular Neuropharmacology, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-344, Poland.
authors: Ryszard
authors: R
authors: Przewlocki
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D044127:Epigenesis, Genetic / Q000235:genetics; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases