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Updated: Mar 25, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

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

Marcin Piechota¹, Michal Korostynski², Joanna Ficek²

¹Department of Molecular Neuropharmacology, Institute of Pharmacology Polish Academy of Sciences, Krakow, 31-344, Poland. marpiech@if-pan.krakow.pl.

BMC Bioinformatics

|February 13, 2016

Summary

This summary is machine-generated.

Seqinspector is a new web tool that identifies shared transcriptional regulators using ChIP-seq and RNA-seq data. It analyzes genomic coordinates to find common gene expression regulators for various RNA types and ChIP-seq peaks.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Gene expression regulation in eukaryotes is complex, involving epigenetic modifications and transcription factors.
Chromatin immunoprecipitation and next-generation DNA sequencing (ChIP-seq) offer sensitive methods for studying gene regulation.
Existing ChIP-seq data can enhance the interpretation of new gene expression profiling experiments.

Purpose of the Study:

To introduce seqinspector, a web-based tool for identifying shared transcriptional regulators.
To provide a resource utilizing a large collection of public ChIP-seq and RNA-seq experiments.
To enable the analysis of genomic coordinates from various sequencing studies.

Main Methods:

Seqinspector accepts genomic coordinates from ChIP-seq or RNA-seq studies.
It utilizes a database of over 1300 public ChIP-seq and RNA-seq tracks from human and mouse.
Over-representation analysis is performed using coverage computed directly from indexed bigwig files.

Main Results:

The tool identifies shared transcriptional regulators from user-provided genomic coordinates.
It is not restricted to pre-computed gene promoter sets, offering broader applicability.
The resource contains data on transcription factors, histone modifications, RNA polymerases, enhancers, and insulators.

Conclusions:

Seqinspector can identify common gene expression regulators for co-expressed transcripts, including miRNAs, lncRNAs, and novel RNAs.
It aids in identifying potential protein-protein interactions or transcriptional co-factors from ChIP-seq peak sets.
The seqinspector tool is accessible online at http://seqinspector.cremag.org.