C4S DB: Comprehensive Collection and Comparison for ChIP-Seq Database

Abstract

Combining multiple binding profiles, such as transcription factors and histone modifications, is a crucial step in revealing the functions of complex biological systems. Although a massive amount of chromatin immunoprecipitation followed by sequencing (ChIP-seq) data is available, existing ChIP-seq databases or repositories focus on individual experiments, and it is difficult to elucidate orchestrated regulation by DNA-binding elements. We developed the Comprehensive Collection and Comparison for ChIP-Seq Database (C4S DB) to provide researchers with insights into the combination of DNA binding elements based on quality-assessed public ChIP-seq data. The C4S DB is based on >16,000 human ChIP-seq experiments and provides two main web interfaces to discover the relationships between ChIP-seq data. "Gene browser" illustrates the landscape of distributions of binding elements around a specified gene, and "global similarity," a hierarchical clustering heatmap based on a similarity between two ChIP-seq experiments, gives an overview of genome-wide relations of regulatory elements. These functions promote the identification or evaluation of both gene-specific and genome-wide colocalization or mutually exclusive localization. Modern web technologies allow users to search for and aggregate large-scale experimental data through interactive web interfaces with quick responses. The C4S DB is available at https://c4s.site.

Keywords: DNA-binding proteins; histone modifications; quality control; transcription factors; transcriptional regulation.