Cis-Cardio: A comprehensive analysis platform for cardiovascular-relavant cis-regulation in human and mouse

Abstract

Cis-regulatory elements are important molecular switches in controlling gene expression and are regarded as determinant hubs in the transcriptional regulatory network. Collection and processing of large-scale cis-regulatory data are urgent to decipher the potential mechanisms of cardiovascular diseases from a cis-regulatory element aspect. Here, we developed a novel web server, Cis-Cardio, which aims to document a large number of available cardiovascular-related cis-regulatory data and to provide analysis for unveiling the comprehensive mechanisms at a cis-regulation level. The current version of Cis-Cardio catalogs a total of 45,382,361 genomic regions from 1,013 human and mouse epigenetic datasets, including ATAC-seq, DNase-seq, Histone ChIP-seq, TF/TcoF ChIP-seq, RNA polymerase ChIP-seq, and Cohesin ChIP-seq. Importantly, Cis-Cardio provides six analysis tools, including region overlap analysis,element upstream/downstream analysis, transcription regulator enrichment analysis, variant interpretation, andprotein-protein interaction-based co-regulatory analysis. Additionally, Cis-Cardio provides detailed and abundant (epi-) genetic annotations in cis-regulatory regions, such as super-enhancers, enhancers, transcription factor binding sites (TFBSs), methylation sites, common SNPs, risk SNPs, expression quantitative trait loci (eQTLs), motifs,DNase I hypersensitive sites (DHSs), and 3D chromatin interactions. In summary, Cis-Cardio is a valuable resourcefor elucidating and analyzing regulatory cues of cardiovascular-specific cis-regulatory elements. The platform is freely available at http://www.licpathway.net/Cis-Cardio/index.html.