About INTRARED

INTRARED is a data platform for promoting the understanding of transcriptional regulation. The platform integrates the data of cis-regulatory elements (CRE), trans-factors, and epigenomes. The data platform consists of two databases. fanta.bio is a database of CREs, which are genomic regions contributing to the regulation of gene and transcript expression on the same chromosome, with their locations and activities in various cell types and states. ChIP-Atlas is a database of trans-factors that bind to CREs, and of epigenomes that affect CREs and trans-factors. Within the data platform, the development and operations teams of both databases cooperate to build datasets of transcriptional regulation and develop interfaces to provide them.

Overview of INTRARED, adopted in the FY2022 NBDC Database Integration Coordination Program. fanta.bio (cis-regulatory elements) provides cis-regulatory element references for human, mouse and non-human primates, their activity by cell type, and neighbouring genomic variations, from bulk 5′ RNA-seq, single-cell 5′-end gene expression and genomic variation data. ChIP-Atlas (trans-factors and epigenomes) provides transcription factor binding sites, chromatin states and DNA methylation, and epigenome functions, from SRA ChIP-seq, ATAC-seq and bisulfite-seq data and from ENCODE, IHEC and Roadmap. The two databases are linked.