Overview
The IGVF Catalog contains genomic elements, which are potential functional regions for regulating gene expression. These elements are identified/tested by functional assays (e.g., MPRA), association studies (e.g., caQTLs), and computational predictions (e.g., the ENCODE-rE2G model). Data sources include:- ENCODE Candidate Cis-Regulatory Elements (cCREs): A unified set of genomic elements predicted to have regulatory potential based on a combination of experimental data (e.g., ChIP-seq, DNase-seq) from the ENCODE project.
Coding Variants
Genomic Elements-Genes Edges
Gene Regulation
Genomic Elements-Biosamples Edges
Variants-Genomic Elements Edges
(also on variants page)- External caQTL studies: variants associated with genomic elements function from external studies (PMID:34038741, PMID:34017130) and AFGR(African Functional Genomics Resource)
- IGVF BlueSTARR: computational model predicts variants affecting the regulatory function in ENCODE cCREs (Candidate Cis-Regulatory Elements)
- IGVF MPRA
Interacting with the Table:
- Click on column headers to sort the table by that column
- Use the search box above the table to filter results
- Adjust the number of rows displayed using the dropdown menu
- Navigate between pages using the “Previous” and “Next” buttons
Biosample Table
The Biosample Table provides information about biological samples associated with the regulatory regions in your selected genomic coordinates. Table Columns:Enhancer-Gene Prediction(s)
This table reports whether the query region contains predicted enhancers from the ENCODE-rE2G model, and their target genes and cell types. Each row reports one predicted enhancer, target gene, and cell type.
Currently, this table includes predictions from the ENCODE-rE2G model across 1700+ ENCODE biosamples (see Gschwind et al. bioRxiv 2023)
The table is initially sorted by Score in descending order, showing the strongest predictions first.