Abstract Integrating single-cell transcriptomes and epigenomes across diverse cell types can link genes with the cis -regulatory elements (CREs) that control expression. Gene co-expression across cell types confounds simple correlation-based analysis and results in high false prediction rates. We developed a procedure that controls for co-expression between genes and integrates multiple molecular modalities, and used it to identify &gt;10,000 gene-CRE pairs that contribute to gene expression programs in different cell types in the mouse brain.

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes