Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the construction of subpopulation-specific cis-regulatory networks. The capability of inferring useful regulatory network is demonstrated by the two-fold increment on network inference accuracy compared to the Pearson correlation-based method and the 27-fold enrichment of GWAS variants for inflammatory bowel disease in the cis-regulatory elements. The R package scREG provides comprehensive functions for single cell multiome data analysis.
Following publication of the original paper [1], the authors have reported an error in reference genome version of the HiC data used for validation of the RE-TG interactions. After using the correct version of the HiC anchor locations, the result in Fig. 4D, supplementary Figure S11, and S12 are all improved.
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