Login / Signup

Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG.

Zhana DurenFengge ChangFnu NaqingJingxue XinQiao LiuWing Hung Wong
Published in: Genome biology (2022)
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.
Keyphrases
  • single cell
  • gene expression
  • transcription factor
  • rna seq
  • data analysis
  • high throughput
  • dna methylation
  • dna damage
  • genome wide
  • stem cells
  • machine learning
  • artificial intelligence
  • bone marrow
  • human health