LRcell: detecting the source of differential expression at the sub-cell-type level from bulk RNA-seq data

Brief Bioinform. 2022 May 13;23(3):bbac063. doi: 10.1093/bib/bbac063.


Given most tissues are consist of abundant and diverse (sub-)cell types, an important yet unaddressed problem in bulk RNA-seq analysis is to identify at which (sub-)cell type(s) the differential expression occurs. Single-cell RNA-sequencing (scRNA-seq) technologies can answer the question, but they are often labor-intensive and cost-prohibitive. Here, we present LRcell, a computational method aiming to identify specific (sub-)cell type(s) that drives the changes observed in a bulk RNA-seq experiment. In addition, LRcell provides pre-embedded marker genes computed from putative scRNA-seq experiments as options to execute the analyses. We conduct a simulation study to demonstrate the effectiveness and reliability of LRcell. Using three different real datasets, we show that LRcell successfully identifies known cell types involved in psychiatric disorders. Applying LRcell to bulk RNA-seq results can produce a hypothesis on which (sub-)cell type(s) contributes to the differential expression. LRcell is complementary to cell type deconvolution methods.

Keywords: cell marker genes; cell-type enrichment; differential gene expression.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computer Simulation
  • Gene Expression Profiling* / methods
  • Humans
  • RNA-Seq
  • Reproducibility of Results
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis* / methods