CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types

Genome Biol. 2016 Sep 29;17(1):201. doi: 10.1186/s13059-016-1062-5.


We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our method, CellMapper, strongly outperforms previous computational algorithms to predict cell type-specific expression, especially for rare and difficult-to-isolate cell types. Furthermore, CellMapper makes accurate predictions for human brain cell types that have never been isolated, and can be rapidly applied to diverse cell types from many tissues. We demonstrate a clinically relevant application to prioritize candidate genes in disease susceptibility loci identified by GWAS.

Keywords: Cell type; Expression; Genome-wide association study; Inflammatory bowel disease; Microarray.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Animals
  • Brain / cytology
  • Brain / metabolism
  • Caco-2 Cells
  • Cell Line
  • Cells, Cultured
  • Computational Biology / methods*
  • Endothelial Cells / cytology
  • Endothelial Cells / metabolism
  • Gene Expression Profiling / methods*
  • Genetic Predisposition to Disease / genetics
  • Genome-Wide Association Study / methods*
  • Hematopoietic Stem Cells / cytology
  • Hematopoietic Stem Cells / metabolism
  • Humans
  • Immune System / cytology
  • Immune System / metabolism
  • Mice, Inbred C57BL
  • Neurons / cytology
  • Neurons / metabolism
  • Polymorphism, Single Nucleotide
  • Reproducibility of Results
  • Spleen / cytology
  • Spleen / metabolism