Cell type-specific gene expression differences in complex tissues

Nat Methods. 2010 Apr;7(4):287-9. doi: 10.1038/nmeth.1439. Epub 2010 Mar 7.


We describe cell type-specific significance analysis of microarrays (csSAM) for analyzing differential gene expression for each cell type in a biological sample from microarray data and relative cell-type frequencies. First, we validated csSAM with predesigned mixtures and then applied it to whole-blood gene expression datasets from stable post-transplant kidney transplant recipients and those experiencing acute transplant rejection, which revealed hundreds of differentially expressed genes that were otherwise undetectable.

Publication types

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

MeSH terms

  • Animals
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation*
  • Graft Rejection / blood
  • Graft Rejection / genetics
  • Humans
  • Kidney Transplantation
  • Linear Models
  • Oligonucleotide Array Sequence Analysis / methods*
  • Rats

Associated data

  • GEO/GSE19830
  • GEO/GSE20300