Cell type-specific gene expression differences in complex tissues.
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.
Shen-Orr
Shai S
SS
Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.
Tibshirani
Robert
R
Khatri
Purvesh
P
Bodian
Dale L
DL
Staedtler
Frank
F
Perry
Nicholas M
NM
Hastie
Trevor
T
Sarwal
Minnie M
MM
Davis
Mark M
MM
Butte
Atul J
AJ
D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006084:Graft Rejection / Q000097:blood / Q000235:genetics; D006801:Humans; D016030:Kidney Transplantation; D016014:Linear Models; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D051381:Rats