title: Cell type-specific gene expression differences in complex tissues.
abstract: 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.
authors.affiliation: Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Shai S
authors.initials: SS
authors.lastname: Shen-Orr
authors.forename: Robert
authors.initials: R
authors.lastname: Tibshirani
authors.forename: Purvesh
authors.initials: P
authors.lastname: Khatri
authors.forename: Dale L
authors.initials: DL
authors.lastname: Bodian
authors.forename: Frank
authors.initials: F
authors.lastname: Staedtler
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Perry
authors.forename: Trevor
authors.initials: T
authors.lastname: Hastie
authors.forename: Minnie M
authors.initials: MM
authors.lastname: Sarwal
authors.forename: Mark M
authors.initials: MM
authors.lastname: Davis
authors.forename: Atul J
authors.initials: AJ
authors.lastname: Butte
mesh_terms: 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