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Cell type-specific gene expression differences in complex tissues. 2010
Shai S Shen-Orr, and
Robert Tibshirani, and
Purvesh Khatri, and
Dale L Bodian, and
Frank Staedtler, and
Nicholas M Perry, and
Trevor Hastie, and
Minnie M Sarwal, and
Mark M Davis, and
Atul J Butte
Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA.
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.
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