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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.

SUBMITTER: Shen-Orr SS

PROVIDER: S-EPMC3699332 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature

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Cell type-specific gene expression differences in complex tissues.

Shen-Orr Shai S SS 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

Nature methods 20100307 4

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 ...[more]

PMID: 20208531

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