Cell type-specific gene expression differences in complex tissues

http://en.wikipedia.org/wiki/Deconvolution - recover signal from noise

so in this case, noise is because we mixed all the different cell types together and we can't tell which differential expression is from which cell type

www.nature.com/nmeth/journal/v7/n4/abs/nmeth.1439.html

Shai S Shen-Orr^1,2,10, Robert Tibshirani^3,4,10, Purvesh Khatri¹, Dale L Bodian^5,9, Frank Staedtler⁶, Nicholas M Perry⁷, Trevor Hastie^3,4, Minnie M Sarwal^1,2, Mark M Davis^2,8,10 & Atul J Butte^1,10

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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.

Nature Methods 7, 287 - 289 (2010)
Published online: 7 March 2010 | doi:10.1038/nmeth.1439


whole-blood cell types: lymphocytes, monocytes, neutrophils, eosinophils and basophils
two groups: 15 acute rejection of kidney, 9 stable after kidney transplant
cell type frequencies: from Coulter counter measurements used for complete blood counts