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Journal Articles Annals of Applied Statistics Year : 2012

More power via graph-structured tests for differential expression of gene networks

Abstract

We consider multivariate two-sample tests of means, where the location shift between the two populations is expected to be related to a known graph structure. An important application of such tests is the detection of differentially expressed genes between two patient populations, as shifts in expression levels are expected to be coherent with the structure of graphs reflecting gene properties such as biological process, molecular function, regulation, or metabolism. For a fixed graph of interest, we demonstrate that accounting for graph structure can yield more powerful tests under the assumption of smooth distribution shift on the graph. We also investigate the identification of non-homogeneous subgraphs of a given large graph, which poses both computational and multiple testing problems. The relevance and benefits of the proposed approach are illustrated on synthetic data and on breast cancer gene expression data analyzed in context of KEGG pathways.
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Dates and versions

hal-00521097 , version 1 (25-09-2010)
hal-00521097 , version 2 (10-06-2016)

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Laurent Jacob, Pierre Neuvial, Sandrine Dudoit. More power via graph-structured tests for differential expression of gene networks. Annals of Applied Statistics, 2012, 6 (2), pp.561-600. ⟨10.1214/11-AOAS528⟩. ⟨hal-00521097v2⟩
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