GeneProgram is a new unsupervised computational framework based on Hierarchical Dirichlet Processes that addresses each of the above challenges. GeneProgram uses expression data to simultaneously organize tissues into groups and genes into overlapping programs with consistent temporal behavior, to produce maps of expression programs, which are sorted by generality scores that exploit the automatically learned groupings.
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PLoS Comput Biol. 2007 Aug;3(8):e148. Epub 2007 Jun 13.
Automated discovery of functional generality of human gene expression programs.
Gerber GK, Dowell RD, Jaakkola TS, Gifford DK.