Additional file 2.
Figure S2. Derivation of digital gene signatures. (A) The 74-gene signature comprised 44 and 30 genes derived from the intersection of four parent gene sets: those up-regulated in HPI ∩ down-regulated in LPI and those down-regulated in HPI ∩ up-regulated in LPI. Each parent gene set was derived using Fisher's summary statistic following one-tailed t-tests on each biological condition in the compendium. Each intersection was found to represent a significantly larger proportion of its two parent gene sets than expected by chance (as determined by hypergeometric test, p < 0.05). (B) Module map resulting from applying Genomica to the log-ratio compendium. Module up-regulation in a given condition is indicated in red, and module down-regulation in green. (C) Expression of Module 5 comprising 265 genes. HPI-associated arrays are indicated in purple, LPI-associated arrays in blue. Values shown are consistent with the overall pattern of module expression in those arrays in which the module is significantly expressed. Module 5 completely subsumed Module 6 and was used in subsequent analysis.
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Chang et al. BMC Systems Biology 2011 5:202 doi:10.1186/1752-0509-5-202