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Fig. 3 | BMC Bioinformatics

Fig. 3

From: polyClustR: defining communities of reconciled cancer subtypes with biological and prognostic significance

Fig. 3

Subtype communities of breast cancer identified using polyClustR. a A hypergeometric (HYP) test and b PMI was used to assess the significance of the overlap between each pair of clusters using the Chin breast cancer data set [21]. The resulting FDR corrected p values/PMI values were plotted as edge colours/weights in this network, with each node representing a cluster. The size of each node represents the number of samples that cluster contains, and those nodes in a lighter shade represent clusters with associations to known subtypes that are not significant (FDR corrected p > 0.05). Gray shading marks dense groups of clusters that are defined as subtype communities by network community detection. bHYP and bPMI represent HYP and PMI subtype breast cancer communities, respectively. Average silhouette width is shown for each of the subtype communities. Here, all the HC, KM and NMF represent bHC, bKM and bNMF breast cancer subtypes, respectively

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