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Fig. 1 | BMC Genomics

Fig. 1

From: Construction and analysis of sample-specific driver modules for breast cancer

Fig. 1

Flowchart of the three-step procedure used to identify the sample-specific driver module. A The sample-specific network (SSN) for each breast cancer sample was constructed based on the expression matrix and gene interaction network. For a group of reference samples (n samples), a reference network was first constructed by the correlation analysis. A new sample d was added to the group, and the perturbed network with this additional sample was constructed based on the combined expression data. The SSN for sample d was constructed by using the SSN theory. B The somatic mutation profile for each breast cancer sample was constructed using the somatic mutation data. The methylation aberration profile for each breast cancer sample was calculated by the outlier detection method of the Hampel filter based on the methylation data. C The sample-specific mutation driver module (ssMutat-DM) and the sample-specific methylation aberration driver module (ssMethy-DM) for each breast cancer patient were constructed based on the 2-order network theory and hub-gene theory. Subsequent analysis of the driver modules was performed including the structure of driver modules, a synergistic collaboration of mutation and methylation, identification of the common pattern of driver modules for breast cancer, identification of subtype-specific driver modules, and encoding of the functional consequences of mutations and methylation aberrations

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