Fig. 1. Systems biology, databases, and network generation. (A) The diversity of types of high-throughput data (genomics, epigenomics, transcriptomics, proteomics, metabolomics) available. The relationships among the data types are connected by edges. (B) The flow (represented by “edges”) of genetic information from DNA to protein is aligned with the diverse data types. Public repositories corresponding to each data type are listed (further description in ). (C) Network differences between correlation-based approaches and Bayesian networks approaches. The correlation (or mutual information) oriented tools, ARACNE () and WGCNA (), do not report directions of edges in networks. Bayesian-driven networks naturally reveal directed edges among the network entries. In other words, the undirected network (in left of the grey-shaded triangular) having G1, G2, and G3 entries by ARACNE and WGCNA can be differentiated into directed networks (in the right of the grey-shaded triangular), using Bayesian networks tools (–).
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