Additional file 1.

Study overview. Integrative network with miRNAs, mRNAs, expressions, and cancer-related contexts in acquired resistance to antiestrogen in breast cancer cells (tamoxifen resistant (MCF7-T), fulvestrant resistant (MCF7-F), and parental drug-sensitive MCF7 cells). For minimizing false positives in network connectivity, we used experimentally validated databases: TransmiR (TFs binding in miRNA promoters, signaling proteins for regulating miRNAs), and miRTarBase (miRNA target information). In addition, biological interpretability was enhanced by incorporating cancer-related context terms suggested by Hanahan and Weinberg [24] into the network connectivity. The cancer contexts were connected with TFs, signaling proteins, and miRNA targets from the two databases by using a text-mining tool, PubGene [26]. The antiestrogen resistant cell line expressions were incorporated into the network connectivity (see the details in the Methods section), and the network clusters underscoring the antiestrogen resistances were identified by the Cytoscape clusterMaker [29].

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Nam et al. BMC Genomics 2012 13:732   doi:10.1186/1471-2164-13-732