We generated an miRNA-mRNA regulatory network by using the intersecting DEGs from TarBase version 8 (http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Findex) and miRTarBase (http://mirtarbase.cuhk.edu.cn/php/index.php). The curated TF-miRNA regulations were derived from the TransmiR version 2.0 database (http://www.cuilab.cn/transmir) 22. The following parameters were selected to reduce false positives during processing: (i) number of supporting experiments ≥1 means that at least one high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (CLIP-Seq) experiment supported the predicted miRNA target site; (ii) up- or downregulated expression patterns between miRNA and mRNA were included; and (iii) level 1 or 2 evidence for supporting the predicted TF in breast tissue was included, and the prediction of literature evidence was excluded. The above interaction information was imported into Cytoscape software version 3.7.2 to construct the TF-miRNA-mRNA regulatory network.

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