10.1371/journal.pone.0184471.g002 David J. Schultz David J. Schultz Penn Muluhngwi Penn Muluhngwi Negin Alizadeh-Rad Negin Alizadeh-Rad Madelyn A. Green Madelyn A. Green Eric C. Rouchka Eric C. Rouchka Sabine J. Waigel Sabine J. Waigel Carolyn M. Klinge Carolyn M. Klinge Enrichment analysis of miRNA-seq data. Public Library of Science 2017 SIN breast cancer cells MicroRNAs MYC TNBC genome-wide microRNA transcriptome MetaCore Gene Ontology cell lines VIM mRNA transcript expression ER miR -20b Whole genome expression 69 AnAc-responsive miRNAs MCF -7 cells AnAc-treated MDA-MB -231 cells breast cancer AnAc-treated MCF -7 cells miRNA arm preference miR -20b target EFNB 2 transcript levels PPAR MCF -7 estrogen receptor α B cell receptor IC Genome-wide miRNA response MDA-MB -231 cells 2017-09-08 18:05:36 Figure https://plos.figshare.com/articles/figure/Enrichment_analysis_of_miRNA-seq_data_/5391823 <p>Differentially expressed genes were identified in pairwise comparisons: MCF-7 AnAc vs. MDA-MB-231 AnAc using the tuxedo suite of programs including cufflink-cuffdiff2. The Venn diagrams show the number of common and differentially expressed genes significantly downregulated (A) and upregulated (B). Pathway analysis was performed using GeneGo Pathways Software (MetaCoreTM). The pathways identified for each comparison are listed in the order provided by MetaCoreTM analysis.</p>