title: Identifying miRNA-mediated signaling subpathways by integrating paired miRNA/mRNA expression data with pathway topology.
abstract: In the road for network medicine the newly emerged systems-level subpathway-based analysis methods offer new disease genes, drug targets and network-based biomarkers. In parallel, paired miRNA/mRNA expression data enable simultaneously monitoring of the micronome effect upon the signaling pathways. Towards this orientation, we present a methodological pipeline for the identification of differentially expressed subpathways along with their miRNA regulators by using KEGG signaling pathway maps, miRNA-target interactions and expression profiles from paired miRNA/mRNA experiments. Our pipeline offered new biological insights on a real application of paired miRNA/mRNA expression profiles with respect to the dynamic changes from colostrum to mature milk whey; several literature supported genes and miRNAs were recontextualized through miRNA-mediated differentially expressed subpathways.
authors.forename: Aristidis G
authors.initials: AG
authors.lastname: Vrahatis
authors.forename: Georgios N
authors.initials: GN
authors.lastname: Dimitrakopoulos
authors.forename: Athanasios K
authors.initials: AK
authors.lastname: Tsakalidis
authors.forename: Anastasios
authors.initials: A
authors.lastname: Bezerianos
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D008892:Milk / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D051381:Rats; D015398:Signal Transduction / Q000235:genetics*; D059467:Transcriptome
chemical_list: D015415:Biomarkers; D035683:MicroRNAs; D012333:RNA, Messenger