Identifying miRNA-mediated signaling subpathways by integrating paired miRNA/mRNA expression data with pathway topology

Annu Int Conf IEEE Eng Med Biol Soc. 2015:2015:3997-4000. doi: 10.1109/EMBC.2015.7319270.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biomarkers / metabolism
  • Databases, Genetic
  • Gene Regulatory Networks
  • MicroRNAs / genetics
  • MicroRNAs / metabolism*
  • Milk / metabolism
  • Oligonucleotide Array Sequence Analysis
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Rats
  • Signal Transduction / genetics*
  • Transcriptome

Substances

  • Biomarkers
  • MicroRNAs
  • RNA, Messenger