Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line

BMC Genomics
Naresh Doni Jayavelu, Nadav Bar

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate genes at the post-transcriptional level in spatiotemporal manner. Several miRNAs are identified as prognostic and diagnostic markers in many human cancers. Estimation of the temporal activities of the miRNAs is an important step in the way to understand the complex interactions of these important regulatory elements with transcription factors (TFs) and target genes (TGs). However, current research on miRNA activities excludes network dynamics from the studies, disregarding the important element of time in the regulatory network analysis. In the current study, we combined experimentally verified miRNA-TG interactions with breast cancer microarray TG expression data to identify key miRNAs and compute their temporal activity using network component analysis (NCA). The computed activities showed that miRNAs were regulated in a time dependent manner. Our results allowed constructing a synergistic network of miRNAs using the computed miRNA activities and their shared regulation of TGs. We further extended this network by incorporating miRNA-TG, miRNA-TF, TF-miRNA and TF-TG regulations in the context of breast cancer. Our integrated network identified several miRNAs known to b...Continue Reading

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Datasets Mentioned

BETA
GSE13009

Software Mentioned

MATLAB
MIRUMIR
mirDREM
Transcriptome Browser
Mathworks
NCA
R
Cytoscape
PPISURV
DAVID ( Database for Annotation , Visualization and Integrated...

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