TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis

Krutik Patel, Sharmilla Chandrasegaran, Ian M. Clark, Carole J. Proctor, David A. Young, Daryl P. Shanley

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)
6 Downloads (Pure)

Abstract

Motivation: The analysis of longitudinal datasets and construction of gene regulatory networks (GRNs) provide a valuable means to disentangle the complexity of microRNA (miRNA)-mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal miRNA-mRNA datasets. Results: We present TimiRGeN, an R package that uses time point-based differential expression results to identify miRNA-mRNA interactions influencing signaling pathways of interest. miRNA-mRNA interactions can be visualized in R or exported to PathVisio or Cytoscape. The output can be used for hypothesis generation and directing in vitro or further in silico work such as GRN construction.

Original languageEnglish
Pages (from-to)3604–3609
Number of pages6
JournalBioinformatics
Volume37
Issue number20
Early online date16 May 2021
DOIs
Publication statusPublished - 15 Oct 2021

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