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

Tools

Patel, Krutik, Chandrasegaran, Sharmilla, Clark, Ian M., Proctor, Carole J., Young, David A. and Shanley, Daryl P. (2021) TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis. Bioinformatics, 37 (20). 3604–3609. ISSN 1367-4803

[thumbnail of Patel et al Bioinformatics 2021 in press]

Preview

PDF (Patel et al Bioinformatics 2021 in press) - Accepted Version
Available under License Creative Commons Attribution.
Download (1MB) | Preview

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.

Item Type:	Article
Additional Information:	Funding Information: K.P., I.M.C. and D.Y. are supported by the Dunhill Medical Trust [R476/ 0516]. D.P.S. is supported by Novo Nordisk Fonden Challenge Programme: Harnessing the Power of Big Data to Address the Societal Challenge of Aging [NNF17OC0027812]. C.P., D.Y. and S.C. by the MRC and Versus Arthritis as part of the Medical Research Council Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA) [MR/R502182/1].
Uncontrolled Keywords:	statistics and probability,biochemistry,molecular biology,computer science applications,computational theory and mathematics,computational mathematics ,/dk/atira/pure/subjectarea/asjc/2600/2613
Faculty \ School:	Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Groups > Musculoskeletal Medicine
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	21 May 2021 00:08
Last Modified:	25 Sep 2024 15:35
URI:	https://ueaeprints.uea.ac.uk/id/eprint/80061
DOI:	10.1093/bioinformatics/btab377

Downloads

Downloads per month over past year

Actions (login required)

View Item