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

Krutik Patel; Sharmilla Chandrasegaran; Ian Clark; Carole Proctor; David Young; Daryl Shanley

doi:10.1093/bioinformatics/btab377

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

Krutik Patel, Sharmilla Chandrasegaran, Ian Clark, Carole Proctor, David Young, Daryl Shanley

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Abstract

Motivation: The analysis of longitudinal datasets and construction of gene regulatory networks provide a valuable means to disentangle the complexity of microRNA-mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal microRNA-mRNA datasets.

Results: We present TimiRGeN, an R package that uses time point based differential expression results to identify miRNA-mRNA interactions influencing signalling pathways of interest. miRNA-mRNA interactions can be visualised 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 gene regulatory network construction.

Availability and implementation: TimiRGeN is available for download on Bioconductor (https://bioconductor.org/packages/TimiRGeN) and requires R v4.0.2 or newer and BiocManager v3.12 or newer.

Original language	English
Journal	Bioinformatics
Early online date	16 May 2021
DOIs	https://doi.org/10.1093/bioinformatics/btab377
Publication status	E-pub ahead of print - 16 May 2021

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10.1093/bioinformatics/btab377Licence: CC BY

Patel et al Bioinformatics 2021 in pressAccepted author manuscript, 1.34 MBLicence: CC BY

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MicroRNAs are key mediators of cartilage destruction in osteoarthritis: in vivo, in vitro and in silico studies
Clark, I., Young, D., Dalmay, T. & Swingler, T.
Dunhill Medical Trust (The)
1/01/17 → 30/06/22
Project: Research

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title = "TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis",

abstract = "Motivation: The analysis of longitudinal datasets and construction of gene regulatory networks provide a valuable means to disentangle the complexity of microRNA-mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal microRNA-mRNA datasets.Results: We present TimiRGeN, an R package that uses time point based differential expression results to identify miRNA-mRNA interactions influencing signalling pathways of interest. miRNA-mRNA interactions can be visualised 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 gene regulatory network construction.Availability and implementation: TimiRGeN is available for download on Bioconductor (https://bioconductor.org/packages/TimiRGeN) and requires R v4.0.2 or newer and BiocManager v3.12 or newer.",

author = "Krutik Patel and Sharmilla Chandrasegaran and Ian Clark and Carole Proctor and David Young and Daryl Shanley",

year = "2021",

month = may,

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doi = "10.1093/bioinformatics/btab377",

language = "English",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

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T1 - TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis

AU - Patel, Krutik

AU - Chandrasegaran, Sharmilla

AU - Clark, Ian

AU - Proctor, Carole

AU - Young, David

AU - Shanley, Daryl

PY - 2021/5/16

Y1 - 2021/5/16

N2 - Motivation: The analysis of longitudinal datasets and construction of gene regulatory networks provide a valuable means to disentangle the complexity of microRNA-mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal microRNA-mRNA datasets.Results: We present TimiRGeN, an R package that uses time point based differential expression results to identify miRNA-mRNA interactions influencing signalling pathways of interest. miRNA-mRNA interactions can be visualised 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 gene regulatory network construction.Availability and implementation: TimiRGeN is available for download on Bioconductor (https://bioconductor.org/packages/TimiRGeN) and requires R v4.0.2 or newer and BiocManager v3.12 or newer.

AB - Motivation: The analysis of longitudinal datasets and construction of gene regulatory networks provide a valuable means to disentangle the complexity of microRNA-mRNA interactions. However, there are no computational tools that can integrate, conduct functional analysis and generate detailed networks from longitudinal microRNA-mRNA datasets.Results: We present TimiRGeN, an R package that uses time point based differential expression results to identify miRNA-mRNA interactions influencing signalling pathways of interest. miRNA-mRNA interactions can be visualised 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 gene regulatory network construction.Availability and implementation: TimiRGeN is available for download on Bioconductor (https://bioconductor.org/packages/TimiRGeN) and requires R v4.0.2 or newer and BiocManager v3.12 or newer.

U2 - 10.1093/bioinformatics/btab377

DO - 10.1093/bioinformatics/btab377

M3 - Article

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

ER -

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

Abstract

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MicroRNAs are key mediators of cartilage destruction in osteoarthritis: in vivo, in vitro and in silico studies

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