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

doi:10.1093/bioinformatics/btab377

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

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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. 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	3604–3609
Number of pages	6
Journal	Bioinformatics
Volume	37
Issue number	20
Early online date	16 May 2021
DOIs	https://doi.org/10.1093/bioinformatics/btab377
Publication status	Published - 15 Oct 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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@article{d6812f77971f4ea8883393a9eaa32d53,

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 (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. 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",

author = "Krutik Patel and Sharmilla Chandrasegaran and Clark, {Ian M.} and Proctor, {Carole J.} and Young, {David A.} and Shanley, {Daryl P.}",

note = "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].",

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AU - Chandrasegaran, Sharmilla

AU - Clark, Ian M.

AU - Proctor, Carole J.

AU - Young, David A.

AU - Shanley, Daryl P.

N1 - 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].

PY - 2021/10/15

Y1 - 2021/10/15

N2 - 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. 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - 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. 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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

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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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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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