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

Research output: Contribution to journal › Article › peer-review

8 Citations (SciVal)

41 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. 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

Access to Document

10.1093/bioinformatics/btab377Licence: CC BY

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

Cite this

@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].",

year = "2021",

month = oct,

day = "15",

doi = "10.1093/bioinformatics/btab377",

language = "English",

volume = "37",

pages = "3604–3609",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "20",

}

TY - JOUR

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

AU - Patel, Krutik

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.

UR - http://www.scopus.com/inward/record.url?scp=85134647645&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btab377

DO - 10.1093/bioinformatics/btab377

M3 - Article

SN - 1367-4803

VL - 37

SP - 3604

EP - 3609

JO - Bioinformatics

JF - Bioinformatics

IS - 20

ER -

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

Abstract

Access to Document

Other files and links

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

Cite this

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

Abstract

Access to Document

Other files and links

Projects

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

Cite this