Projects per year
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.
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 |
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Pages (from-to) | 3604–3609 |
Number of pages | 6 |
Journal | Bioinformatics |
Volume | 37 |
Issue number | 20 |
Early online date | 16 May 2021 |
DOIs | |
Publication status | Published - 15 Oct 2021 |
Projects
- 1 Active
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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.
1/01/17 → 31/12/22
Project: Research