miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets

Lu, Tzu-Pin; Lee, Chien Yueh; Tsai, Mong-Hsun; Chiu, Yi-Chang; Hsiao, Chuhsing Kate; Lai, Liang‐Chuan; Chuang, Eric Y.

doi:10.1371/journal.pone.0042390

Cited by 286 publications

(275 citation statements)

References 51 publications

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“…Since miRNA names in GSE14473 were old (miRBase, release 9.1), they were converted to miRNA names used in the present version of the MiRaGE software package (miRBase release 18) and by the miRConverter implemented in miRSystem 24 .…”

mentioning

confidence: 99%

Correlation between miRNA-targeted-gene promoter methylation and miRNA regulation of target genes

Taguchi

2013

F1000Res

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Science and Technology Norway Discuss this article AbstractmiRNA regulation of target genes and promoter methylation are Background known to be the primary mechanisms underlying the epigenetic regulation of gene expression. However, how these two processes cooperatively regulate gene expression has not been extensively studied.Gene expression and promoter methylation profiles of 271 distinct Methods human cell lines were obtained from gene expression omnibus. P-values that describe both miRNA-targeted-gene promoter methylaion and miRNA regulation of target genes were computed using the MiRaGE method proposed recently by the author.Significant changes in promoter methylation were associated with Results miRNA targeting. It was also found that miRNA-targeted-gene promoter hypomethylation was related to differential target gene expression; the genes with miRNA-targeted-gene promoter hypomethylation were downregulated during cell senescence and upregulated during cellular differentiation. Promoter hypomethylation was especially enhanced for genes targeted by miR-548 miRNAs, which are non-conserved, primate-specific miRNAs that are typically expressed at lower levels than the frequently investigated conserved miRNAs.It was found that promoter methylation was affected by miRNA Conclusions targeting. Furthermore, miRNA-targeted-gene promoter hypomethylation is suggested to facilitate gene regulation by miRNAs that are not strongly expressed (e.g., miR-548 miRNAs).

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mentioning

confidence: 99%

Correlation between miRNA-targeted-gene promoter methylation and miRNA regulation of target genes

Taguchi

2013

F1000Res

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“…Typically, predicted target genes are used as input for functional enrichment to infer the potential functions of miRNAs. Furthermore, several tools are also used to correlate the expression levels of miRNAs with mRNA in a particular experiment to infer miRNA function such as miRnet [110], miRSystem [111] and DIANAmiRPath v3.0 [107]. Several tools have also been developed to directly link miRNAs to biological processes such as DMirNet [188], miRnet [110] and DIANA-miRPath v3.0 [107].…”

Section: Integrated Tools For Mirna Analysismentioning

confidence: 99%

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Ngoc¹,

Dudemaine²,

Fomenky³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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The recent remarkable development of transcriptomics technologies, especially next generation sequencing technologies, allows deeper exploration of the hidden landscapes of complex traits and creates great opportunities to improve livestock productivity and welfare. Non-coding RNAs (ncRNAs), RNA molecules that are not translated into proteins, are key transcriptional regulators of health and production traits, thus, transcriptomics analyses of ncRNAs are important for a beter understanding of the regulatory architecture of livestock phenotypes. In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identiication of ncRNAs and functional inference of identiied ncRNAs, with emphasis on tools for livestock species. We also discuss future challenges and perspectives for ncRNA transcriptome data analysis in livestock species.

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“…Pathway analysis was performed using miRSystem (http://mirsystem.cgm.ntu. edu.tw/) 33 with default parameters.…”

Section: Microrna Profilingmentioning

confidence: 99%

Nutrition has a pervasive impact on cardiac microRNA expression in isogenic mice

et al. 2016

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The complex interaction between obesity, Western-style diets, and cardiovascular disease is of increasing interest, with a growing number of children being born to obese parents with poor lifestyle choices. These offspring have themselves an increased susceptibility to obesity and subsequent cardiovascular disease in adult life, which may be 'programmed' by their intrauterine environment. Cardiac microRNAs (miRNAs) are affected by multiple disease states, and have also been shown to be capable of exerting a hormone-like control on whole body metabolism. Here we sought to determine the effect of prenatal exposure to maternal obesity and/or postnatal exposure to a Western diet on miRNA expression in the heart. Unbiased small RNA sequencing was carried out on cardiac tissue from young adult mice born to lean or obese mothers; offspring were weaned onto either a low-fat control diet or a high-fat Western-style diet. We found 8 cardiac miRNAs that were significantly altered in response to maternal obesity, but only when the offspring were challenged postnatally with the Western diet. In contrast, postnatal exposure to the diet alone induced significant changes to the expression of a much larger number of miRNAs (33 in offspring of lean and 46 in offspring of obese). Many of the affected miRNAs have previously been implicated in various cardiac pathologies. The pervasive cardiac miRNA changes induced by a Western diet suggest that an individual's lifestyle choices outweigh the impact of any programming effects by maternal obesity on miRNA-related cardiac health.

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miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets

Cited by 286 publications

References 51 publications

Correlation between miRNA-targeted-gene promoter methylation and miRNA regulation of target genes

Correlation between miRNA-targeted-gene promoter methylation and miRNA regulation of target genes

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Nutrition has a pervasive impact on cardiac microRNA expression in isogenic mice

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