Systematic miRNA Target Prediction

Target genes for selected miRNAs were predicted by using TargetScan Release 6.0 (http://www.targetscan.org/) [32] (link) and miRanda (http://www.microrna.org/microrna). The target genes that were predicted by both TargetScan (default parameters) and miRanda (Total score> = 145, Total energy< = −10) for each miRNA were further analyzed through IPA (Ingenuity Systems, www.ingenuity.com). The multiple testing corrected P value calculated by Benjamini-Hochberg method (FDR) [28] was used to determine the significance of the predicted function in IPAs. A threshold of FDR <0.05 and molecule number >1 were applied to enrich significant biological functions of each miRNA.

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Liang G., Malmuthuge N., McFadden T.B., Bao H., Griebel P.J., Stothard P, & Guan L.L. (2014). Potential Regulatory Role of MicroRNAs in the Development of Bovine Gastrointestinal Tract during Early Life. PLoS ONE, 9(3), e92592.

Publication 2014

IPA

Biological functions Genes Ipas Mirna

Corresponding Organization :

Other organizations : University of Alberta, University of Missouri, University of Saskatchewan

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Variable analysis

independent variables

Target genes for selected miRNAs were predicted by using TargetScan Release 6.0 and miRanda

dependent variables

The target genes that were predicted by both TargetScan (default parameters) and miRanda (Total score>=145, Total energy<=-10) for each miRNA were further analyzed through IPA (Ingenuity Systems)

control variables

The multiple testing corrected P value calculated by Benjamini-Hochberg method (FDR) was used to determine the significance of the predicted function in IPAs.

positive controls

None specified

negative controls

None specified

Annotations

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