The tools for 'MicroRNA Set Enrichment Analysis' can identify risk pathways(or prior gene sets) regulated by microRNA set in the context of microRNA expression data. (1) This package constructs a correlation profile of microRNA and pathways by the hypergeometric statistic test. The gene sets of pathways derived from the three public databases (Kyoto Encyclopedia of Genes and Genomes ('KEGG'); 'Reactome'; 'Biocarta') and the target gene sets of microRNA are provided by four databases('TarBaseV6.0'; 'mir2Disease'; 'miRecords'; 'miRTarBase';). (2) This package can quantify the change of correlation between microRNA for each pathway(or prior gene set) based on a microRNA expression data with cases and controls. (3) This package uses the weighted Kolmogorov-Smirnov statistic to calculate an enrichment score (ES) of a microRNA set that co-regulate to a pathway , which reflects the degree to which a given pathway is associated with the specific phenotype. (4) This package can provide the visualization of the results.
|Author||Junwei Han, Siyao Liu|
|Date of publication||2015-07-01 11:30:03|
|Maintainer||Junwei Han <email@example.com>|
|License||GPL (>= 2)|
Corrp2miRfile: create a pathway-microRNA(miRNA) profile and a p value matrix
EnrichmentScore: Computes the enrichment score
EnrichmentScore2: Computes the enrichment score faster
envData: The variables in the environment include predefine pathway,...
GetExampleData: Get the example data
GetMiRTargetData: Get the data of microRNA(miRNA) and target genes
GetPathwayData: Get the gene sets of pathways
HeatMapPlot: Plot a heatmap
MirSEA: Identify dysregulated pathways based on microRNA (miRNA) set...
MiRSEA-internal: MiRSEA internal functions
MiRSEA-package: MicroRNA Set Enrichment Analysis
MsReport: Produce report for a microRNA (abbreviated miRNA) set
PlotCorrelation: Plot global microRNA(miRNA) correlation profile
PlotHeatMap: Plot a heat map
PlotRunEnrichment: Plot running microRNAs(miRNAs) enrichment score
S2N: calculate signal to noise ratio for microRNAs(miRNAs)