MiRSEA: 'MicroRNA' Set Enrichment Analysis
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.
- Junwei Han, Siyao Liu
- Date of publication
- 2015-07-01 11:30:03
- Junwei Han <email@example.com>
- GPL (>= 2)
- create a pathway-microRNA(miRNA) profile and a p value matrix
- Computes the enrichment score
- Computes the enrichment score faster
- The variables in the environment include predefine pathway,...
- Get the example data
- Get the data of microRNA(miRNA) and target genes
- Get the gene sets of pathways
- Plot a heatmap
- Identify dysregulated pathways based on microRNA (miRNA) set...
- MiRSEA internal functions
- MicroRNA Set Enrichment Analysis
- Produce report for a microRNA (abbreviated miRNA) set
- Plot global microRNA(miRNA) correlation profile
- Plot a heat map
- Plot running microRNAs(miRNAs) enrichment score
- calculate signal to noise ratio for microRNAs(miRNAs)
Files in this package