eisa (version 1.24.0)

ISAmiRNA: Calculate (predicted) miRNA target enrichment for transcription modules

Description

This function performs enrichment calculations with respect to predicted miRNA targets to check whether an ISA module contains many genes that are targets of the same miRNA.

Usage

ISAmiRNA (modules, ann = annotation(modules), features = featureNames(modules),  hgCutoff = 0.05, correction = TRUE, correction.method = "holm")

Arguments

modules

An ISAModules object, a set of ISA modules.

ann

Character scalar. The annotation package to be used. By default it is taken from the modules argument.

features

Character vector. The names of the features. By default it is taken from the modules argument.

hgCutoff

Numeric scalar. The cutoff value to be used for the enrichment significance. This can be changed later, without recalculating the test.

correction

Logical scalar, whether to perform multiple hypothesis testing correction.

correction.method

Character scalar, the multiple testing correction method to use. Possible values: “holm”, “hochberg”, “hommel”, “bonferroni”, “BH”, “BY”, “fdr”, “none”. See the p.adjust function for details on these.

Value

miRNAListHyperGResult object.

Details

miRNAs are short RNA fragments that specifically regulate (usually inhibit) the expression of genes. Some genes have been experimentally validated as targets of a given miRNA, but we currently don't know the target genes of most miRNAs.

TargetScan is a database of predicted miRNA targets. The predictions are done based many factors, including the conservation of the target region during evolution.

The hypergeometric test, a version Fisher's exact test, takes a miRNA and a gene set (in our case coming from an ISA module) and asks whether the number of genes in the set regulated by the miRNA is significantly more (or less) than what one would expect by chance. ISAmiRNA performs the hypergeometric test for every module, for all miRNAs in the TargetScan database.

In order to use this function, TargetScan annotation packages are needed.

References

Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets Benjamin P Lewis, Christopher B Burge, David P Bartel. Cell, 120:15-20 (2005). Bergmann S, Ihmels J, Barkai N: Iterative signature algorithm for the analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.

See Also

ISAGO, ISAKEGG and ISACHR for other enrichment calculations.

The Category package.

Examples

data(ALLModulesSmall)

if (require(targetscan.Hs.eg.db)) {
  miRNA <- ISAmiRNA(ALLModulesSmall)
  summary(miRNA, p=0.1)[[7]]
}