GO enrichment for miRNA targets

Description

Given a list of miRNA IDs, performs enrichment analysis of Gene Ontology (GO) terms in predicted target genes.

Parameters

• Ontology category (all, biological process, molecular function, cellular component) [biological process]
• P-value threshold (0-1) [0.05]
• Minimum population (1-1000000) [5]
• Conditional testing (yes, no) [yes]
• P-value adjustment method (none, BH, BY) [none]
• Search for over or under-represented genes (under, over) [over]
• Species (human, mouse, rat) [human]
• Database for human miRNA targets (PicTar, TargetScan, both) [both]

Details

This tool takes a list of miRNA IDs, fetches the predicted target genes, and runs a hypergeometric test for over-representation of GO terms in this list. For human miRNAs it is possible to specify whether to use gene predictions from both PicTar or TargetScan database, or from both in order to decrease false positives. For mouse and rat miRNAs the gene targets come from miRBase.

Analysis can be restricted to GO terms which have a minimum, user-specified number of genes mapped to them (by default 5).

In order to avoid the identification of directly related GO terms, conditional testing is used by default: First the terms with no child terms are tested. All genes annotated at significant children are then removed before testing the parent terms. This continues until all terms have been tested. It is also possible to perform unconditional testing, and in this case you can use multiple testing correction too.

Output

Output is a text file and an HTML file with a list of significant categories.