Overview
Enrichment – A tool that calculate gene function enrichment for a selected gene set. Ther tool displays Gene Ontology enrichments as a tree.
Example work flow:
- Add a group of genes to the gene list.
- Go to the tool and display the enrichments.
- Scroll down to view all enrichment tests.
- Select the GO details tab to view more options for gene ontology enrichment.
- Choose one of the three domains and calculate enrichment.
- Select a minimum p-value and minimum number of genes in a category to reduce the number of results.
- Change the layout to tree view.
Basic Usage
The enrichment tool calculates the statistical enrichment of a set of functional annotations, currently Gene ontology, miRNA, and Pfam, in a gene list. There is one page with an overview of all enrichment tests, and a GO details tab with advanced settings for GO enrichment as well as a visualization of the Gene Ontology trees (biological process, molecular function and cellular component). The results can be filtered by specifying a p-value threshold (default is 0.05) and a minimum number of genes annotated with the specific function (default 2). False Discovery Rate (FDR) corrected p-values are reported by default. Under-enrichment, that is significantly fewer annotations in the gene list than one would expect by chance, is hidden by default. Statistics column in the Enrichment table indicate (number of genes in test list | number of test genes in GO term | Number of genes in GO term | Total genes with GO assignment). A new genelist can be created by clicking the number of genes within the GO term.
Implementation
The Enrichment tool uses Cytoscape Web (flash) to display the Gene Ontology tree. The webpage is coded with PHP, HTML and JavaScript, the calculations are coded in Python, and the statistical test (fisher´s exact test) is calculated with the fisher 0.1.4 package.
Ref http://github.com/brentp/fishers_exact_test