Haynes:GOEnrichment

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Gene Ontology

So you discovered that a set of genes all become activated when you treat cells with a drug. What do the genes "do?" How will the phenotypes of the cells change as a consequence of activating these genes?

To help answer such questions, a group of scientists built a large list of standard terms to describe the functions of genes. It's very important to have a standard vocabulary, especially when many scientists are sharing information. For instance, one scientist might write about "secretion of extracellular matrix proteins" while another, who is studying the same gene reports the function as "cell surface matrix component delivery." It is important to establish which phrase is acceptable, especially when most scientists are comparing hundreds and thousands of genes that all need to be described.

Another interesting problem...when more than one gene cooperates to control a single function, if the function has many different names, then it is hard to correctly classify the genes into a single functional group.

"The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products across databases." Read more at the Gene Ontology Consortium home page at http://geneontology.org/

Tool: GOrilla

Intro: These instructions will help you to use the Gene Ontology enRIchment anaLysis and visuaLizAtion tool (GOrilla) to search for enriched GO terms in a target list of genes compared to a background list of genes. The software searches for GO terms that are enriched in the target set compared to the background set using the standard Hyper Geometric statistics.

1. Go to http://cbl-gorilla.cs.technion.ac.il/
2. Set "Choose organism" to the relevant organism (e.g., Homo sapiens = human, Mus musculus = mouse)
3. Set "Choose running mode" to "Two unranked lists of genes (target and background lists)"
4. In the "Target Set" field, paste or upload a list of genes that you want to analyze. txt format, one gene symbol per line, is recommended for the upload option
5. For the "Background Set," copy-paste or upload a complete list of all gene symbols for your organism. Use your own or one of the following:
   1. Human genes - GOBg_Human_092014.txt
   2. Mouse genes - GOBg_Mouse_092014.txt
6. Set "Choose an Ontology" to one of the three options. It is recommended that you run an analysis for each separately (do not select "All") for publishable results...
   1. "Process" - should be labeled "Biological Process" in figures; describes the specific activity of the gene product (e.g. enzymatic, structural, etc.)
   2. "Function"