Wednesday, October 19, 2011

How to search for enriched GO terms in the gene list

If you have a gene list that came out from your experiment and that is ranked for example by p-value there is an easy way to check for the enrichment of specific GO (gene ontology) terms.
Go to
Paste your gene list separated by /n
Chose the species

Chose running mode: Single ranked list of genes
In case you got as an output a ranked list of genes paste in total list of your genes in a ranked order (e.g. in you had 20.000 genes tested and ranked in your experiment, paste in all 20.000 genes in the order of ranking).

Chose an ontology: All
Select all 3 groups of ontologies to be shown as output.

The output is a table:

null Description P-value Enrichment (N, B, n, b) Genes
GO:0030695 GTPase regulator activity 5.45E-6 1.72 (13439,402,1552,80) [+] Show genes
GO:0060589 nucleoside-triphosphatase regulator activity 7.46E-6 1.70 (13439,412,1552,81) [+] Show genes
GO:0005488 binding 3.36E-5 1.07 (13439,9544,1560,1185) [+] Show genes
GO:0042578 phosphoric ester hydrolase activity 2.42E-4 1.83 (13439,311,1110,47) [+] Show genes
GO:0005509 calcium ion binding 3.77E-4 1.49 (13439,515,1591,91) [+] Show genes
GO:0005083 small GTPase regulator activity 4.58E-4 1.71 (13439,258,1552,51) [+] Show genes
GO:0005096 GTPase activator activity 4.66E-4 1.75 (13439,233,1552,47) [+] Show genes
GO:0005085 guanyl-nucleotide exchange factor activity 6.01E-4 1.91 (13439,161,1484,34) [+] Show genes
GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity 6.25E-4 11.71 (13439,7,656,4) [+] Show genes
GO:0005515 protein binding 8.63E-4 1.12 (13439,5545,1458,672) [+] Show genes

In case you don't have a ranked list of genes, but just a group of genes that are came out of the experiment, select as running mode: Two unranked lists of genes (target and background lists).
In this case you will need to provide a background list of genes for the analysis. If for example your gene list comes from a microarray experiment the background should be all the genes from the array.

1 comment:

  1. In this situation I used DuplicateFilesDeleter for great effect. It searches two or more duplicate files in one or more selected search paths and removes them.