I am wondering if someone can recommend a convenient webserver or software program to calculate the enrichment of GO terms in one gene list over another gene list. If only one gene list is provided, the program should be able to use a 'background" gene list containing all genes in a particular species. Ideally, it could also handle various types of identifiers (e.g. refseq, entrez id, UniGene,etc) in the input gene lists.
I know there are a lot of tools out there for a simple GO enrichment analysis, but I haven't found one that I particularly like.... Fatigo cannot calculate enrichment score if only one gene list is provided. I also tried GOStat, but the links to AmiGO from individual GO terms on the result page seem broken...
Comments (2)
hi,
You might want to have a try of a perl package GO::TermFinder. It could take an annotation file (GO anntation of some genes) and calculate the enrichment p-values and corrected p-values of a partial list of genes.
We may have a discussion about how to use it, if you are not familiar with perl.
fengfeng
Posted by Fengfeng Zhou | March 10, 2007 8:26 PM
Posted on March 10, 2007 20:26
you could try david:
http://david.abcc.ncifcrf.gov/
Posted by jhxiong | April 17, 2007 7:51 AM
Posted on April 17, 2007 07:51