We want to do Gene Set Enrichment Analysis (GSEA) for a zebrafish transcriptome data set. But when it comes to choosing a "gene set" most of them are built for human or mouse.
We found these nice zebrafish sets based on gene ontologies (GO), but I wish there were more choices:
http://www.go2msig.org/cgi-bin/prebuilt.cgi?taxid=7955
1) Are there others sources of zebrafish gene sets?
2) Is there a converter that would map the gene names from a human gene set to a zebrafish gene set?
Thanks for any advice or resources.
Dear Elizabeth
I think that a nice resource is represented by the Ensembl Biomart tool. You can access it from the Danio rerio page: http://grch37.ensembl.org/Danio_rerio/Info/Index
With Biomart you can build a lot of queries that let you, for instance:
1) Extract all the orthologs between zebrafish and human/mouse. So you could put a list of gene names or loci and retrieve the corresponding human/mouse genes and viceversa.
2) Extract all the GO annotation of zebrafish genes
3) Extract the gene names associated to a specific GO, KEGG, keyword, etc.
I always use this tool for many organisms and I think it is very powerful.
I hope this information might be useful.
Riccardo
Bioinformatics data analyst at www.sequentiabiotech.com
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