Gene lists and calculated Ka/Ks ratio per gene
Hi all,
I have a lists of human genes up and down regulated in a case control study. I'm looking for enrichments in certain gene classes/groups/families. So I was wondering if there are somewhere pre-made gene lists. For example transcription factors or the ZNF gene family...
-edit- http://www.genenames.org/genefamilies/a-z -->
Download the HGNC Gene Family dataset
Click here for the complete HGNC Gene Family dataset in text format."
Besides I was wondering if there is somewhere a list of pre calculated Ka/Ks ratio's for all human genes present?
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Ram
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Floris Brenk
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Floris Brenk
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Since Ka/Ks ratios are compared to for a reference species with respect to another, which species do you want to compare it to? Ensembl has the calculated dN/dS in their ortholog comparison for each of the genes searched, also ensembl biomart has the calculated dN and dS (seperately) for the orthologs (Attributes -> Homologues -> Species) when you check the features comparison
did you visit this site? It might help, it has nice R scripts https://github.com/a1ultima/kaks_error_bars