Question: Gene lists and calculated Ka/Ks ratio per gene
gravatar for Floris Brenk
6.2 years ago by
Floris Brenk980
Floris Brenk980 wrote:

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...

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"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?



family gene conservation • 2.0k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 6.2 years ago by Floris Brenk980

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

ADD REPLYlink written 3.7 years ago by Rohit1.4k

did you visit this site? It might help, it has nice R scripts

ADD REPLYlink written 3.7 years ago by Manvendra Singh2.1k
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