Question: Gene lists and calculated Ka/Ks ratio per gene
0
gravatar for Floris Brenk
6.2 years ago by
Floris Brenk980
USA
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...

-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?

 

 

family gene conservation • 2.0k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 6.2 years ago by Floris Brenk980
1

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 https://github.com/a1ultima/kaks_error_bars

ADD REPLYlink written 3.7 years ago by Manvendra Singh2.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1687 users visited in the last hour
_