Question: HGNC gene family hierarchy
0
gravatar for email2mrna
8 months ago by
email2mrna0
email2mrna0 wrote:

Where can I download the HGNC gene family hierarchy? In the download section https://www.genenames.org/cgi-bin/statistics I can find the data as flat file ("New HGNC Gene Family dataset"). However I want the data which indicated the tree as at the top of the page https://www.genenames.org/cgi-bin/genefamilies/set/358

Note: I am looking for the data describing "which gene family is part of the which bigger gene super-family". For example in the page https://www.genenames.org/cgi-bin/genefamilies/set/358 figure (tree) on the top shows that "RGK type GTPase family" (most right) is part of the bigger family "RAS type GTPase family" which inter part of "Ras small GTPases superfamily". I want to download this data.

ADD COMMENTlink modified 8 months ago • written 8 months ago by email2mrna0
0
gravatar for Santosh Anand
8 months ago by
Santosh Anand3.7k
Santosh Anand3.7k wrote:

FTP site : ftp://ftp.ebi.ac.uk/pub/databases/genenames/

There you can see gene family files

ftp://ftp.ebi.ac.uk/pub/databases/genenames/genefam_list.txt.gz

ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/genefamilies.txt

See README there for full details ftp://ftp.ebi.ac.uk/pub/databases/genenames/README.txt

ADD COMMENTlink written 8 months ago by Santosh Anand3.7k

Thanks for the response. However I am looking for the data describing the relationship between different gene family. The file ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/genefamilies.txt describes is same to what I have but do not contains gene family hierarchy information. See my Note for details.

ADD REPLYlink written 8 months ago by email2mrna0
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