This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Databases For Gene Family?

I have got some lists of gene families. For example, list1 and list2. I'd like to know whether there are some databases recording genes that can form gene families in genome.

gene database
• 9,309 views • link
updated by Biostar Biostar • written by Dejian Dejian

3 answers

I would start at TreeFam: http://www.treefam.org/

• 0 views • link
written by Chris Evelo Chris Evelo

Pretty good. "The ultimate goal of TreeFam is to present a curated resource for all the families." I think this db will be a good help to me. Thank you, Chris.

• 0 views • link
written by Dejian Dejian

Treefam is dead, for now. If you want to find the latest gene build, you will be disappointed. The treefam pipeline has been largely adopted and improved by EnsemblCompara.

• 0 views • link
written by lh3 lh3

Treefam is dead, for now. If you want to find the latest gene build, you will be disappointed (if you do not care, treefam is still fairly good IMO). The treefam pipeline has been largely adopted and improved by EnsemblCompara.

• 0 views • link
written by lh3 lh3

Update: Treefam is reborn and a new release is coming. The Pfam/Rfam group at Sanger has taken it over.

• 0 views • link
written by lh3 lh3

Ensembl has excellent gene family calculations. Check out the family of ensembl databases here if you are not looking at vertebrate model organisms. biomart provides query access to most of these if needed

• 0 views • link
updated by Ram Ram • written by Alastair Kerr Alastair Kerr

Of course, part of what drives where you search and is what you're looking for. I know of two excellent database for cytochrome P450 (basically xenobiotic and drug metabolizing enzymes) genes, one of which has a focus on gene variants and implications in drug treatment/dose. This means, you may need to search the literature for "gene family" + "database." Or similarly search the internet.

Added in edit on 16 Feb 2012: In looking closely at the UniProtKB entry for human albumin, P02768, I see that there is listed in the COMMENT field: [WEB RESOURCE] Name=Albumin Website; URL='http://www.albumin.org'. This could be an approach to identify if there is a database for a gene family of interest. Find the protein in UniProtKB and scan this COMMENT field.

• 1 views • link
written by Larry_Parnell Larry_Parnell

Many thanks. One of my colleagues is going to work on p450. I have forwarded this message to her. :)

• 0 views • link
written by Dejian Dejian

Several P450 subfamilies from treefam: treefam.org/cgi-bin/search2.pl?f=P450 The nice thing about treefam is you see trees, which are much more intuitive than looking at a list of genes/ortholog pairs.

• 0 views • link
written by lh3 lh3

Log in to answer this question.

More posts like this