Databases For Gene Family?
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13.2 years ago
Dejian ★ 1.3k

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 • 7.6k views
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13.2 years ago

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

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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.

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

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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.

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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.

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13.2 years ago

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

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13.2 years ago

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.

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

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Several P450 subfamilies from treefam. The nice thing about treefam is you see trees.

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