[BiO BB] Gene Ontology

[Mike Marchywka]

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> Date: Wed, 27 Oct 2010 00:37:54 -0700
> From: ngadewal at yahoo.com
> To: bbb at bioinformatics.org
> Subject: [BiO BB] Gene Ontology
>
> Dear All,
>
> I have a list of genes with gene symbol (entrez) which has to be annotated by
> gene ontology.
>
> I am looking for online tool which takes genelist as input and will give
> output the genes which are involved in bioloical process and molecular funtion.
> For eg. Out of 100 genes (genelist) submitted, will give output say 30 genes are
> involved in "Signal transduction" (biological process).
> If anyone know such kind of tool than please let me know.
> Thankyou in advance.

There may be specific tools for this but one option is eutils.

http://eutils.ncbi.nlm.nih.gov/

 For example,I have a script that can go search the gene db and return and xml file 
with an entry for each gene of interest. You can then parse or do whatever you want to 
associate attributes with each gene and pick the ones you want. If I type this,

eutilsnew -v -out xxx -gene human

I get a bunch of genes in "xxx" that relate to the search term "human".
Apparently there is a field called Prot-ref_desc that is close to what you
want but you would need to look a little more - not sure if looking up
protein would be needed to get classification you want etc.


more xxx | grep "track_geneid\|rot-ref_desc"

      <Gene-track_geneid>253461</Gene-track_geneid>
      <Prot-ref_desc>zinc finger and BTB domain-containing protein 38</Prot-ref_
desc>
      <Gene-track_geneid>55245</Gene-track_geneid>
      <Prot-ref_desc>ubiquinol-cytochrome c reductase complex chaperone CBP3 hom
olog</Prot-ref_desc>
      <Gene-track_geneid>8353</Gene-track_geneid>
      <Prot-ref_desc>histone H3.1</Prot-ref_desc>
      <Gene-track_geneid>8091</Gene-track_geneid>
      <Prot-ref_desc>high mobility group protein HMGI-C</Prot-ref_desc>
      <Gene-track_geneid>79145</Gene-track_geneid>
      <Prot-ref_desc>coiled-coil-helix-coiled-coil-helix domain-containing prote
in 7</Prot-ref_desc>
      <Gene-track_geneid>3007</Gene-track_geneid>
      <Prot-ref_desc>histone H1.3</Prot-ref_desc>
      <Gene-track_geneid>195814</Gene-track_geneid>
      <Prot-ref_desc>epidermal retinol dehydrogenase 2</Prot-ref_desc>
      <Gene-track_geneid>57211</Gene-track_geneid>
      <Prot-ref_desc>G-protein coupled receptor 126</Prot-ref_desc>
      <Gene-track_geneid>57188</Gene-track_geneid>
      <Prot-ref_desc>ADAMTS-like protein 3</Prot-ref_desc>





>
> Nikhil
>
>