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GO annotations for lists of genes

Anand Kumar anand.kumar at ifomis.uni-leipzig.de
Tue May 25 08:55:31 PDT 2004


Hello Wendy,

You should take genes with both single and multiple annotations, since multiple annotations help to understand the relations between GO terms present in its three orthogonal axis. This is important since there are many patterns one can find and it you trace them, you could get a whole pathway or parts of it. 
We have recently written a paper to be presented at Coputerm/Coling 2004 and the draft version is at:

http://www.uni-leipzig.de/~akumar/coling.pdf

This paper only deals with TIGR database and can be useful to your work.

Not sure if this interests you but furthermore if you connect GO cellular component axis to a lower granularity larger anatomy like FMA, then you can even goto disease levels, making a bridge between bio and medical informatics. We are doing this work for colon carcinoma.

Your work on GO looks quite interesting. We are having a GO workshop in Leipzig next week, the details of which are at:
http://www.ifomis.uni-leipzig.de/Events/GeneOntology_2004/

As an outcome of the workshop, I plan to propose a study group on the topics you have raised your email. It would be good if you could let me know about your work, so that I could share it with the GO consortium members which will be present at the workshop, and can post it back to you and on the list here. 

Kind Regards,
Anand.



Am Di 25.05.2004 17:29, Wendy Parris <wendy.parris at duke.edu> schrieb:

>  
> 
> I have obtained Go annotations (and chosen broad terms, such as cell
> communication, protein metabolism, nucleoside etc metabolism, transport etc)
> ) for a list of genes I am analyzing under Biological Function.  My goal is
> to try and detect differences in annotations between subsets of genes from
> this list.  Of course each gene may have multiple annotations. When
> performing such an analysis is there a norm for dealing with this.  ie
> Should the "differences in annotation analyses" be done using only those
> genes with unique annotations, or is it appropriate to include genes with
> multiple annotations.  Any input about the conventions other people use
> would be greatly appreciated.
> 
> Thank you,
> 
> Wendy
> 
>  
> 

Anand Kumar MBBS, PhD
IFOMIS
Faculty of Medicine
University of Leipzig
Härtelstraße 16-18
04107 Leipzig
Germany
http://www.uni-leipzig.de/~akumar/







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