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News: J-Express 2011 released. Download from jexpress.bioinfo.no
 
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Author Topic: Gene ontology problem  (Read 6265 times)
sainitin
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« on: August 17, 2007, 06:48:11 AM »

Dear sir,
             I have downloaded Gene ontology for human from http://www.geneontology.org/GO.current.annotations.shtml and placed in Jexpress go folder
but when i perform Gene ontology analysis in jexpress wen i click mapdataset it is not mapping genes

plz tell me the solution sir

regards
sainitin
« Last Edit: August 17, 2007, 08:20:19 AM by sainitin » Logged
Bjarte Dysvik
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« Reply #1 on: September 04, 2007, 08:12:25 PM »

Are you sure your gene association file contains the same identifiers as your data?
Please see the GO documentation and make sure the annotation is the same in your dataset as in the downloaded gene ontology file.

This is the only reason I can think of...

Bjarte
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annekristin
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« Reply #2 on: November 06, 2007, 11:07:10 AM »

This is always a problem with the human GO association file downloaded from geneontology.. J-Express uses column 3 or column 11 in the association file. You can toggle between these two columns by selecting or deselecting 'Use synonyms'.

For the human file column 3 contains Gene Symbols (amongst other types of id's, see the readme file on the download page). The problem is that they have added the suffix '_HUMAN' to the end of each id. To get this to work you will either have to add this suffix to the end of the gene symbols in your datafile or remove it from the end of the gene symbols in the association file.

Column 11 contains IPI id. If you can map your probe id's to IPI id's then this may be a better option. Since there is only one type of id in this column it is easier to get a better coverage of the go terms
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