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Question: problem in probeID conversion in Staphylococcus aureus
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gravatar for nazaninhoseinkhan
3.9 years ago by
nazaninhoseinkhan • 410
Iran, Islamic Republic Of
nazaninhoseinkhan • 410 wrote:

Dear all,

I want to do functional clustering of large number of co-expressed genes belong to bacterium Staphylococus aureus . I have the transcript Ids of these genes, but unfortunately DAVID functional annotation tool does not recognize them.

I tried to convert these ids using Biodbnet, but it did not work either. ds The ids belong to gpl1339.

Does any body have any idea what should I do?

Thank you in advance

Nazanin
affyid conversion gpl1339 staphylococcus aureus • 1.1k views
ADD COMMENT • link •
modified 3.9 years ago by zjhzwang • 180 • written 3.9 years ago by nazaninhoseinkhan • 410
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gravatar for zjhzwang
3.9 years ago by
zjhzwang • 180
zjhzwang • 180 wrote:

You can get ID information from GEO database directly.
For your dataset GPL1339, the URL is :
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GPL1339&id=13187&db=GeoDb_blob89
ADD COMMENT • link written 3.9 years ago by zjhzwang • 180

Thank u. But I had already downloaded this annotation file. When I open gpl1339 in excel, unfortunately gene symbol column is empty and no other columns has gene symbols

ADD REPLY • link written 3.9 years ago by nazaninhoseinkhan • 410

Maybe you can use the second column Protein accession numbers

ADD REPLY • link written 3.9 years ago by zjhzwang • 180
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