Question: problem in probeID conversion in Staphylococcus aureus
0
gravatar for nazaninhoseinkhan
3.9 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan410 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

ADD COMMENTlink modified 3.9 years ago by zjhzwang180 • written 3.9 years ago by nazaninhoseinkhan410
0
gravatar for zjhzwang
3.9 years ago by
zjhzwang180
zjhzwang180 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 COMMENTlink written 3.9 years ago by zjhzwang180

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 REPLYlink written 3.9 years ago by nazaninhoseinkhan410

Maybe you can use the second column Protein accession numbers

ADD REPLYlink written 3.9 years ago by zjhzwang180
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