Question: Gene ID determination (to be used in DAVID) from OrthoDB6 OG Ids and Transcription Start Site
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gravatar for saswati.s2010
2.3 years ago by
saswati.s20100 wrote:

I have a .bed file with the OrthoDB6 IDs (for example: EOG698VMB, EOG6ZPFGT) and the transcription start sites of respective IDs. I have to find out the gene ID that can used in DAVID tool for GO term analysis. Is there any file (apart from the one in the OrthoDB6 website) that can help me find out the gene IDs?

[The file which I found on the orthoDB6 site has some values missing. I want to find out the gene ID of all the orthologous sequences between D.melanogaster and D.pseudoobscura.]

Thank you for the help. :)

david orthodb6 gene • 1.3k views
ADD COMMENTlink written 2.3 years ago by saswati.s20100

Not a solution to your problem, but (if you browse around on this forum) you'll find a few hundred times that people say not to use DAVID since it hasn't been updated for a long long time. It's badly outdated. If I understand it correctly, you are working on Drosophila, it that case you could have a look at http://pantherdb.org/

ADD REPLYlink written 2.3 years ago by WouterDeCoster32k

Okay. But my main problem is how do I convert these orthoDB6 IDs (or even by using the TSS values) to FlyBase IDs or any ID that is processed by PantherDB? I am not being able to convert my data into usable form. I am using the data that I found in the supplementary files of : http://genome.cshlp.org/content/suppl/2014/05/21/gr.159384.113.DC1.html

ADD REPLYlink written 2.3 years ago by saswati.s20100
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