What's your problem? Open Thread

q_mark2.jpgWelcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.

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4 thoughts on “What's your problem? Open Thread

  1. azalea

    Hi,
    My friend has a question:
    How to find gene ontology annotation by ensembl ID?
    the Gene Ontology Database does not seem to accept an ensembl ID.
    Thank you in advance,

    azalea

  2. Mary

    Hi azalea:

    Actually, I think there is a way to do it at the GO site. I will step through a search that worked for me below. However, there are also a lot of other useful GO tools for analysis of lists and we discussed some here: http://www.openhelix.com/blog/?p=158 You can check those out as well.

    To use Ensembl IDs at GO:
    1. Go to http://www.geneontology.org/
    2. Click the word AmiGO above the quick search box. (I know, it looks like the same quick search box).
    3. On the new quick search page, click the Search link in the top navigation area. This should get you to the “Advanced Search”. The direct URL for that is here: http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?action=advanced_query&session_id=9225amigo1209041291
    But I’m not sure that link will work on the blog. I wanted to give you the path to reproduce it anyway.
    4. On the Advanced Search page, enter an ensembl ID in the text box (I’m using one I just pulled out of ensembl: ENSG00000141510. You can find a box there to upload a list, though, too.
    5. Very important: change the “search type” radio button to “Genes or Proteins”. I would also check Database ID.
    6. Submit query.
    7. Results: for some reason it clicks back to the other radio button search the first time (may be a bug–I clicked near the box and it un-selects it for some reason). I re-ran it with the Genes/Prots button clicked and it worked. I get 2 genes that match this.
    You can then perform a bunch of things on your results list.

    Another thing I thought of while writing this was BioMart. I’ll bet you can get what you want from there too: http://www.ensembl.org/biomart/martview/737c0d37b0cea4e6ee8b24f837f7d198

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