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.

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6 thoughts on “What's Your Problem? Open Thread

  1. Shirley

    I’m looking for tools or methods that provide descriptive information about lists of genes or proteins. I have a few criteria that have made the search difficult:

    1. The tool should provide information that is representative (as much as possible) of the list as a whole, not just individual members.
    2. The list can be composed of genes/proteins from multiple species.
    3. The tool should use literature or text rather than or in addition to controlled vocabularies / ontologies.

    At a minimum, #1 and #2 need to be satisfied – GO TermFinder and DAVID are examples. I’m interested in any other tools that satisfy at least #1 and #2, but especially all three.

    Thanks in advance for any suggestions!

  2. Mary

    That is remarkable–just yesterday we were having this discussion at a lunch following a talk at the Whitehead Institute. We thought of these:

    FatiGO: http://fatigo.bioinfo.cnio.es/bioinfo/
    Also at their site is this intriguing tool–but I haven’t used it: IDconverter light: http://idclight.bioinfo.cnio.es/

    SkyPainter at Reactome might work for some genes in pathways that have been curated. You enter a list, and the genes (if present) are color coded on the pathways. So you could spot over-represented pathways: http://reactome.org/cgi-bin/skypainter2?DB=gk_current

    GOstat was a favorite of someone else at lunch:

    I think if GoPubMed had an upload option that would solve it, but I can’t see one: http://www.gopubmed.org/

    And there are a lot we are investigating on the GO tools page: http://www.geneontology.org/GO.tools.shtml

    But we are still in the evaluation phase of which ones we want to focus on. It would be a big help if they even just had some descriptions next to each one.

    This question frequently comes across the GO mailing list–let me search there and see what I find.

  3. Shirley

    Thanks for the quick reply, and I’m excited to see what else you find. Just to reiterate, I’d be especially interested if you happen to come across something that uses literature rather than GO! Looking forward to the update.

  4. Mary

    On the GO mailing list, the Onto tools were mentioned:

    FABLE came up for literature, and I see now they have a copy of the UCSC Genome Browser added to it–you *might* be able to get a nice custom query build up that combined literature and GO terms with that…? But it looks like that is only for human right now–and I don’t see a table browser option, just visual browsing. http://fable.chop.edu/ I don’t see any type of upload feature for lists here, that would be handy.

    PubSearch sounds like it is getting closer to one tool for that–but I’m not having a lot of luck there with the links: http://pubsearch.org
    The abstract with the concept is here: http://mrw.interscience.wiley.com/emrw/9780471250951/cp/cpbi/article/bi0907/current/abstract

    Chilibot sounds promising for some aspects of what you need: http://www.chilibot.net/

    PubGene: http://www.pubgene.org/ might work for you.

    I was going to do a post on this very topic soon asking for input from people on their favorite tools for handling lists of genes–anyone with a suggestion is welcome to tell us!

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