What’s Your Problem? Open Thread

wyp_q_mark2_thumbnail1Welcome 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.

We’d also like to invite resource providers to let us know if they have something new to talk about, or something they want to mention to the bioinformatics community. We’ve had some people email us because they weren’t sure if they should post something, and we want to say that’s fine.

So What’s Your Problem? And What’s Your Solution? :)

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4 thoughts on “What’s Your Problem? Open Thread

  1. Adrian


    Here is my problem:

    I want to retrieve, say from the EnsEMBL database, all genes annotated to be transcription factors, or interleuking (receptor) genes. I guess I could use the GO but I can not find a GO term for interleukin for example.

    What do you suggest?


  2. Jennifer Post author

    Hi Adrian,

    * There are several ways to find ‘the GO term of your dreams’, or even research needs, but an easy one is to directly to the Gene Ontology website: http://www.geneontology.org/. As soon as the page opens you will see a search box – change the radio button from ‘gene or protein name’ to ‘GO term or ID’. Then enter any term, or partial term you’d like to search on. When I searched on ‘interleukin’ I got back 489 hits in all categories. I can use the tools at the top of the results page to filter these results by product type, species, data source, GO branch and more. If I search specifically for ‘interleukin receptor’ and specified that I wanted GO terms rather than genes or proteins, I narrowed my results down to 83 hits, which included complexes, interleukin binding proteins, etc. On the right side of the results page you can click links to see genes associated with the term, either as a list or a tree. If the gene list that you receive isn’t satisfactory, you could query directly at EnsEMBL, where there are very powerful filtering & querying tools.

    * To find a list of genes associated with a particular GO term directly at EnsEMBL http://www.ensembl.org, I suggest using the BioMart tool. From the EnsEMBL homepage at , open the BioMart tool – either from the link labeled ‘Mine Ensembl with BioMart’ on the right, or from the link at the top of the page (in the dark blue bar). The BioMart tool will open as an almost blank page because it follows a ‘less is more’ philosophy. To use the tool you will need to specify a dataset to search by choosing a database (I chose Ensembl genes 59) and then a dataset (Homo sapiens genes(GRCh37), for example).

    Next, in order to specify that you want to search for specific GO terms, you will set filters and then possibly attributes. In the blue area on the left of the interface, click the word ‘Filters’. A set of expandable filter tools will appear on the right side of the interface. Expand the Gene Ontology tools by clicking its plus sign. When open you will see many filtering options that allow you to enter a GO term from any of the three GO branches (BP, MF or CC; either using the term name or ID#) & specify the level of evidence you desire. I entered the term ‘GO:0005897′ (which is CC ‘interleukin-9 receptor complex’) into the ‘ GO Cellular Component Term Accession’ box, clicked enter. My results came back as a text file of Ensembl gene IDs that I could either save or open. I could have further refined my BioMart query to specify whatever information I wanted included in my output file. We’ve go several tutorials on these sorts of things, if you’ve got a subscription to us.

    If neither of these techniques work for you feel free to let us know & I’ll suggest other options. I also strongly recommend checking out the GO wiki http://wiki.geneontology.org/index.php/Main_Page, or if you still need help emailing the GO help desk gohelp@geneontology.org. GO consortium members take user help VERY seriously and are excellent at answering emails & solving problems, in my experience.

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