What's your problem? Open Thread

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to askq_mark2.jpg 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.You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

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

  1. Laura

    We recently received reviewer comments back on a manuscript and they suggested that we use the Allen Brain Atlas to find out how our eight candidate genes correlate in different regions of the mouse brain. I have searched the site, but only find the NeuroBlast tool that shows only the top 250 genes correlated with a particular gene. I also looked at their API tool and found the code to actually download the expression energies, but they are labeled in a grid and I haven’t found the information that links the grid point to brain regions. I appreciate any help that you can offer. Thanks!

  2. OHNews

    Hi Laura,

    We have just started developing a tutorial on the Allen Brain Atlas. I’m at a conference through tomorrow, but as soon as I get home I will look into your question in more detail.

    You might also want to look for this type of info at MGI (http://www.informatics.jax.org). I know they have nice expression data.

    (comment by Jennifer)

  3. Laura

    Thanks Jennifer! I did find the Atlas Annotation data on the website which links the x,y,z coordinates with brain regions. There were three atlas annotation files, but they did not cover all the x,y,z coordinates in the expression energies. Maybe I am missing something.

  4. Jennifer

    Hi Laura,

    We have emailed the ABA with your question and will post any answers we receive.

    In the meantime I have been digging a bit more & found a few things that I hope you find helpful. I can’t tell from you comment exactly what type of information you want (images vs expression values), or at what level of detail you want to look at the correspondence of the gene expression.

    If you want to compare expression images across genes, you can do a gene search for multiple genes, and then use the multiple image viewer to look at up to three images and the reference atlas at once. The viewer has ALL sorts of cool functions which allow you to layer images, filter images to see expression details etc. I think their help is pretty nice for these viewer functions, and you can access that here:

    I’ve created a little demo movie in which I search for a list of 6 genes. From my list (cdc28, ddit4, Gnas, llgl2, sic1, slc35f3, tbcld8) cdc28 is not found, a synonym is found for sic1 but the data is not available yet, and the other four genes are available from my search results. Again, I can only look at 3 genes at a time.
    ABA demo movie 1

    If you just need to compare expression levels on a gross anatomical level, you can download each gene’s ‘Expression Summary’ data into Excel & compare the values. I show how to go from the viewer in movie 1 to each gene’s expression summary data.
    ABA demo movie 2

    Hope that helps, and that we get others submitting their suggestions too!

    Take care,

  5. preeti

    hi jennifer,
    first its amazing to see the healthy interaction of science taking place around here,and providing helping hands to new research students like me.. congrates…!

    coming to my problem…..let me confess tht being a graduate student i am all new to molecular research, but learning this things in time. my problem is, i want to amplify the sequence of gene displayed at NCBI. now if i want to design primer manually how can i do that? i know some tools for primer design but tht doesnt give the amplification of the region i wnat. so what shoudl i do?

    and another thing, how do i standardize the PCR condition for 400bp sequence?
    do u have any tutorial or something where i can find all these stuff?
    i know i sound bit..irritating here. but try to help me if possible…


  6. Mary

    Hi Preeti–

    I would recommend Primer3, or Primer3 Plus for your work. You can enter the sequence of interest, and then ask the software to provide the primers based on a variety of criteria.

    We did a blog post about these tools here: http://www.openhelix.com/blog/?p=135, and we do have a tutorial on Primer3 in our catalog.

    If your sequence is one from a species in the UCSC Genome Browser, you can also check the amplification products in the genomic sequence from the In Silico PCR tool. We have a free tutorial on the UCSC Genome Browser.

  7. Jennifer

    Hi Laura,

    I just found an article that describes using ABA as part of a screen for genes with specific or enriched expression in target regions. If you haven’t seen the paper yet, you might want to check it out:

    “Identification of a set of genes showing regionally enriched expression in the mouse brain” D’Souza et. al.
    BMC Neuroscience 2008, 9:66

  8. vincent


    May I check what does it mean when the SNP association trend deviates towards the x-axis instead of the usual y-axis in a Q-Q plot?


    Have a great day!


  9. Mary Post author

    Oh, maybe this wasn’t about GRAIL? I saw the other question first and couldn’t figure out what you meant.

    Trey is our SNP maven, but he’s on the road right now. I’ll let him know there’s a question on this and try to have him take a look at this.

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