What's Your Problem? Open Thread

q_mark2.jpgWe’re back this week!  Welcome 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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6 thoughts on “What's Your Problem? Open Thread

  1. Wesley Brooks, D.Sc.

    I am a physiology researcher in heart failure (HF) with little knowledge of genomic data bases. I have found two ESTs (public ID # AA892765 and AI008646) that are significantly downregulated in the LV from spontaneously hypertensive rats with HF, and markedly reversed (i.e. returned to non-failing levels)with treatment which are of particular interest. Is there anyway of identifying the possible biological function of these transcripts? I think they maybe energy related based on changes of other identified transcripts from the same LV samples, but have no evidence to support this hypothesis. I would gretly apprechiate your help in gaining any further information about these unknown ESTs.

  2. Mary

    Hi Wesley–

    I’m going to look further into these sequences. I pulled them out of GenBank and I see that they actually match each other. That actually makes them kind of their own replicates and makes sense that both show the same response.

    (I took them both over the NCBI BLAST and used the feature to compare 2 sequences to each other to look at them. My job ID is YEGZ0RXT113, I’m not sure if you can take it to BLAST and enter that to see the alignment http://blast.ncbi.nlm.nih.gov/ and use the tab for recent results and put the job ID in the box and try.)

    I’m going to look around at other aspects now, but I wanted you to know I was beginning to look.

  3. Mary

    Ok, my next step was to BLAST vs the rat. I took one of those two sequences (your second one) and BLASTed vs rat genomic. It is clear that the top match is mitochondrial. My BLAST job is YEHB0CVY011 for that next one.

    So that makes sense from an energy perspective.

    But I’m going to look more into Rat and mitochondrial resources to learn more about the specific sequences. I’m going to poke around RGD first, and then mito databases.

  4. Mary

    I went over to UCSC and used their BLAT sequence alignment tool to see what the genomic view was for this region. I created a session here:
    http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Mary%20Mangan&hgS_otherUserSessionName=Rat_EST_blat You should be able to load that and see my result. It appears to match to a predicted protein. See the rat mRNAs from genbank, X52757. If you click on that item you get details about that sequence. That record at NCBI is here: http://www.ncbi.nlm.nih.gov/nuccore/288288

    It says mitochondrial D-loop region.

  5. Mary

    I think the next step is reading up on mitochondrial D-loop topics. It’s not an area I know at all.

    Hmm…this old paper speculates on rat D-loop issues in rat heart:
    http://www.ncbi.nlm.nih.gov/pubmed/7632322

    I’m not convinced there is a real protein there based on that Genbank x52757, that looks like an ORF call prediction. But it looks like d-loop may be important in mitochondrial regulation.

    I think that’s where I’d start looking for clues in the literature.

  6. Wesley Brooks, D.Sc.

    Thanks Mary,
    I was out most of yesterday, but you have given me a number of good suggestions. I am reading up on mitochondrial D-loops.
    Thanks again
    Wes Brooks

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