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  • Determining the biological process or function of genes

    I have a list of DEGs from DESeq from A.digitifera coral. I put them into DAVID software as a list, selected Identifier as "OFFICIAL_GENE_SYMBOL", chose Gene List, and then submitted the list. Then, I chose "Option 1: Convert the gene list to DAVID". None of the genes were in the DAVID database, was what was indicated as the result.

    Is there any software I could use that might be better for my species? I just need to do this (very) quick and dirty (for now). I am interested to determine biological processes or functions of these DEGs I have. Here is a sublist of the DEGs, in case:

    (I appreciate any help!!!!)

    aug_v2a.00154.t1
    aug_v2a.00307.t1
    aug_v2a.00601.t1
    aug_v2a.00603.t1
    aug_v2a.00823.t1
    aug_v2a.00990.t1
    aug_v2a.01279.t1
    aug_v2a.01408.t1
    aug_v2a.01492.t1
    aug_v2a.01496.t1
    aug_v2a.01618.t1
    aug_v2a.02238.t1
    aug_v2a.02239.t1
    aug_v2a.02459.t1
    aug_v2a.03293.t1
    aug_v2a.03318.t1
    aug_v2a.03417.t1
    aug_v2a.03732.t1
    aug_v2a.03955.t1
    aug_v2a.04041.t1
    aug_v2a.04353.t1
    aug_v2a.04482.t1
    aug_v2a.04679.t1
    aug_v2a.04822.t1
    aug_v2a.05042.t1
    aug_v2a.05093.t1
    aug_v2a.05179.t1
    aug_v2a.05185.t1
    aug_v2a.05514.t1
    aug_v2a.05561.t1
    aug_v2a.05667.t1
    aug_v2a.05723.t1
    aug_v2a.05776.t1
    aug_v2a.05823.t1
    aug_v2a.05859.t1
    aug_v2a.05896.t1
    aug_v2a.05945.t1
    aug_v2a.06125.t1
    aug_v2a.06180.t1
    aug_v2a.06372.t1
    aug_v2a.06390.t1
    aug_v2a.06468.t1
    aug_v2a.06469.t1
    aug_v2a.06517.t1
    aug_v2a.06763.t1
    aug_v2a.06991.t1
    aug_v2a.07140.t1
    aug_v2a.07189.t1
    aug_v2a.07227.t1
    aug_v2a.07393.t1
    aug_v2a.07523.t1
    aug_v2a.07683.t1
    aug_v2a.07824.t1
    aug_v2a.08028.t1
    aug_v2a.08251.t1
    aug_v2a.08395.t1
    aug_v2a.08398.t1
    aug_v2a.08439.t1
    aug_v2a.08791.t1
    aug_v2a.08951.t1
    aug_v2a.09028.t1
    aug_v2a.09216.t1
    aug_v2a.09226.t1
    aug_v2a.09253.t1
    aug_v2a.09307.t1
    aug_v2a.09322.t1
    aug_v2a.09376.t1

  • #2
    You are working with a very uncommon genome so this is not going to be a trivial task. You are going to have to start blasting the sequences and doing some legwork to assign a putative function to the proteins you have identified as DE.

    You can find the protein sequence for the gene models at the link Devon had posted yesterday: http://marinegenomics.oist.jp/genome...s?project_id=3

    Only 13 proteins from Acropora appear to be in RefSeq: http://www.ncbi.nlm.nih.gov/protein?...from_uid=10529

    Comment


    • #3
      This was also cross-posted on Biostars, where Jeremy Leipzig and I both already replied. Please don't cross-post, it creates double work.

      Comment

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