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I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest associated with each of those genes in the other (the important part is that the genes are identified by the CG number). The second dataset is this study from multiple species where genes are identified by "GLEANR" ID's like this one: "dsim_GLEANR_10060".

I would like to extract all of the values from this study for the D.melanogaster and D.simulans data, then link that to the Annotation ID's in the first dataset (to connect my variable of interest to the sex bias in expression for each species). The trouble I am having is connecting the orthologous genes within the second study to each other, and then connecting them to the CG identifiers in the first study.

Does anyone have any suggestions on resources which can be used to get this all to link up?

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This is the FlyBase page for the example gene: Dsim\GD10095. There, you have a section "orthologs", linking to OrthoDB. So my suggestion is: Find the list of synonyms for D. simulans on FlyBase (perhaps here?), download the Drosophila section of OrthoDB, and finally find the 1:1 orthologs.

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Thanks, I am looking at this now - I assume each gene has a unique FBgn and their orthologs are identified by the ODB6_OG_ID (?) and the species identified by DROME, DROSI, DROSE... taking just those three variables I can create a data frame of each ODB6_OG_ID in the first column and columns for each species giving its orthologous FBgn ID for each species of interest? But how do I "Find the 1:1 orthologs"? –  GriffinEvo Mar 8 '13 at 10:30
    
Sometimes you have a strain-specific gene duplication, which you probably want to exclude to keep things simple. So you can check for each species if there's more than one gene associated with an ODB6_OG_ID, and remove those. –  Michael Kuhn Mar 8 '13 at 11:18
    
I got this all working after a good ol' fashioned wrestle with R today - thanks a lot for the help! –  GriffinEvo Mar 11 '13 at 20:02
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You could also use biomart for this purposes.

Click on the "ID Converter" tab in the "Tools" section (on the left).

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