We've conducted an RNA-Seq study where we're trying to find a gene signature for a particular condition. We found a ten-gene signature, where two of the genes that were very specific to the condition are listed with the gene symbols "AC092165.4" and "AP001610.5" in the GTF file (from Ensembl gene ids ENSG00000237412 and ENSG00000228318, respectively). I now wish to learn more about these and have tried a number of strategies, but none of them seem to be panning out.
- I googled for the names, which gives me the Ensembl genome browser among the first hits. Here I see that these gene symbols seem to overlap with other genes, but not exactly. AP001610.5 overlaps with MX1, whereas the other one gives a 404 error message on the genome browser.
- I searched for these symbols in Integrated Genome Viewer, which again seems to show me a certain amount of overlap with other genes, such as PRSS56 and CHRND. An additional point of confusion here: if I search for the original Ensembl gene id's, entirely different areas seem to pop up.
- I searched on PubMed Gene, where a number of results come up for AC092165.4 but not for AP001610.5. Among this list are some of the aforementioned overlap genes. However, the relationship with these genes is not described in any detail. They don't seem to be among the alternative aliases even.
At this point, I'm stuck. Can anyone explain to me what these symbols mean, since they don't appear to be "standard" gene symbols? Also, if you have any tips for how to interpret these better so that we can go ahead with validating them, that would be great.