Gene Mapping Issue
Hello everyone, I hope you're all doing well.
I'm currently facing an issue with DAVID—it doesn't accept certain gene names when I upload them. I managed to map some genes successfully, but now I'm stuck because these specific genes won’t map: AC140912.1 (ENSG00000261227.2), RP11-71E19.1 (ENSG00000250934.2), RP11-879F14.3 (ENSG00000267316.5), RP11-740P5.4 (ENSG00000287396.1).
Since I can't move forward with my work, I’d really appreciate any advice or solutions.
Thanks in advance!
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lieven.sterck
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won •
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won •
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DAVID List Upload/Gene Conversion Tool
written by b5708137 •
welcome won ,
A word of advise to a newbie on the forum :) : do put some work in the posts you make. The more info your provide the better and the more meaningful answers you will receive (in this specific case: eg what is the response/error you get, where did you get the gene names from , ... ) . I also always helps to indicate what you have tried already which shows that you have put effort in this to solve it yourself and not just hoping some-else to just do it for you ;)
Hey, thanks for the advice! I get what you mean, and I usually try to include as much detail as possible.
Right now, I’m working on RNA-seq analysis for cancer, specifically looking at gene expression in response to certain treatments. The issue I’m facing is with gene ID conversions.
For example:
RP11-545E17.3 = In Ensembl BioMart, it appears as ZDHHC12-DT.
RP5-1028K7.2 = BioMart didn’t return a gene name, so I used SyngoPortal, which identified it as LOC105371773. DAVID accepts this format just fine.
But for AC140912.1 and RP11-879F14.3, no matter what I try, DAVID keeps giving me an error: "You are either not sure which identifier type your list contains, or less than 80% of your list has mapped to your chosen identifier type. Please use the Gene Conversion Tool to determine the identifier type."
I’ve already tried everything I know, including checking different databases, formats, and conversion tools, but nothing seems to work. Any ideas on what else I can try?
great , thanks.
Have you tried that Gene Conversion Tool it is referring to? what was the result?
(I don't have much hands-on experience with DAVID though)