Question: Uniprot/Gene ID to Go id for Goseq many-to-many
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gravatar for nyoegut
6 days ago by
nyoegut0
Vienna
nyoegut0 wrote:

Hi there Biostars-Community, I want to perform Goseq with my non model organism and therefore have to generate a manual Category mapping for the goseq(pwf, gene2cat = Category_mapping,) function. Category mapping should look like the following

(...)a data frame with two columns. One column should contain the gene IDs and the other the name of an associated category. (...)mapping between categories and genes is usually many-to-many. (...)

The problem: I looked at multiple websites that provide mappings like http://geneontology.org/, bioDBnet, http://pantherdb.org/ and DAVID and everywhere the mapping output contains muliple GO IDs in one or multiple columns, often with GO terms,or you can only download each Gene ID with respective GO ID seperately . Eg like this:
Q9RTT3 (GO:0016491)(GO:0055114)(GO:0016020)(GO:0016021)

Of course I can do one of the options but I have more than 3000 genes that I want to analyse so manual formating would cost me hours, if not days (and I´m unfortunately not proficient enough in any programming language to write myself a code that can do that). Therefore I wanted to aks if somebody knows a website/mapping tool that provides many-to-many mappings of some identifier to GO IDs, so that the output would give me two columns, each containing only one GO ID (not the complete term) and one Gene Identifier/Uniprot ID per row?

Any input is highly appreciated. Thank you very much!

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