I am working on RNA sequencing data analysis of Pichia pastoris (Komagataella phaffi)CBS 7435. I have an excel sheet of differentially expressed genes. I want to cluster the genes on the basis of functional similarity. The gene IDs in the excel sheet are given in the following format ACIB2EUKG772156, I also have the gene locus- BQ9382_C4-0695, protein product- SOP83056.1 and Uniref100 IDs- F2QY27. The online tools available for clustering genes require abbreviated gene names or UniprotKB IDs to perform analysis. I also have Gene Ontology for each gene. Can someone please guide me in how to get these gene/ protein IDs converted to abbreviated gene names and UniprotKB IDs? Or any other gene or protein IDs that the online tools can recognize.
You may take the help of ID retrieval option in UNIPROT database.
There you can convert gene id s to UNIPROT IDs
You can also try g:profiler, specifically g:Convert;
http://biit.cs.ut.ee/gprofiler/convert
Note that one protein can lead to a number of genes, so converting gets messy very quickly.
It depends on the ID. You may obtain references from places like ncbi, but still there will be an Id for each. This means the IDs will be different in each place. However they do share some similarity. This means if you search pichia pastoris, on uniprot, you could find any label,names and Id. Ncbi and uniprot normally do match. This means the information may be shared. Maybe you could make a list when you download. (txt or CSV)