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String db knows some gene symbols of DEGs for more than one protein and after entering gene symbols ask to select the desiered gene.

I performed a differential expression analysis with R. Now I have a list of differential expressed gene symbols and I want to visualize them with Cytoscape. When I enter DE gene symbols to sring db plugin of Cytoscape, it knows some of the gene symbols for more than one protein and asks to choose between them and I don't know how to sure which one is my desired one. So I have to choose a safer way to transfer DEGs to string. Does exist a way to transfer exactly the DEGs themselves to sring by R?

r cytoscape string app network visualization
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updated by scooter scooter • written by Sib • Sib

1 answer

There are several approaches here, but fundamentally, gene symbols are not unique (as you discovered) and are not a great way to identify differentially expressed genes. I would suggest translating your gene symbols to uniprot or ensemble identifiers. These should work much better when you hand them off to string-db.

-- scooter

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written by scooter scooter

thanks to reply my question. I also have tried ensemble IDs. But the same problem occurs is about ensemble IDs. I saw in many related articles researchers used GENE-SYMBOLs for transferring genes from GEO to STRING and I was wondering about that because they lose many DEGs.

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written by Sib • Sib

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