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Find the number of genes exist in dataset with GO functional annotation

Suppose, I have a yeast dataset containing 6100 genes with 93 samples. I want to find the number of genes in dataset which is with GO functional annotation? For example :Output will be 3957 genes.

Sample dataset are in this link. I downloaded the goslim terms by SGD from here and yeast annotation from here , gene ontology from here.

gene r go
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updated by EagleEye EagleEye • written by animesh_10kuet • animesh_10kuet

Could you show us how looks a line with the GO annotation in your file ?

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written by Juke34 Juke34

Please check the question again. I made a modification in the question. I add the link of difference sources which I already downloaded.

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written by animesh_10kuet • animesh_10kuet

1 answer

Have you tried GeneSCF. if your are worried about using updated functional database for the annotation, GeneSCF v1.1 uses current database from the source.

Gene Set Clustering based on Functional annotation (GeneSCF)

If you would like to use your own reference. You can also use your custom reference db in GeneSCF v1.0

A: GO enrichment analysis using a Text file with all the genes and GO ids associat

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written by EagleEye EagleEye

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