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

Question

[animesh_10kuet]

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.

[Juke34]

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

[animesh_10kuet]

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

Answer 1

[EagleEye]

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

[animesh_10kuet]

Is there any solution of this problem in R ??

[EagleEye]

I do not have much idea about R based tools which accepts custom annotation. But try with GSEA where you can create custom annotation file as .gmt and use it as reference. It is available For R,

http://software.broadinstitute.org/gsea/downloads.jsp