Enrichment analysis specifically by topGO

Question

[Ram]

Hello all,

I am having data frame in R with name of genes in one column and GO description in second column .

Is it possible to know how to get p-value as part of enrichment for each genes in third column .

So through TopGO I am getting different errors.

1 RALBP1 ATPase activity, coupled to movement of substances 2 RALBP1 Rac GTPase binding 3 RALBP1 Ral GTPase binding

Thanks a lot

[ivivek_ngs]

Take a look at this thread as to how to work programmtically in R

Have your tried to check the manual? You have to download the required db and then parse your list of genes as a vector and select the GO category and output the GO terms. The enrichment is Fisher test. Take a look at the manual from page 3

This R code is for Human micro-array data using topGO

There is also GOstats package which has the R code in this link that can do the enrichment and generate reports. Take a look

If you want GO enrichment pvalues you can use DAVID/EnrichR/ GOrilla/ Panther. They will give the number of genes enriched with also pvalue from the fisher test score. Just supply your gene list and put your desired species or even a background set of genes and perform GO enrichment.

There are many ways to perform this.

Answer 1

[Guangchuang Yu]

You can use clusterProfiler.

Answer 2

[EagleEye]

Why don't you try this tools which exactly does the same, Gene Set Clustering based on Functional annotation (GeneSCF)

[ivivek_ngs]

Ah yes I forgot to mention your new tool. Thanks for putting it.