GO enrichment and exclusion of genes without GO terms

Question

[linelr]

Hi!

I´m new to this forum, so first of all I´d just want to say that the biostars community has been a really important platform for me to learn more about bioinformatics. So, thank you!

I´m doing an GO enrichment analysis with Blast2GO for a set of approx. 500 differentially expressed genes. Quite a few of the DE genes do not have a GO term. Can I (and should I) exclude them from the enrichment analysis? And if yes, why?

Line

[linelr]

Thank you!

and thanks for the links, I will definitely read them.

[ivivek_ngs]

It is indeed a great place to learn . Just a note. Please move this as a comment rather than putting it up as answer. Take a look at this tutorial for effective usage of the forum for your own benefits in coming future.

[linelr]

sure!

the link does not work, though.

[ivivek_ngs]

Ah so it was there when I posted probably the moderators are working on it to make some changes , that is the reason it is down now.

Answer 1

[Sukhi Singh]

Welcome to Biostars.

I reckon, if the genes have no terms associated with them, they anyways will not be included in the enrichment analysis. You do not have to manually remove them. Although, you can cross-check, your results, by taking the genes that you are interested and using one of the open-source web tools like Enrichr, David, Panther etc.

Further pointers, if interested

Tools To Find Gene Ontology Term Enrichment

Pointers To Learn About Functional Enrichment And Go Analysis

Best Way To Do Pathway Analysis Of A Set Of Genes?

[ivivek_ngs]

I would not reckon using DAVID if you look at this link, the other 2 tools are great for usage and quite easy to learn for for a newbie. Another tool I prefer using is GOrilla, quite updated as well. +1 for the pointers.

[linelr]

Thank you!

and thanks for the links, I will definitely read them.

[Sukhi Singh]

Personally, I never use DAVID, its just some people have made it as their standard GO tool. So, I just added not to disappoint them :)

[ivivek_ngs]

I can understand the crossed eye brows when one of the developers or even most frequented users come across my comment. I have been using DAVID in my earlier days but learnt it over a year and half about its non-frequent updates , so stopped it. It is not about disappointing or disapproving, it is just that things make much more sense if we use updated stuffs for research purpose. Thats what I have learnt past few years from the Biostars community and then draw eventful meaning out of results. It all boils down to mostly data driven hypothesis for me.