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?
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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
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.
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 :)
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.
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Thank you!
and thanks for the links, I will definitely read them.
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.
sure!
the link does not work, though.
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.