BinGo customerized work flow

Question

[Chao.wang2]

Hi everyone,

Is there anyone who familiar with BiNGO for gene ontology enrichment. How to make your own annotation and ontology file based on the ensemble ID? And also a naive question, what is difference between these to file?

Thanks guys

[Chao.wang2]

I can easily retrieve the GO term accession from the ensembl Biomart, is that the right way to do it?

Answer 1

[David Quigley]

The ontology file describes the structure of the ontology tree. It has three root nodes (Biological Process, Molecular Function, Cellular Compartment) and gets more specific from there, e.g. "M phase mitosis". It does not link any particular gene to an ontology entry. The Annotation file indicates which gene symbols correspond to the ontology terms specified in the ontology file.

The BiNGO documentation has a step-by-step guide to customizing the annotation files. Google is your friend!

[Chao.wang2]

Thanks David. That makes sense now for me.