Dear all,
I have a list of 200 genes which I have obtained from microarray analysis. I want to classify them on the basis of their function whether some of them are involved in cell proliferation, cell migration and differentiation. How can I perform this functional classification of these genes.
3 answers
You can use mygene.info to obtain the GO terms. There's a python client for mygene.info (if you prefer python), as well as an R client (available via bioconductor.) See this post for how to use the R client to get GO terms. It's so easy even someone who had never touched R prior to that (like me) was able to do it.
Use the Gene Ontology annotations. If the species you're working with is annotated in Ensembl, then you can get associated GO terms using BioMart or the API. If your species is not annotated, you can annotate the genes yourself by transferring GO terms across orthologs using e.g. TreeFam.
If you are looking for human genes:
Gene Set Clustering based on Functional annotation (GeneSCF)
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