Getting Gene Ontology information for functional analysis from appropriate databases
The Gene Ontology (GO) is a very useful restricted vocabulary of annotation terms for genes and gene products that describe the biological process, molecular function, or cellular component of an annotated entity. As such, the terms are helpful as data in gene-set enrichment analysis and other functional -omic approaches. In this recipe, we’ll look at how we can prepare a list of gene IDs in a genomic region and get the GO IDs and descriptions for them.
Getting ready
We will just need the biomaRt package from Bioconductor and an internet connection.
How to do it…
Getting GO information can be done using the following steps:
- Make connections to Ensembl BioMart and find attributes:
library(biomaRt)ensembl_connection <- useMart(biomart = "ENSEMBL_MART_ENSEMBL")listDatasets(ensembl_connection)data_set_connection <- useMart("hsapiens_gene_ensembl"...
