Retreive and filter GO annotations for a list of genes using mygene.info via R
The annotate-genes.R script contains a set of functions that you can source in order to make them available in your R environment.
Note: the dependency on the mygene package proved to be tricky on a M1X Mac (see notes in script).
Once you have successfully sourced the function-containting script, annotate-genes.R, then you can simply pass a list of genes to the makeAnnotationDF function to generate an R-friendly data.frame with the GO annotations you want. Query genes can be provided as symbols, NCBI Gene IDs or Ensembl IDs. Refer to the annotate-genes.R script for all parameter options per function.
For example:
my.gene.list <- c("sox9", "tbx5")
#annotate with GO terms from the molecular function branch
my.df <- makeAnnotationDF(my.gene.list, species='mouse', go.branch = "MF")
#or, annotate only with MF GO terms that contain "transcription factor"
my.df2 <- makeAnnotationDF(my.gene.list, species='mouse', go.branch = "MF", pattern="^.*transcription factor.*$")
And the output include the query gene, GO term name, GO ID, evidences and qualifiers:
gene term id evidences qualifiers
1 sox9 beta-catenin binding GO:0008013 IDA,IPI enables,enables
2 sox9 cis-regulatory region sequence-specific DNA binding GO:0000987 IDA enables
3 sox9 DNA binding GO:0003677 IDA enables
4 sox9 DNA-binding transcription activator activity, RNA polymerase II-specific GO:0001228 IDA enables
5 sox9 DNA-binding transcription factor activity GO:0003700 IDA,IMP enables,enables
6 sox9 DNA-binding transcription factor activity, RNA polymerase II-specific GO:0000981 IDA enables
7 sox9 pre-mRNA intronic binding GO:0097157 IDA enables
8 sox9 protein binding GO:0005515 IPI enables
9 sox9 RNA polymerase II cis-regulatory region sequence-specific DNA binding GO:0000978 IDA enables
10 sox9 sequence-specific DNA binding GO:0043565 IDA enables
11 sox9 transcription cis-regulatory region binding GO:0000976 IDA enables
12 tbx5 DNA binding GO:0003677 IDA enables
13 tbx5 DNA-binding transcription activator activity, RNA polymerase II-specific GO:0001228 IDA enables
14 tbx5 DNA-binding transcription factor activity GO:0003700 IDA enables
15 tbx5 protein binding GO:0005515 IPI enables
16 tbx5 RNA polymerase II cis-regulatory region sequence-specific DNA binding GO:0000978 IDA enables
17 tbx5 RNA polymerase II transcription regulatory region sequence-specific DNA binding GO:0000977 IDA enables