gene ontology annotation

 GAF

DNA mutation GO and deep learning

 

https://www.ebi.ac.uk/QuickGO/term/GO:0006281

Peyton used 153 genes in DNA mutaion module. 

Peyton reversed the direction of GO direction, with the top-GO term as the output layer to phenotype. Following the DCell paper. 

yeast GO terms

I was surprised at the number of GO terms in yeast genome provided by Dr. Guo.
230 for BF biological process
112 for CC Cellular location
 131 for MF. molecular function.

When I analyzed geneontology downloaded files, there are many more terms.

tb = read.table("gene_association.sgd", skip=25, sep="\t", stringsAsFactors=FALSE, quote = "", row.names = NULL)

paste("There are", length(unique(tb[,3])), "genes.")

## [1] "There are 6445 genes."

paste("There are", length(unique(tb[,9])), "types of GO terms.")

## [1] "There are 3 types of GO terms."

paste("There are", length(unique(tb[,5])), "GO terms.")

## [1] "There are 6051 GO terms."

converting GO IDs to terms

Here is a flat file from gene ontology that lists the GO ids and the description string: http://www.geneontology.org/doc/GO.terms_alt_ids

https://www.biostars.org/p/50564/

GO annotation

http://www.geneontology.org/page/download-annotations