Preparing functional gene set for DECODE program

Question

[nazaninhoseinkhan]

Dear all, I want to identify pairs of differential co-expressed genes between two conditions.

I used to apply DiffCorr package for this purpose, however I get the following error:

"Error in if (max(x) > 1 | min(x) < 0) stop("input p-values must all be in the range 0 to 1!") : missing value where TRUE/FALSE needed"

Since I could not solve this problem, I switched to DECODE program. However I do not know how to prepare Functional gene set for this program that its structure have to be like this:

Column 1: positive regulation of epidermal growth factor-activated receptor activity

Column 2: GO 0045741

Column 3: EREG

Column 4: FBXW7

....

Can any one tell me how to make this table.

I searched GO but I could not find what I wanted.

Thank you in advance

Nazanin

Answer 1

[h.mon]

Not pretty, but it (almost) works:

library( gage )
library( org.Hs.eg.db )

go.bta <- go.gsets( "bovine" )

gs <- NULL
for( i in 1:length( names(gocc.bta) ) ){
  gs <- rbind ( gs, c( names(gocc.bta)[[i]], 
                       substr( names(gocc.bta)[[i]], 1,10 ), 
                       paste0( gocc.bta[[i]], collapse="\t") ) )
}
write.table( gs, file = "gene.set", sep = "\t", quote = F, row.names = F, col.names = F )

It uses the go.gsets() function from gage to compile the GO sets from a Org.Db package. You will have to convert ENTREZ gene ids to gene names, use the geneannot.map() function from the pathview package.

Now, please provide links to the packages you are using, makes our lifes easier. And please use the formatting buttons to make your post more readable. And why didn't you just copy/pasted DECODE explanation of the gene set format? It is more intuitive and general than your explanation.

Input gene set data format

Rows:

Each row consists of a gene set (including gene set names, id, and genes)

Columns (columns are tab separated):

Column 1: Name of gene set

Column 2: Gene set ID (e.g. GO ID)

Starting from column 3: Genes (using official gene symbols) in the gene set