GOseq analysis

1. Ge the up and down regulated gene list. “bothDF” is the dataframe that contains both up and down-regulated genes from both EdgeR and DEseq2.

bothDF_down <- bothDF[bothDF$log2FoldChange <= -1,]
bothDF_up <- bothDF[bothDF$log2FoldChange >= 1,]

Convert to these dataframes into table with True or False values. Write the table to local directory.

DE_list_boolup <- as.data.frame(row.names(d) %in% bothDF_up$Row.names,
      row.names = row.names(d))
DE_list_booldown <- as.data.frame(row.names(d) %in% bothDF_down$Row.names,
                        row.names = row.names(d))

    col.names = F)

col.names = F)
  1. Perform the GOseq analysis in Galaxy. You will need to perform the analysis for up and down regulated genes separately.


  1. Combine gene descriptions with up and down regulated genes. You can get the S_lycopersicum_Feb_2014.bed file from the Dropbox link on Bb.
annots_file <- 'S_lycopersicum_Feb_2014.bed'
# keep gene id and gene description columns
annots <- read.delim(annots_file,sep='\t',header=F)[,13:14]
# name the columns
names(annots) <- c('gene','description')
# combine gene expression and annotations
bothDF_genedesc  <- merge(bothDF,annots, by.x = "Row.names",by.y='gene')
  1. To order your data using FDR, you use the following command in R.
bothDF_genedesc  <-  bothDF_genedesc[order(bothDF_genedesc$FDR), ]