Question: GOSeq gene ontology enrichment analysis in rice
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gravatar for Bioinfonext
6 weeks ago by
Bioinfonext220
Korea
Bioinfonext220 wrote:

I need your help for Goseq R code for gene ontology enrichment analysis for differentially expressed gene identified by DESeq2.

I got the differentially expressed genes and I can also download the mapping file from biomart for all the rice gene ID like below:

Gene stableID   Transcript stable ID           GO term accession
BGIOSGA013239  BGIOSGA013239-TA                   GO:0009098
BGIOSGA013239  BGIOSGA013239-TA                   GO:0003862
BGIOSGA013239  BGIOSGA013239-TA                   GO:0009082
BGIOSGA013239  BGIOSGA013239-TA                   GO:0016616
BGIOSGA013239  BGIOSGA013239-TA                   GO:0051287

.....................

Goseq code:
d <- read.csv("deseq2res.csv", header=T, row.names=1)
all_genes <- row.names(d)
 DE_genes <- all_genes[d$padj<0.05]

I am not sure how should I proceed further after this? I am not able to understand how should I get the genes.vector and length.vector.names for the below code and then GO_data.frame?

pwf <- nullp(genes.vector,bias.data=length.vector.names)
head(pwf)

# calculate GO enrichment using default method
GO.WALL <- goseq(pwf, gene2cat=GO_data.frame)

Many thanks, Bioinfonext

goseq R • 114 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Bioinfonext220

Not a GOSeq solution but since you are working with Oryza sativa indica you could use AgriGO v2.

The input file will be a list of gene_id i.e, the gene_id of your differentially expressed genes

ADD REPLYlink written 6 weeks ago by andres.firrincieli600
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