Dear Seniors and all members,
Me again!! I hope you do not mind me as a junior in RNAseq and tried to learn and finish my degree. Sorry for another question. I have done WGCNA and was able to identify the module associated with traits and exported data for Gene Ontology and network via cytoscape. I worked on mouse tumour tissue untreated or treated with radiation.
I had a module, which contains almost a 1000 genes and I would like to do gene ontology particularly over representative analysis for that module. Basically, I had gene symbol in my output and to do gene ontology, I had to convert it to entrezID. I use the following code chunk from Biomart library.
gene_id<- getBM(attributes = c("ensembl_gene_id", "external_gene_name", "entrezgene_id"), mart = useDataset("mmusculus_gene_ensembl", useMart("ensembl")))
Here is the output I got.
and I used the following code chunk to map entrezID to my gene symbol
d1<- merge(d, gene_id[,c(2,3)], by.x="GeneID", by.y="external_gene_name")
## Gene Ontology
I first used ClusterProfiler to perform GO over representative analysis using the following code after creating genelist.
ego <- enrichGO(gene = gene, universe = names(geneList), OrgDb = org.Mm.eg.db, ont = "BP", pAdjustMethod = "BH", pvalueCutoff = 0.01, qvalueCutoff = 0.05, readable = TRUE)
I got error as shown in the following
--> No gene can be mapped.... --> Expected input gene ID: 75002,70099,50796,104310,71099,18663 --> return NULL...
I guess I had the correct entrezID in my genelist, which is integer. Why there was no gene that can be mapped? I had read previous posts in biostar from members, who had experienced the same problem and our members said these are not mouse entrezID. May I ask whether my code chunk used to generate generate entrezID is correct for mouse organism.
Also, I have try another option in R using
testing<- new("GOHyperGParams", geneIds= selectgene, universeGeneIds= unversegene, annotation= "org.Mm.eg.db", ontology= "BP", pvalueCutoff= cutoff, conditional= FALSE, testDirection="over")
Here is the output
1 GOBPID Pvalue OddsRatio ExpCount Count Size Term
<0 rows> (or 0-length row.names)
Warning message: No results met the specified criteria. Returning 0-row data.frame >
Does this mean my genelist is not found in any GO geneset or just because the error with entrezID conversion? it is weird because I had lots of genes and I should have gotten some outputs. Thank for taking time reading my question. Is there any online web-interface to do gene ontology outside R? looking forward to hearing from all seniors and members soon.