Column that include Enterez ID converted from wheat Ensemble ID using biomart package is empty!

Question

[Yunus ŞAHİN]

I have Triticum monoccoccum ssp. monococcum transcriptome data performing DEG analysis by Deseq2 package. I filtered the genes that less than 0.05 p-values. While i convert Ensemble ID to Enterez ID using biomart package in R, the column that include Enterez ID is empty. The codes are here;

DGEgenes <- rownames(subset(DESeq.ds.results, padj < 0.05))

features <- getBM(attributes = c("ensembl_gene_id",
                                 "go_id",
                                 "entrezgene",
                                 "description",
                                 "interpro",
                                 "kegg_enzyme",
                                 "pfam"),
                  filters = c("ensembl_gene_id"),
                  values = DGEgenes, 
                  mart = ensembl)

How can i get enterez id that is required for KEGG enrichment analyisis or can someone please recommend other way to get them.

[Lila M]

Hi, I assume that you have loaded the data set of interest as:

mart <- useDataset("dataset", useMart("ensembl"))

and your genes are in ensembl_gene_id format:

features <- getBM(attributes = c("ensembl_gene_id",  "go_id",  "entrezgene",  "description", "interpro", "kegg_enzyme", "pfam"), 
 filters = "ensembl_gene_id", 
 values = DGEgenes,
 mart = mart)

Do you get any error message? DO you get the other attributes?

[Kevin Blighe]

In addition to Lila's questions, please show how you create the connection to the database, i.e., your commands prior to getBM()

[Yunus ŞAHİN]

Hi Kevin thank you so much replying,

here it is;

library("biomaRt") 

ensembl <- useMart(biomart = "plants_mart",
                   dataset = "taestivum_eg_gene",
                   host = "plants.ensembl.org")

[Yunus ŞAHİN]

Hi Dear Lila thank you so much for replying

I do not have error message and I have got some of other ones. here the codes before getBM() function;

library("biomaRt")

ensembl <- useMart(biomart = "plants_mart", dataset = "taestivum_eg_gene", host = "plants.ensembl.org")

[Kevin Blighe]

It is quite possible that no annotation yet exists for the genes for which no value is returned. This occurs even in human gene annotations. Can you provide some example IDs that have no match?

[Yunus ŞAHİN]

now i got error message.

library("biomaRt") #annotation
ensembl <- useMart(biomart = "plants_mart",
                   dataset = "taestivum_eg_gene",
                   host = "plants.ensembl.org")

features <- getBM(attributes = c("ensembl_gene_id",
                                  "go_id",
                                  "entrezgene",
                                  "description",
                                  "interpro",
                                  "kegg_enzyme",
                                  "pfam"),
                   filters = c("ensembl_gene_id"),
                   values = DGEgenes, 
                   mart = ensembl)

Error in getBM(attributes = c("ensembl_gene_id", "go_id", "entrezgene",  : 
  Invalid attribute(s): entrezgene 
Please use the function 'listAttributes' to get valid attribute names

[Lila M]

The column has been created but is empty? Or is there not column at all? Try first with entrezgene only and see if any error or warning message appears.

[Yunus ŞAHİN]

opps now i got error message

library("biomaRt") #annotation
 ensembl <- useMart(biomart = "plants_mart",
                    dataset = "taestivum_eg_gene",
                    host = "plants.ensembl.org")

 features <- getBM(attributes = c("ensembl_gene_id",
                                  "go_id",
                                  "entrezgene",
                                  "description",
                                  "interpro",
                                  "kegg_enzyme",
                                  "pfam"),
                   filters = c("ensembl_gene_id"),
                   values = DGEgenes, 
                   mart = ensembl)


Error in getBM(attributes = c("ensembl_gene_id", "go_id", "entrezgene",  : 
  Invalid attribute(s): entrezgene 
Please use the function 'listAttributes' to get valid attribute names

[Lila M]

I guess that, so use the function listAttributes and find entrezgene (copy and paste to your code). However, as @Kevin suggest, is possible that not annotation exist at all for your genes.

[GenoMax]

Yunus ŞAHİN : Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[Yunus ŞAHİN]

I am sorry. i am begginer to use this forum. Thank you for that