Question: Column that include Enterez ID converted from wheat Ensemble ID using biomart package is empty!
0
gravatar for Yunus ŞAHİN
10 days ago by
Turkey/Istanbul/Altınbaş University
Yunus ŞAHİN0 wrote:

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.

rna-seq next-gen R • 115 views
ADD COMMENTlink modified 10 days ago by genomax69k • written 10 days ago by Yunus ŞAHİN0
1

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?

ADD REPLYlink modified 10 days ago • written 10 days ago by Lila M 780
2

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

ADD REPLYlink written 10 days ago by Kevin Blighe45k

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")
ADD REPLYlink modified 9 days ago by genomax69k • written 9 days ago by Yunus ŞAHİN0

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")

ADD REPLYlink written 9 days ago by Yunus ŞAHİN0
1

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?

ADD REPLYlink written 9 days ago by Kevin Blighe45k

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
ADD REPLYlink modified 9 days ago by genomax69k • written 9 days ago by Yunus ŞAHİN0

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.

ADD REPLYlink modified 9 days ago • written 9 days ago by Lila M 780

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
ADD REPLYlink modified 9 days ago by genomax69k • written 9 days ago by Yunus ŞAHİN0
1

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.

ADD REPLYlink written 9 days ago by Lila M 780

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

Thank you!

ADD REPLYlink written 9 days ago by genomax69k

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

ADD REPLYlink written 6 days ago by Yunus ŞAHİN0
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