Gene symbols to Entrez Gene ID for S. pombe

Question

[Parham]

Hi, I want to use my Cufflinks output in order to use them in gage! I have to convert the Gene IDs to Entrez gene IDs I guess?! For that can some body help me for the species? I have gage data preparation manual but it doesn't include pombe when I print(bods)! Please give me feedback or a link that explains how to do this.

Cheers,

Answer 1

[Neilfws]

Ah, a "convert ID X to ID Y" question. The answer is almost always BioMart. In this case it's a little trickier as the organism is less widely-used, so I'll get you started:

library(biomaRt)
mart.sp <- useMart(biomart = "fungal_mart", dataset = "spombe_eg_gene", host = "fungi.ensembl.org")

# some example gene IDs
ids <- c("SPAC11D3.02c", "SPAC18B11.02c")

getBM(attributes = c("ensembl_gene_id", "entrezgene"), filters = "ensembl_gene_id", values = ids, mart = mart.sp)
#   ensembl_gene_id entrezgene
# 1    SPAC11D3.02c    2542974
# 2   SPAC18B11.02c    2542607

You could then use e.g. match() to match your list of gene IDs to the first column returned using getBM() and replace with the entrezgene column.

[Emily]

You can also do the same thing with a point and a click. See the help video here.

[Neilfws]

You can but in this case, they're using the R/Bioconductor gage package, so my example lets them stay in R.

[Emily]

Indeed, but here's hoping that other people will stumble across this by searching, rather than creating their own post. We don't want them looking at your lovely R example and thinking Oh no - I don't know what that means and creating another post asking for a pointy-clicky method.

[Parham]

But there I cannot find dataset for S. pombe!

[Neilfws]

The fungal web interface to BioMart is here.

[Parham]

Thanks, but I want to convert all the genes in gene_exp.diff out of Cufflink, not few specific genes, and I am not an advanced user. So if you could do a favour and provide few more lines on how to incorporate the whole file and convert all the IDs in the file to Entrez I extremely appreciate it.

[Neilfws]

Well, I showed those "few specific genes" just as an example. You will need to use your own list of IDs; I do not know what your data looks like or how they would be derived from it.

If, for example, you have a data frame or matrix where the gene IDs are row names, you might use something like:

ids <- rownames(mydataframe)

Presumably your gene_exp.diff file is some kind of delimited data that you can read into R using e.g. read.table().

[Parham]

OK, here I have a link to my data and a link to the workflow I am trying. Section 6.5 when it is converting IDs, I wonder what should I change in the code lines, if you could do a favour and have a look on it. Probably it is this code line that needs a change?

> gnames.eg=pathview::id2eg(gnames, category ="symbol")

Thanks!