Entering edit mode
10 weeks ago
Bioinfo • 0
I have a list of 2000 genes that I want to classify them based on gene ontology . I am only interested in those that are located in nucleus.
as an example, I selected some genes that I know couple of them are in nucleus and cytoplasm. I want to pick those that are at least in cellular compartment of nucleus
I am doing it in R
df<- structure(list(Gene = c("YAP1", "TPM3\xca", "LUZP1\xca", "MYL9\xca", "SCC1L\xca", "DBN1\xca", "MYO18A\xca", "MPRIP\xca", "MPRIP2", "PLS3\xca", "TPM3\xca", "TUBB\xca", "KIAA1671\xca", "SCRIB\xca", "PPP1R12A\xca", "SCRIB2", "TUBB\xca", "FLNA\xca")), class = "data.frame", row.names = c(NA, -18L))
then I do gene ontology
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") tb_id <- getBM(attributes=c("uniprot_gn_id","ensembl_gene_id","entrezgene_id", "external_gene_name"), filters = 'external_gene_name', values = df, mart = ensembl) sig_genes <- unique(tb_id$entrezgene_id) sig_genes <- sig_genes[!is.na(sig_genes)]
but now how would you go to get those that are only in nucleus ?
any other approach or database etc?
Please consider using the search functionality in the future:
@Matthias Zepper thank none is giving the answer. I didn't find a proper answer on the web, otherwise I would not ask here ,
Are you sure? These answers look very helpful. i.e., They mention human protein atlas which has subcellular localizations. You can get a list like this:
@barslmn one by one, will take me forever and they don't match to Uniprot
I didn't match these one by one neither I said you should. I am just saying threads above looks helpful and just picked one of those to demonstrate. If you want to match with UniProt there is also solutions about that in the threads above.