gene ontology of a certain gene names
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10 weeks ago
Bioinfo • 0

Hi guys,

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?

R • 576 views
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@Matthias Zepper thank none is giving the answer. I didn't find a proper answer on the web, otherwise I would not ask here ,

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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:

ENSG00000058272  PPP1R12A  Actin filaments;Cytosol
ENSG00000102024  PLS3      Cytosol;Plasma membrane
ENSG00000113758  DBN1      Actin filaments;Plasma membrane
ENSG00000133030  MPRIP     Actin filaments
ENSG00000137693  YAP1      Nucleoplasm
ENSG00000143549  TPM3      Actin filaments
ENSG00000169641  LUZP1     Actin filaments
ENSG00000180900  SCRIB     Cell Junctions;Plasma membrane
ENSG00000196230  TUBB      Microtubules
ENSG00000196924  FLNA      Actin filaments;Cytosol;Plasma membrane
ENSG00000197077  KIAA1671  Microtubules
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@barslmn one by one, will take me forever and they don't match to Uniprot

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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.

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