NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
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@f83463b2
Last seen 11 weeks ago
United States

Hello all, I was wondering if it is possible to convert an NCBI protein, say, CPB2 (acc. no. NP_001265470.1) to its respective cDNA value? I must be frank, I am not entirely familiar with what cDNA is (or how one would find it on CPB2's NCBI's NLM site), so any clarifications would be appreciated. I am also wondering how the process would look like for Ensembl genes, as well as if one could put an NCBI protein or accession number into an R program and get the respective Ensembl cDNA value. Thank you for any help, Rob

Rstudio cDNA ensembldb NCBI • 351 views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States

I don't know what you mean by 'cDNA value'. That could mean any number of things, I suppose, particularly if you don't know what cDNA is (probably not really a thing in this context - cDNA stands for 'complementary DNA', and is what you get when you use reverse transcriptase to generate DNA from RNA).

In addition, CPB2 might be a protein symbol, or it might be an HGNC gene symbol. In this case it's both.

> library(org.Hs.eg.db)
## map CPB2 to NCBI ID
> select(org.Hs.eg.db, "CPB2", c("ENTREZID","SYMBOL"), "ALIAS")
'select()' returned 1:1 mapping
between keys and columns
  ALIAS ENTREZID SYMBOL
1  CPB2     1361   CPB2

## add Ensembl
> select(org.Hs.eg.db, "CPB2", c("ENTREZID","SYMBOL","ENSEMBL"), "ALIAS")
'select()' returned 1:1 mapping between keys and columns
  ALIAS ENTREZID SYMBOL         ENSEMBL
1  CPB2     1361   CPB2 ENSG00000080618

Here I assume it's an HGNC gene symbol. But I don't believe that HGNC gene symbols and protein symbols (like from UniProt) are necessarily the same, so you could also use UniProt to map.

> library(UniProt.ws)
> ws <- UniProt.ws()
> z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensembl","organism_name"), "Gene_Name")

## check that we can get a tractable number of rows
> dim(subset(z, Organism == "Homo sapiens (Human)"))
[1] 4 6

## looks OK
> subset(z, Organism == "Homo sapiens (Human)")
    From      Entry Gene.Names GeneID                        Ensembl             Organism
2   CPB2     Q96IY4       CPB2  1361; ENST00000181383.10 [Q96IY4-1]; Homo sapiens (Human)
6   CPB2 A0A087WSY5       CPB2  1361;             ENST00000439329.5; Homo sapiens (Human)
161 CPB2 A0A6Q8PG06       CPB2   <NA>             ENST00000675730.1; Homo sapiens (Human)
162 CPB2 A0A6Q8PHS9       CPB2   <NA>             ENST00000674625.1; Homo sapiens (Human)
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It does look like CBP2 is an HGNC symbol, not a protein ID though.

> z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensembl","organism_name", "id"), "Gene_Name")
> subset(z, Organism == "Homo sapiens (Human)")
    From      Entry Gene.Names GeneID                        Ensembl             Organism       Entry.Name
2   CPB2     Q96IY4       CPB2  1361; ENST00000181383.10 [Q96IY4-1]; Homo sapiens (Human)      CBPB2_HUMAN
6   CPB2 A0A087WSY5       CPB2  1361;             ENST00000439329.5; Homo sapiens (Human) A0A087WSY5_HUMAN
161 CPB2 A0A6Q8PG06       CPB2   <NA>             ENST00000675730.1; Homo sapiens (Human) A0A6Q8PG06_HUMAN
162 CPB2 A0A6Q8PHS9       CPB2   <NA>             ENST00000674625.1; Homo sapiens (Human) A0A6Q8PHS9_HUMAN

Apparently the protein ID is CBPB2.

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Thank you, this works well. As for CDNA, I figured out what I need to find, and have made a new post regarding it.

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