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Question: Missing GenBank accession numbers in the org.Hs.egACCNUM object?
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gravatar for colaneri
8 months ago by
colaneri30
United States
colaneri30 wrote:

I am trying to convert GenBank accession numbers to Entrez ID or Symbol using the org.Hs.egACCNUM object. However many of the GenBank accnum in my list do not exist in the object. The description of this object says: “This object is a simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers”.

For example if I search for AA725246 in ncbi I found this record:

=====================

ai16b08.s1 Soares_parathyroid_tumor_NbHPA Homo sapiens cDNA clone 1342935 3- similar to contains Alu repetitive element;, mRNA sequence

410 bp expressed sequence tag.

Accession: AA725246.1GI: 2742953

====================

however if I try to find AA725246 in org.Hs.egACCNUM I can not find it. 

e.g. in R

> k <- keys(org.Hs.eg.db, keytype="ACCNUM")

>"ABF01637" %in% k

[1] TRUE

 >"AA725246" %in% k

[1] FALSE

How can I convert this kind of accession number to gene symbol?

ADD COMMENTlink modified 8 months ago by James W. MacDonald45k • written 8 months ago by colaneri30
0
gravatar for James W. MacDonald
8 months ago by
United States
James W. MacDonald45k wrote:

The org.Hs.eg.db package is based on the Entrez Gene table, so by definition anything that doesn't have an Entrez Gene ID is invisible to that annotation package.

Put another way, as you noted, the description for the ACCNUM table is “This object is a simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers”. So if there isn't an Entrez Gene ID that maps to AA725246, which is just an EST that never seems to have made the leap to the big time, then the mapping can't be made.

ADD COMMENTlink written 8 months ago by James W. MacDonald45k

I see, thanks for the clarification. Then I guess the question is: is there any available tool to convert this accnum to gene identifiers.

Because those accnum I am having problem to convert comes from papers reporting gene expression differences measured by micro array. That means that they were used with the intention to represent a gene.

ADD REPLYlink written 8 months ago by colaneri30
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