How to pull-down gene/protein names from the database search, using R ?
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ALOK • 0
@6930566a
Last seen 7 weeks ago

Hi to all,

I'm dealing with a problem that looked so simple, but I'm able to solve...

I have a list of protein accession numbers:

for example:

"M57423" "Z70218" "L17328" "S81916" "U63332" "M77235"

and I would like to find ( in a repository for ex.) the names as:

[1] "hypothetical protein LOC221823" [2] "meningioma (disrupted in balanced translocation) 1" [3] "fasciculation and elongation protein zeta 2 (zygin II)" [4] "Phosphoglycerate kinase {alternatively spliced}" [5] "---" [6] "sodium channel, voltage-gated, type V, alpha polypeptide"

anyone can help me ?

Thanks in advance,

proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics • 99 views
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@gordon-smyth
Last seen 41 minutes ago
WEHI, Melbourne, Australia

The IDs that you list are GenBank human nucleotide accessions. They are not protein accession numbers and they should not appear in any proteomics workflow.

The human organism package org.Hs.eg.db provides a way to map GenBank accessions to Entrez Gene Ids.

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