How to pull-down gene/protein names from the database search, using R ?
1
0
Entering edit mode
ALOK • 0
@6930566a
Last seen 3.3 years 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 • 912 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 51 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.

ADD COMMENT

Login before adding your answer.

Traffic: 522 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6