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Date : Fri, 24 Jun 2011 09:48:20 +0100
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--- Begin Message ---
Hi,
I am not sure whether there is a mailing list to share my (lack of)
experience!
However, I am contacting you because I found the following issue with
queries for Entrez Gene IDs.
Actually, initially, this was using biomaRt Bioconductor package but it
is clearly not an issue of biomaRt.
When I interrogate ENTREZ, duplicated items are returned: one with the
correct Entrez ID, the others empty.
For example:
Input:
ENSMUSG00000026073
ENSMUSG00000026180
ENSMUSG00000053846
ENSMUSG00000035208
ENSMUSG00000069830
ENSMUSG00000078853
ENSMUSG00000020826
ENSMUSG00000030077
ENSMUSG00000050075
ENSMUSG00000070501
Normal output:
Ensembl Gene ID Associated Gene Name MGI symbol Chromosome Name Gene
Start (bp) Gene End (bp)
ENSMUSG00000020826 Nos2 Nos2 11 78734289 78773756
ENSMUSG00000026073 Il1r2 Il1r2 1 40141613 40182064
ENSMUSG00000026180 Cxcr2 Cxcr2 1 74200563 74207812
ENSMUSG00000030077 Chl1 Chl1 6 103460870 103699671
ENSMUSG00000035208 Slfn8 Slfn8 11 82815660 82834312
ENSMUSG00000050075 Gpr171 Gpr171 3 58900370 58905743
ENSMUSG00000053846 Lipg Lipg 18 75098976 75120917
ENSMUSG00000069830 Nlrp1a Nlrp1a 11 70904699 70958290
ENSMUSG00000070501 BC094916 BC094916 1 175449848
175466088
ENSMUSG00000078853 Igtp Igtp 11 58013058 58021093
Output with Entrez Gene ID:
Ensembl Gene ID Associated Gene Name MGI symbol Chromosome Name Gene
Start (bp) Gene End (bp) EntrezGene ID
ENSMUSG00000020826 Nos2 Nos2 11 78734289 78773756
18126
ENSMUSG00000026073 Il1r2 Il1r2 1 40141613 40182064
16178
ENSMUSG00000026073 Il1r2 Il1r2 1 40141613 40182064
ENSMUSG00000026180 Cxcr2 Cxcr2 1 74200563 74207812
12765
ENSMUSG00000026180 Cxcr2 Cxcr2 1 74200563 74207812
12765
ENSMUSG00000030077 Chl1 Chl1 6 103460870 103699671
ENSMUSG00000030077 Chl1 Chl1 6 103460870 103699671
12661
ENSMUSG00000030077 Chl1 Chl1 6 103460870 103699671
ENSMUSG00000035208 Slfn8 Slfn8 11 82815660 82834312
276950
ENSMUSG00000035208 Slfn8 Slfn8 11 82815660 82834312
100505399
Ten items, but only 5 distinct, are returned. So we are missing 5 items.
Of course the issue might be at the level of ENTREZ.
In anticipation, I thank you for your help.
Kind regards
Dr Henri-Jean Garchon
Henri-Jean Garchon, MD, PhD
Director of Research
Cochin Institute and Inserm U1016
Department of Immunology
Laboratory of Chronic Inflammation
Pavillon Hardy A 1st floor
27 rue du Faubourg Saint-Jacques
75014 Paris
France
phone +33 1 40 51 66 06
fax:+33 1 40 51 66 41
mail: [email protected]
--- End Message ---
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