Dear Henri-Jean, In order to receive the full query result, if you use the BioMart web query interface (martview), in the result page you need to choose "All" rows and select the "Unique results only" checkbox. Below is the result I got after doing so:
Ensembl Gene ID MGI ID MGI symbol EntrezGene ID ENSMUSG00000020826 MGI:97361 Nos2 18126 ENSMUSG00000026073 MGI:96546 Il1r2 16178 ENSMUSG00000026073 MGI:96546 Il1r2 ENSMUSG00000026180 MGI:105303 Cxcr2 12765 ENSMUSG00000030077 MGI:1098266 Chl1 ENSMUSG00000030077 MGI:1098266 Chl1 12661 ENSMUSG00000035208 MGI:2672859 Slfn8 276950 ENSMUSG00000035208 MGI:2672859 Slfn8 100505399 ENSMUSG00000035208 MGI:2672859 Slfn8 ENSMUSG00000050075 MGI:2442043 Gpr171 229323 ENSMUSG00000053846 MGI:1341803 Lipg 16891 ENSMUSG00000069830 MGI:2684861 Nlrp1a 195046 ENSMUSG00000069830 MGI:2684861 Nlrp1a ENSMUSG00000070501 MGI:3584522 BC094916 545384 ENSMUSG00000070501 MGI:3584522 BC094916 ENSMUSG00000078853 MGI:107729 Igtp 16145 ENSMUSG00000078853 MGI:107729 Igtp The result does not miss any of your 10 input mouse genes, and all of them have at least one corresponding EntrezGeneID. In terms of rows with missing EntrezID, you can safely ignore them. The reason such duplicate happens has something to do with how data is organized internally. If you use biomaRt, there should be a way to remove size limit of result to be returned so you do just see the first 10 rows. Let us know if you still have any questions. Best regards, Junjun On 11-06-24 5:00 AM, "Henri-Jean GARCHON" <[email protected]> wrote: From: Henri-Jean GARCHON <[email protected]> Reply-To: <[email protected]> Date: Fri, 24 Jun 2011 04:48:24 -0400 To: <[email protected]> Subject: biomaRt and ENTREZ issue 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]
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