Hi Henri-Jean,
1. Regarding: " I cannot switch to the next step to select attributes: the "Output" and "Next" buttons on the top are not working." Can you please describe what is not working? What happens when you click on these buttons? 2. The ID Converter can be accessed here: http://central.biomart.org/converter/#!/ID_converter/gene_ensembl_config_2 Elena Rivkin Outreach and Training Coordinator, Informatics and Bio-computing Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 647-258-4316 Toll-free: 1-866-678-6427 www.oicr.on.ca This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. From: Henri-Jean Garchon <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Mon, 8 Aug 2011 10:44:35 -0400 To: Microsoft Office User <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, Junjun Zhang <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] Mouse EnsemblTranscriptID retrieval Hi Elena, Do you get 93805 transcript from the same list of Ids that you sent us? Can you please describe how you get all the Ensembl genes (n = 36814)? This was partly a mistake of mine. As I mentioned yesterday to Junjun (I realize I didn't cc the Biomart Users list, sorry about it): "I am speaking only of the 0.8 version Biomart server, using Internet Explorer (IE9). I was puzzled by the fact that when I had uploaded the 22308 Ensembl Gene ID list I am working with, a list of 36814 genes ID and 93805 transcripts ID was returned, actually corresponding to the unfiltered database. Uploading a subset of 5000 gene IDs, the output was the same. But I realized that in the "Filters" section, altough I had checked the "ID list limit" box, I had not selected "Ensembl Gene IDs" option in the popdown menu (that doesn't exist in the 0.7 version). So there was no filtering, even though I had uploaded my gene list, making complete sense. Indeed, if I select "Ensembl Gene IDs" in the popdown menu under the 'ID list limit" checkbox and l upload the list, I can now see the proper gene ID list appear in the "Filters" section of the summary panel on the left (nicely done!). However: my new problem is that I cannot switch to the next step to select attributes: the "Output" and "Next" buttons on the top are not working." In addition to the method described by Junjun, there is another quick way to get the transcript ID for a list of genes. In central.biomart.org, under Tools – select ID Converter. Select Mus musculus dataset, and upload your list of genes. Select Transcript ID in the TO box. Using this method I get 75,966 rows, as before. I can't find this tool Best regards Henri-Jean From: Henri-Jean Garchon <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Sun, 7 Aug 2011 06:28:57 -0400 To: Junjun Zhang <[email protected]<mailto:[email protected]>> Cc: Microsoft Office User <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] Mouse EnsemblTranscriptID retrieval Dear Junjun, Following my previous mail, the issue was with the browser: I was using Opera (my default). With Internet Explorer, the "upload file" button works fine. There are no duplicates in the output transcript list (93805 transcripts). So this is good. The issue however is that all the Ensembl genes (n = 36814) are retrieved. Identical result if I upload a 5000 gene list. Best wishes Henri-Jean Le 05/08/2011 22:45, Junjun Zhang a écrit : Dear Henri-Jean, After executing the same query directly using SQL SELECT statement against the database and testing the same query on a BioMart 0.8 server. It is confirmed that they both do not have any problem of missing or duplicating results. So problem is caused by BioMart 0.7 query batching. Please try this if you'd like to test your gene IDs: http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+63+(WTSI%2C+UK)&step=1&datasets=mmusculus_gene_ensembl<http://central.biomart.org/martwizard/#%21/Genome?mart=Ensembl+Genes+63+%28WTSI%2C+UK%29&step=1&datasets=mmusculus_gene_ensembl> Cheers, Junjun From: jzhang <[email protected]<mailto:[email protected]>> Date: Fri, 5 Aug 2011 01:33:34 -0400 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, Elena Rivkin <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] Mouse EnsemblTranscriptID retrieval Dear Henri-Jean, Thanks for sending the lists of IDs to us for testing. Based on Elena's test here, we can confirm the problem exists, however, we have not had a chance to look into it closely enough to figure out what exactly causes the problem. It very likely has something to do with BioMart 0.7's query batching (that I described a few days ago in another thread), which may result in missing/duplicating rows in the result. As I mentioned earlier, this will not happen in 0.8 where batching is implemented in a different way. We will continue the investigation and get you back when we found something concrete. Best regards, Junjun From: Henri-Jean Garchon <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Thu, 4 Aug 2011 09:49:43 -0400 To: Elena Rivkin <[email protected]<mailto:[email protected]>>, jzhang <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] Mouse EnsemblTranscriptID retrieval Dear Elena, Dear JunJun, Many thanks to both of you for having taken the time to address my request a month ago. I agree that using the viewer with limit set to 10 to illustrate my issue was not very bright! Apologies. I must say that things have changed substantially since then and look much better today. The output file generated after retrivieving "EntrezGene.ID" is a lot more consistent than a month ago. There are fewer duplicates (and actually no duplicate rows in the output table as there used to be), much fewer "NA" entries from Entrez (although I checked these null entries have an associated gene name). I guess these are issues with the Entrez database. Perhaps, what is most important: all input Ensembl.Gene.ID are present in the outpout table. My concern now is an issue with the retrieval of Ensembl.Transcript.ID, the default attributes of Biomart: Actually I am working with a list of 22308 Ensembl gene ID mapped on the Affymetrix Mouse Gene 1.0 ST microarray. I uploaded this list on the Biomart.org website to filter my query. The database is Ensembl build 63, the dataset is NCBIM37. I retrieve the output as a TSV file ("export all results to", not checking "unique results only"). I then go to R to check this output file. The output table has 75966 row, of which 59458 are unique. In other words, 42950 rows are unique and 16508 are duplicated. Why some rows are duplicated and others not perhaps might be explained. My main concern is that 6467 input Ensembl.Gene.IDs are not retrieved and are missing from the output table. These are bona fide genes with regular associated gene names. If I upload the list of these missing guys, I now get the corresponding transcripts. All of them are retrieved and there are no duplicate rows! In anticipation I thank you very much for your valuable help and comments Best regards Henri-Jean Le 24/06/2011 15:24, Elena Rivkin a écrit : Dr. Henri-Jean Garchon, The reason for only seeing a subset of EntrezGeneID is b/c only some transcripts do not have EntrezGene ID associated with them. If you select Ensembl Transcript ID as an attribute, you will se which transcripts correspond to which EntrezGene ID. For example. ENSMUSG00000026073 (Illr2) - only one of transcripts (ENSMUST00000027243) has EntrezGene ID And ENSMUSG00000035208 (Slfn8) - has two different EntrezGEneIDs, although only one transcript (ENSMUST00000038141). I hope it helps. Elena From: Henri-Jean GARCHON <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Fri, 24 Jun 2011 05:00:03 -0400 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [BioMart Users] Fwd: Returned mail: see transcript for details -------- Message original -------- Sujet: Returned mail: see transcript for details Date : Fri, 24 Jun 2011 09:48:20 +0100 De : Mail Delivery Subsystem <[email protected]><mailto:[email protected]> Pour : <[email protected]><mailto:[email protected]> The original message was received at Fri, 24 Jun 2011 09:48:20 +0100 from mx1.ebi.ac.uk [193.62.197.214] ----- The following addresses had permanent fatal errors ----- [email protected]<mailto:[email protected]> (reason: 550 Host unknown) (expanded from: <[email protected]><mailto:[email protected]>) ----- Transcript of session follows ----- 550 5.1.2 [email protected]<mailto:[email protected]>... 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