biomart Paty

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Oct 16, 2013, 10:34:20 PM10/16/13

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Hi,

I have noticed that different orthologs are being retrieved from biomart.org than from ensembl.org/biomart/martview.

Why?

You get 5 zebrafish ortholog genes by doing the following on the ensembl biomart page: http://useast.ensembl.org/biomart/martview:

1)DATABASE = Ensembl Gene 73

2) DATASET = Homo Sapiens Gene

3) Then in the Filters section:

Open the "Gene" section, select "HGNC symbol" in the ID list limit drop down and paste "CDH1" in the box.

4) In the Attributes section:

Click on the "Homologs" radio button, open the ORTHOLOGS section and select all the "Zebrafish Orthologs" attributes.

Open the Gene section and un-tick "Ensembl Gene ID" and "Ensembl Transcript ID".

5) click on result and you should get all the zebrafish ortholog genes back for the Human gene

You should get the same result by pasting the following URL in your browser:

In Biomart, I get no orthologs:

http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+73+Genes+%28WTSI%2C+UK%29&step=4&id_list_limit_filters[]=hgnc_symbol&id_list_limit_filters[]=CDH1&id_list_limit_filters[]=HGNC+symbol%28s%29+[e.g.+ZFY]&attributes=drerio_inter_paralog_ensembl_gene%2Cdrerio_inter_paralog_perc_id%2Cdrerio_inter_paralog_dn%2Cdrerio_inter_paralog_ds

Paty

Arek Kasprzyk

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Oct 18, 2013, 4:24:03 AM10/18/13

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Hi Paty,

I don't think you can paste exactly the same URL into central.biomart.org. This instance runs off a different code base (java BioMart v08) as opposed to Ensembl instance (perl BioMart v07). If you want to try to do equivalent request on BioMart site please use our portal running off the 07 version (ie "www.biomart.org" rather than "central.biomart.org")

a

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biomart Paty

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Oct 21, 2013, 6:12:24 PM10/21/13

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Hi Arek,

Thanks for your reply. I did not post the same URL, my bad, for implying that. I "clicked" my way through the options and I am just showing you the links for you to see that the results are different.
Now that I understand that the 0.7 version should return different results than 0.8, my question is why? Those homologs are still in the latest Compara database. Why are they not shown in version 0.8?

Paty

Arek Kasprzyk

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Oct 22, 2013, 3:37:43 AM10/22/13

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Hi Paty

I am sorry for misreading your email first time round. You are right.

Although the 08 and 07 portals are implemented differently they should return the same results for the same query.

This appears to be a problem on our side that needs fixing.

Thank you for reporting this,

a

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Arek Kasprzyk

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Oct 22, 2013, 4:06:52 AM10/22/13

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Hi Paty,

I think I jumped the gun yet again :)

After careful testing I can in fact get identical results for this query for both instances. My initial confusion was due to using 'Zebra Fish Possible Orthologs' instead 'Zebrafish Orthologs' box in the 08 instance.

The former does not produce any results, while the latter produces identical results to the 07 instance (Please see below):

ENSG00000039068 ENSDARG00000058546

ENSG00000039068 ENSDARG00000092450

ENSG00000039068 ENSDARG00000068137

ENSG00000039068 ENSDARG00000024371

ENSG00000039068 ENSDARG00000035796

LRG_301 no data

This appears to be the same as obtained from the 07 instance:

Ensembl Gene ID Zebrafish Ensembl Gene ID

ENSG00000039068 ENSDARG00000058546

ENSG00000039068 ENSDARG00000092450

ENSG00000039068 ENSDARG00000068137

ENSG00000039068 ENSDARG00000024371

ENSG00000039068 ENSDARG00000035796

LRG_301

From the URL that you provided It seems that you might have made the same mistake. Try this one instead:

http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+73+Genes+(WTSI%2C+UK)&step=3&id_list_limit_filters%5B%5D=hgnc_symbol&id_list_limit_filters%5B%5D=CDH1&id_list_limit_filters%5B%5D=HGNC+symbol(s)+%5Be.g.+ZFY%5D&attributes=drerio_homolog_ensembl_gene%2Chomologs_ensembl_gene_id

a

biomart Paty

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Oct 22, 2013, 3:59:22 PM10/22/13

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Hi Arek,

That's it! Very easy to confuse 'Possible Orthologs' with 'Orthologs'! What is the difference, where is this documented?

Thank you for clarifying this!

Paty

On Wednesday, October 16, 2013 10:34:20 PM UTC-4, biomart Paty wrote:

Arek Kasprzyk

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Oct 23, 2013, 3:43:55 AM10/23/13

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Hi Paty,

I am not sure if this is documented but you can certainly get all the relevant information regarding this issue from help...@ensembl.org

Please drop them an email

a

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Thomas Maurel

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Oct 23, 2013, 4:49:02 AM10/23/13

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Dear Paty,

The difference between "Possible Orthologs" and "Orthologs" in ensembl is explained on the following page: http://www.ensembl.org/info/genome/compara/homology_method.html

If want more informations, please don't hesitate to contact help...@ensembl.org.

Hope this helps,

Thomas

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

biomart Paty

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Oct 23, 2013, 2:32:55 PM10/23/13

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Hi Arek,

Thank you so much for your responses! Now the mystery is solved and everything is clear about the meaning of "possible orthologs": when the duplication node is weakly-supported (species-intersection-score ≤ 0.25).

Paty

On Wednesday, October 16, 2013 10:34:20 PM UTC-4, biomart Paty wrote:

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Different orthologs retrieved from biomart.org than from ensembl.org/biomart/martview

biomart Paty

Arek Kasprzyk

“Everybody has a plan until they get punched in the face.”

biomart Paty

Arek Kasprzyk

Arek Kasprzyk

biomart Paty

Arek Kasprzyk

Thomas Maurel

biomart Paty