[ensembl-dev] Biomart inconsistency

[Ivan Kel]

Greetings,

I am using Ensembl Biomart to map Ensembl Gene IDs to Transcript IDs and
UniProt/SwissProt Accession numbers.
Surprisingly, in several cases the corresponding Transcript IDs found for a
Gene ID deffer depending on whether or not I add the UniProt number to the
search.
To clarify here is an example:
Ensembl Gene ID: ENSG00000072110
Result using only GeneID and TranscriptID:
Ensembl Gene ID Ensembl Transcript ID
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000193403<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000193403>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000556083<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556083>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000553882<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553882>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000394419<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000394419>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000438964<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000438964>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000376839<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000376839>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000555075<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555075>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000538545<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000538545>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000544964<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000544964>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000553290<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553290>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000556432<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556432>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000556343<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556343>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000555616<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555616>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000556433<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556433>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000554508<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000554508>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000554158<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000554158>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000553370<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553370>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000553779<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553779>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000556571<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556571>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000553659<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553659>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000556203<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556203>

Result using only GeneID and TranscriptID and UniProtID:
Ensembl Gene ID Ensembl Transcript ID UniProt/SwissProt Accession
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000193403<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000193403>
P12814 <http://www.uniprot.org/uniprot/P12814>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000394419<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000394419>
P12814 <http://www.uniprot.org/uniprot/P12814>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000438964<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000438964>
P12814 <http://www.uniprot.org/uniprot/P12814>
ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000376839<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000376839>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000555075<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555075>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000538545<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000538545>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000544964<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000544964>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000553290<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553290>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000555616<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000555616>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000556433<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556433>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000553370<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553370>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000553779<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553779>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000556571<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556571>
 ENSG00000072110<http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000072110>
ENST00000553659<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000553659>



Please notice that the transcripts found for the Gene ENSG00000072110
differ between the two cases (e.g.
ENST00000556083<http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000556083>is
not present in the second results)
.

For this analysis I use the current Biomart version. This problem does not
occur if I use the older Biomart (hg18, Biomart archive from 2009, NCBI36).

Am I missing something?

Thank you very much in advance.

Ivan
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