On 22 Feb 2007, at 15:48, Rosienne wrote:
Hi,
a few weeks ago I was attending an Open Door Workshop at the Sanger.
I had occasion to speak to one of your team and mention a couple of
problems we regularly encounter when using biomart. I was advised to
post to this address.
I, and my colleagues, use biomart to output gene related information
for lists of microarray feature IDs. Even though we untick the ensembl
transcript ID box we still get an output for each transcript. In some
cases, where genes have 9 documented transcripts we get 9 perfectly
replicated entries. When dealing with lists of over a thousand genes
each time this gets very confusing and generally makes excel stop
responding!
We wonder if in future re-works of the tool a gene specific rather
than a transcript specific output can be made available. We are aware
that for people working on only one, or a handful of genes, getting
all the transcript specific information is essential. However, it
would make life a lot easier for scientists like us who handle large
gene lists if we could specifically select to obtain only gene
specific outputs, 1 gene = 1 row of output.
Dear Rosienne,
this particular problem is really specific to Ensembl data. Ensembl
annotates on per transcript rather than on per gene basis while
most people 'outside' seem to want the latter :) The ideal solution
would be if 'per gene' annotation was provided at the source of
Ensembl annotation but failing that we are now looking for the ways of
simply altering the output such that it will artificially introduce
'per gene' annotation
so that users like yourself would be able to avoid the annoying
repetitions. You must be aware however that such approach has a
potential of introducing
conflicting annotation as it will be totally artificial. The correct
'per gene' annotation can only be corrected at the source.
a.
Our second major problem stems from the fact that sometimes there is
no information linked to particular microarray feature IDs. The count
tab tells you how many out of your list were found but there is no
information whatsoever about the ones that were not found. Manually
finding which 50 out of a list of 1000 were not found is not easy. An
output list of features not found, or inclusion of the not found items
within the output with a short 'not found' comment next to them would
be very useful.
In summary, for us the ideal situation would be if we could input a
list of 1000 feature IDs and as output get a list of 1000 rows, 1 gene
per row, in the same sequence as the input list, with either empty
cells or a not found comment against those not found.
Besides this particular feature, biomart is great and has made data
mining of large data sets so much more accessible!
Thank you.
Regards
Rosienne
_______________________________________________________
Rosienne Farrugia
Division of Transfusion Medicine
Department of Haematology
University of Cambridge
Long Road
Cambridge
CB2 2PT
Tele: 01223 548008
Fax: 01223 548136
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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