Hi,
I have recently downloaded the dataset accompanying the 2002 article
"A gene expression signature as a predictor of survival in breast
cancer" by van De Vijver et al. published in the New England Journal
of Medicine.
There are a total of 24,496 spots on the array out of which 10,159 are
contigs with unknown annotations, i.e. 41% of the total data are not
annotated.
The data set is now almost 4 years old. Have these contigs been
annotated now, and if so where can I find information on them.
Thanks in advance.
Narinder S. Sahni
On Wednesday 18 October 2006 01:44, Narinder Singh Sahni wrote:
> Hi,
>
> I have recently downloaded the dataset accompanying the 2002 article
"A
> gene expression signature as a predictor of survival in breast
cancer" by
> van De Vijver et al. published in the New England Journal of
Medicine.
>
> There are a total of 24,496 spots on the array out of which 10,159
are
> contigs with unknown annotations, i.e. 41% of the total data are not
> annotated.
>
> The data set is now almost 4 years old. Have these contigs been
annotated
> now, and if so where can I find information on them.
What are the accessions used? Genbank or IMAGE Clone ID?
Sean
I have used this dataset for a practical. The attached script shows
how
I have annotated the data using data that translates the contig to
accession numbers and batchgenefinder to retrieve EntrezGene ids and
Locuslink. I hope the comments are clear enough to help you on your
way.
Jan
>I have recently downloaded the dataset accompanying the 2002 article
"A
gene expression signature as a predictor
>survival in breast cancer" by van De Vijver et al. published in the
New
England Journal of Medicine.
>
>There are a total of 24,496 spots on the array out of which 10,159
are
contigs with unknown annotations, i.e. 41% of the
>total data are not annotated.
>
>The data set is now almost 4 years old. Have these contigs been
annotated now, and if so where can I find information on
>them.