Hi,
Working with the Illumina Human WG6 chips, and lumiHumanAll.db. After
linear model fitting and clustering, I have identified a cluster of
~130
loci that show an interesting profile. However, as 125 of them have
no
GeneName or EntrezID, I am struggling to figure out what they might be
biologically.
>From a closer inspection of lumiHumanALl.db, I find that approx. half
of
the features have no EntrezID, so I wasn't just unlucky with the
constituents of my cluster!
Does anyone have any recommendations as to the best approach to get
around this problem (which came to light when I tried to run GOstats,
which requires EntrezID for mapping of terms)?
Many thanks in advance.
Cheers,
a
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On Tue, Jun 10, 2008 at 1:40 AM, Al Ivens <alicat at="" sanger.ac.uk="">
wrote:
> Hi,
>
> Working with the Illumina Human WG6 chips, and lumiHumanAll.db.
After
> linear model fitting and clustering, I have identified a cluster of
~130
> loci that show an interesting profile. However, as 125 of them have
no
> GeneName or EntrezID, I am struggling to figure out what they might
be
> biologically.
>
> >From a closer inspection of lumiHumanALl.db, I find that approx.
half of
> the features have no EntrezID, so I wasn't just unlucky with the
> constituents of my cluster!
>
> Does anyone have any recommendations as to the best approach to get
> around this problem (which came to light when I tried to run
GOstats,
> which requires EntrezID for mapping of terms)?
You could use one of the illuminaHuman... (rather than
lumiHumanAll.db) annotation packages which look to have a larger
number of mapped probes.
Sean
?The illuminaHuman... annotation packages are based on accession IDs
taken from BLAST results from Nuno Barbosa-Marais. Check out
www.compbio.group.cam.ac.uk for more details.
Lynn
Sean Davis wrote:
> On Tue, Jun 10, 2008 at 1:40 AM, Al Ivens <alicat at="" sanger.ac.uk="">
wrote:
>
>> Hi,
>>
>> Working with the Illumina Human WG6 chips, and lumiHumanAll.db.
After
>> linear model fitting and clustering, I have identified a cluster of
~130
>> loci that show an interesting profile. However, as 125 of them
have no
>> GeneName or EntrezID, I am struggling to figure out what they might
be
>> biologically.
>>
>> >From a closer inspection of lumiHumanALl.db, I find that approx.
half of
>> the features have no EntrezID, so I wasn't just unlucky with the
>> constituents of my cluster!
>>
>> Does anyone have any recommendations as to the best approach to get
>> around this problem (which came to light when I tried to run
GOstats,
>> which requires EntrezID for mapping of terms)?
>>
>
> You could use one of the illuminaHuman... (rather than
> lumiHumanAll.db) annotation packages which look to have a larger
> number of mapped probes.
>
> Sean
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
Hi Al:
I would suggest mapping the sequences of your ~130 probes to the
genome directly using "blat" in the UCSC genome browser. You should be
able to get genes which these probes can be sequence matched to
(perfectly or not perfectly). And also you need to check if probes are
matched with the exon regions of the genes. The probe sequences can be
retrieved from Illumina's manifest file.
Hope this helps.
Cheers,
Wei
Al Ivens wrote:
> Hi,
>
> Working with the Illumina Human WG6 chips, and lumiHumanAll.db.
After
> linear model fitting and clustering, I have identified a cluster of
~130
> loci that show an interesting profile. However, as 125 of them have
no
> GeneName or EntrezID, I am struggling to figure out what they might
be
> biologically.
>
> >From a closer inspection of lumiHumanALl.db, I find that approx.
half of
> the features have no EntrezID, so I wasn't just unlucky with the
> constituents of my cluster!
>
> Does anyone have any recommendations as to the best approach to get
> around this problem (which came to light when I tried to run
GOstats,
> which requires EntrezID for mapping of terms)?
>
> Many thanks in advance.
>
> Cheers,
>
> a
>
>
>
>
>
On Thu, Jun 12, 2008 at 10:57 PM, Wei Shi <shi at="" wehi.edu.au=""> wrote:
> Hi Al:
>
> I would suggest mapping the sequences of your ~130 probes to the
genome
> directly using "blat" in the UCSC genome browser. You should be able
to get
> genes which these probes can be sequence matched to (perfectly or
not
> perfectly). And also you need to check if probes are matched with
the exon
> regions of the genes. The probe sequences can be retrieved from
Illumina's
> manifest file.
For affy probes, this works reasonably well. However, for longer
probes, it might be easier to map to a transcript database like RefSeq
or Ensembl genes.
Sean
> Al Ivens wrote:
>>
>> Hi,
>>
>> Working with the Illumina Human WG6 chips, and lumiHumanAll.db.
After
>> linear model fitting and clustering, I have identified a cluster of
~130
>> loci that show an interesting profile. However, as 125 of them
have no
>> GeneName or EntrezID, I am struggling to figure out what they might
be
>> biologically.
>> >From a closer inspection of lumiHumanALl.db, I find that approx.
half of
>> the features have no EntrezID, so I wasn't just unlucky with the
>> constituents of my cluster!
>>
>> Does anyone have any recommendations as to the best approach to get
>> around this problem (which came to light when I tried to run
GOstats,
>> which requires EntrezID for mapping of terms)?
>>
>> Many thanks in advance.
>>
>> Cheers,
>>
>> a
>>
>>
>>
>>
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
