Hi Michael et al,
What do we mean by differentially expressed genes? One definition is
that differentially expressed genes are genes with significantly
different expression in two samples/conditions/experimental
factors/dimensions (e.g., treated vs. untreated, disease vs, normal,
time point1 vs. time point 2) of microarray experiments.
How to measure or infer gene expression (e.g., from mRNA) is a whole
complex question that may be beyond the scope of our use case.
Cheers,
-Kei
mdmiller wrote:
hi scott,
i think you, jim and lena are doing a great job moving the technical
aspect of this work forward. i'm looking forward to seeing the end
results.
cheers,
michael
----- Original Message ----- From: "M. Scott Marshall"
<marsh...@science.uva.nl>
To: "mdmiller" <mdmille...@comcast.net>
Cc: "Kei Cheung" <kei.che...@yale.edu>; "HCLS"
<public-semweb-lifesci@w3.org>
Sent: Tuesday, May 25, 2010 10:21 AM
Subject: Re: BioRDF Telcon
Hi Michael,
Thanks for the clarification. I also explained those concepts during
the BioRDF teleconference but it is difficult for the scribe to
capture such details accurately from a phone conversation. Just
knowing that a gene has changed (either up or down) already gives us
something to work with. Since we started with the microarray use case,
we have aimed to focus on the list of differentially expressed genes
as our entry point into related molecular information, phenotypes,
pathways, diseases, etc.
In addition to the gene list and experimental factors, there is some
data provenance information that characterizes the origins of the gene
list, such as the type of significant analysis or technique that was
performed (ANOVA, LIMMA, ..) and p-value cutoff for the list discussed
in the associated article(s), software packages used (specific R
package from BioConductor, GeneSpring, NextBio, ..). It would be handy
if there was a common vocabulary for this type of information (URI's
for statistical techniques and software packages). I think that some
related resources have been described by myGrid/myExperiment. However,
lacking a complete vocabulary, it is still possible to make use of the
gene list without such a fine grained description of its provenance.
Cheers,
Scott
On Tue, May 25, 2010 at 9:35 AM, mdmiller <mdmille...@comcast.net>
wrote:
hi all,
sorry i ended up not being able to make the call.
"P value
The probability (ranging from zero to one) that the results observed
in a
study could have occurred by chance if the null hypothesis was true.
A P
value of ? 0.05 is often used as a threshold to indicate statistical
significance." (1)
the exact meaning of p-value depends on what is being measured.
also, sometimes it isn't so important that a gene is up or down
regulated
but whether its expression changes from up or down regulated over the
experimental factors, e.g. if you increase the dose of the drug do the
target genes go from non-expressed to up regulated.
cheers,
michael
1)
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=antiepi&part=appendixes.app2
----- Original Message ----- From: "Kei Cheung" <kei.che...@yale.edu>
To: "HCLS" <public-semweb-lifesci@w3.org>
Sent: Monday, May 24, 2010 11:40 AM
Subject: Re: BioRDF Telcon
Today's minutes are available at:
http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/05-24_Conference_Call
Thanks to Matthias for scribing.
Cheers,
-Kei
mdmiller wrote:
hi kei,
look forward to joining the call,
michael
----- Original Message ----- From: "Kei Cheung" <kei.che...@yale.edu>
To: "mdmiller" <mdmille...@comcast.net>; "HCLS"
<public-semweb-lifesci@w3.org>
Sent: Saturday, May 22, 2010 12:10 PM
Subject: Re: BioRDF Telcon
Hi Michael,
Yes, May 24 was what I meant. It was a typo.
Thanks,
-Kei
mdmiller wrote:
hi kei,
do you mean monday (may 24)?
cheers,
michael
----- Original Message ----- From: "Kei Cheung"
<kei.che...@yale.edu>
To: "JunZhao" <jun.z...@zoo.ox.ac.uk>
Cc: <public-semweb-lifesci@w3.org>
Sent: Friday, May 21, 2010 2:28 PM
Subject: Re: BioRDF Telcon
Since there were only Jun and Scott who attended the last
BioRDF call
(I was not able to attend due to some emergency meetings), we
decided to
have the next BioRDF call on the coming Monday (May 21) at 11
am (EDT). The
agenda will be the same (see below).
Cheers,
-Kei
JunZhao wrote:
This is a reminder that the next BioRDF telcon call will be
held at
11
am EDT (4 pm CET) on Monday, May 17 (see details below).
Cheers,
-Jun
== Conference Details ==
* Date of Call: Monday, May 17, 2010
* Time of Call: 11:00 am Eastern Time (4 pm CET)
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6152 (Bristol, UK)
* Participant Access Code: 4257 ("HCLS")
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC
page
for
details, or see Web IRC), Quick Start: Use
http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
for
IRC access.
* Duration: ~1 hour
* Frequency: bi-weekly
* Convener: Jun
* Scribe: to-be-determined
==Agenda==
* Introduction
* Gene list RDF representation
* iPhone demo
