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Re: BioRDF Telcon

From: Kei Cheung <kei.cheung@yale.edu>
Date: Tue, 25 May 2010 23:52:05 -0400
Message-ID: <4BFC9AE5.8060403@yale.edu>
To: mdmiller <mdmiller53@comcast.net>
CC: "M. Scott Marshall" <marshall@science.uva.nl>, HCLS <public-semweb-lifesci@w3.org>
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" 
> <marshall@science.uva.nl>
> To: "mdmiller" <mdmiller53@comcast.net>
> Cc: "Kei Cheung" <kei.cheung@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 <mdmiller53@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.cheung@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.cheung@yale.edu>
>>>>> To: "mdmiller" <mdmiller53@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.cheung@yale.edu>
>>>>>>> To: "JunZhao" <jun.zhao@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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>
>
>
Received on Wednesday, 26 May 2010 03:52:49 GMT

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