Re: BioRDF Telcon

hi kei,

> 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.

yes, this was my meaning.

this is to differentiate between a gene that is always expressed under 
normal conditions because it is part of an essential pathway that is always 
running, that gene is only interesting if its expression level 
changes--similarly for a normally unexpressed gene.

> 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.

yes, which i think was scott's point in his reply.  in fact, for the BioRDF 
use case, initially at least, it is probably sufficient that the authors of 
the paper state that a gene is part of the significant gene list.

cheers,
michael


----- Original Message ----- 
From: "Kei Cheung" <kei.cheung@yale.edu>
To: "mdmiller" <mdmiller53@comcast.net>
Cc: "M. Scott Marshall" <marshall@science.uva.nl>; "HCLS" 
<public-semweb-lifesci@w3.org>
Sent: Tuesday, May 25, 2010 8:52 PM
Subject: Re: BioRDF Telcon


> 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 13:41:56 UTC