- From: Kei Cheung <kei.cheung@yale.edu>
- Date: Tue, 25 May 2010 23:52:05 -0400
- 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 UTC