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Re: Differentially Expressed Gene Lists

From: Kei Cheung <kei.cheung@yale.edu>
Date: Mon, 23 Nov 2009 10:38:27 -0500
To: mdmiller <mdmiller53@comcast.net>
Cc: Helen Parkinson <parkinson@ebi.ac.uk>, marshall@science.uva.nl, Misha Kapushesky <ostolop@ebi.ac.uk>, Eric Prud'hommeaux <eric@w3.org>, Matthias Samwald <samwald@gmx.at>, HCLS <public-semweb-lifesci@w3.org>
Message-id: <4B0AAC73.1040305@yale.edu>
Since there seems to be an interest in exploring how to represent 
differentially expressed gene list, I'm cc'ing this to the HCLS list 
(Scott also suggested doing this). In addition to Michael's suggestion 
(see below), the following is a reference to Structured Digital Abstract 
(SDA) for those who are interested.

http://www.nature.com/nature/journal/v447/n7141/full/447142a.html

Cheers,

-Kei

mdmiller wrote:
> hi all,
>
> SDA does sound useful but it still has the hurdle that the writers of 
> the abstract need to be aware and care to use such structures or 
> someone else needs to add such structure afterwards.
>
> as i mentioned at the F2F, there is GeneSigDB [1] hosted at dana 
> farber, which is curating gene lists from papers.  this is very useful 
> in that it pulls out into a structured database the genes of interest 
> from papers but has the limitation that it doesn't provide the 
> signatures of interest.
>
> there is also the matter of the algorithm that, given a new gene 
> expression profile, provides a score as to inclusion or exclusion from 
> the biomarker. i'm not a bioinformaticists but my understanding is 
> such algorithms may depend on more than just the signatures, they 
> might depend on the values of some higher level algorithm, i.e. there 
> may not be one size fits all algorithms to determine membership.
>
> i also won't be able to make the call.
>
> cheers,
> michael
>
> [1]: http://compbio.dfci.harvard.edu/genesigdb/
>
> Michael Miller
> mdmiller53@comcast.net
>
> ----- Original Message ----- From: "Helen Parkinson" 
> <parkinson@ebi.ac.uk>
> To: "Kei Cheung" <kei.cheung@yale.edu>
> Cc: <marshall@science.uva.nl>; "mdmiller" <mdmiller53@comcast.net>; 
> "Misha Kapushesky" <ostolop@ebi.ac.uk>; "Eric Prud'hommeaux" 
> <eric@w3.org>; "Matthias Samwald" <samwald@gmx.at>
> Sent: Monday, November 23, 2009 5:58 AM
> Subject: Re: Differentially Expressed Gene Lists
>
>
>> I should have read the spec for the SDA. Sounds useful.
>>
>> Kei Cheung wrote:
>>> Helen Parkinson wrote:
>>>
>>>>
>>>>>
>>>>> I've been wondering how structured digital abstract (SDA) can be 
>>>>> applied to gene lists. There has been a pilot application of SDA 
>>>>> by FEBS in terms of interactions with links to MINT. Perhaps, a 
>>>>> similar thing can be done for gene lists with links to databases 
>>>>> like ArrayExpress and GEO. Mark Gerstein and I are working on a 
>>>>> paper describing some extension of SDA (Matthias is also a 
>>>>> co-author).
>>>>>
>>>> Gene lists don't really appear in abstracts either often, one or 
>>>> two genes of interest are mentioned. I'd be happy to take a look at 
>>>> a subset of papers though to confirm/deny this. If that would help
>>>
>>> Many people misunderstood that structured digital abstract applies 
>>> only to abstracts (I know the name is misleading unforunately), it 
>>> can be applied to representing key findings described in the paper. 
>>> The abstract I'm looking at is the following:
>>>
>>> http://www.ncbi.nlm.nih.gov/pubmed/16242812
>>>
>>> It mentions explicitly that one of the key findings is a differently 
>>> gene list of 225 genes across different conditions. Four of the 
>>> validated genes are also mentioned in the abstract:
>>>
>>> apolipoprotein J, interleukin-1 receptor-associated kinase 1, tissue 
>>> inhibitor of metalloproteinase 3, and casein kinase 2, beta.
>>>
>>>
>>>
>>>
>>>>>
>>>>>>
>>>>>> The job of creating an OWL/RDF representation of microarray 
>>>>>> experiement results should *start* with differentially expressed 
>>>>>> genes and experimental conditions. I would hope that it doesn't 
>>>>>> start with text mining ill-defined text sources (such as 
>>>>>> figures). On the bright side, if the experiment of interest is 
>>>>>> included in Gene Expression Atlas, we are all set, right? We just 
>>>>>> need a way to export the RDF.
>>>>>
>>>>>
>>>>>
>>>>> I'm planning  to give a short presentation including an example 
>>>>> during the BioRDF call tomorrow.
>>>>
>>>>
>>>> I'll miss this unfortunately, as will Misha. Yes, if the experiment 
>>>> is in Atlas we can now export rdf and we have a prototype working.
>>>
>>>
>>> Look forward to seeing the protoype. SDA can be seen as a bridge 
>>> between databases and literature. It fits both bottom-up and 
>>> top-down approach.
>>>
>>>>>
>>>>>>
>>>>>> BTW, I've pasted Kei's reminder below for the next BioRDF call 
>>>>>> (tomorrow). It would be great if you could call in and help us to 
>>>>>> figure this out.
>>>>>
>>>> Apologies, I have 30 days holiday to use before the end of the 
>>>> year, so I won't make this.
>>>
>>> Have a good vacation.
>>>
>>> -Kei
>>>
>>>>>>
>>>>>> Cheers,
>>>>>> Scott
>>>>>>
>>>>>> n.b. Does anybody mind if I post this to the mailing list?
>>>>>
>>>>>
>>>>> It's fine with me if people think nothing is controversal or 
>>>>> premature here. :-)
>>>>>
>>>>> Cheers,
>>>>>
>>>>> -Kei
>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------- 
>>>>>>
>>>>>>
>>>>>>
>>>>>> This is a reminder that the next BioRDF telcon call will be held 
>>>>>> at 11 am EDT (5 pm CET) on Monday, November 23 (see details below).
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> -Kei
>>>>>>
>>>>>> == Conference Details ==
>>>>>> * Date of Call: Monday November 23, 2009
>>>>>> * Time of Call: 11:00 am Eastern Time
>>>>>> * 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: Kei Cheung
>>>>>> * Scribe: to-be-determined
>>>>>>
>>>>>> == Agenda ==
>>>>>> * Roll call & introduction (Kei)
>>>>>> * RDF representation of microarray experiment and data (All)
>>>>>> * Provenance and workflow (All)
>>>>>>
>>>>>>> mdmiller wrote:
>>>>>>>
>>>>>>>> hi scott,
>>>>>>>>
>>>>>>>> typically it will not, the data will be the raw data, usually 
>>>>>>>> in the format from the feature extractor at the feature/spot 
>>>>>>>> level and then the error corrected and normalized data at the 
>>>>>>>> sequence/gene/transcript level.  one could include the final 
>>>>>>>> gene list in the MAGE-TAB by adding the appropriate columns to 
>>>>>>>> the MAGE-TAB and have the Derived Data File column contain the 
>>>>>>>> name of the appropriate file but in general the gene list is 
>>>>>>>> only in the paper, often as supplemental data.  in fact i can't 
>>>>>>>> think of a single case where it is included, helen, can you?
>>>>>>>>
>>>>>>>> cheers,
>>>>>>>> michael
>>>>>>>>
>>>>>>>> ----- Original Message ----- From: "M. Scott Marshall" 
>>>>>>>> <marshall@science.uva.nl>
>>>>>>>> To: <mdmiller53@comcast.net>
>>>>>>>> Cc: "kc28" <kei.cheung@yale.edu>
>>>>>>>> Sent: Friday, November 13, 2009 6:50 PM
>>>>>>>> Subject: BioRDF
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi Michael,
>>>>>>>>>
>>>>>>>>> One of the things that has come up during the BioRDF call is 
>>>>>>>>> "we need to confirm whether MAGE-TAB contains gene lists or 
>>>>>>>>> not". In other words, we will need to represent gene lists in 
>>>>>>>>> RDF.
>>>>>>>>>
>>>>>>>>> Ok, my quick interpretation between other things,
>>>>>>>>> Scott
>>>>>>>>>
>>>>>>>>> -- 
>>>>>>>>> M. Scott Marshall
>>>>>>>>> Leiden University Medical Center / University of Amsterdam
>>>>>>>>> http://staff.science.uva.nl/~marshall
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>
>>
>> -- 
>> Helen Parkinson, PhD
>> ArrayExpress Production Coordinator,
>> Microarray Informatics Team, EBI
>>
>> EBI 01223 494672
>> Skype: helen.parkinson.ebi
>>
>>
>
>
Received on Monday, 23 November 2009 15:39:03 GMT

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