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Adding to GoSurfer website RE: A couple comments on http://bioinformatics.oxfordjournals.org/cgi/reprint/bti565v1

Sorin Draghici sorin at wayne.edu
Fri Aug 5 14:57:08 PDT 2005


Sheng,

Thanks for your email. Sure, feel free to add the paper on the GoSurfer 
website. I will make sure I reference the papers you indicated in any 
future publications. It would be nice if you could also refer to our 
previous work on this topic. I noticed for example that the recent paper 
that you just sent me, does not refer to any of our 6 papers on this 
topic published between 2001 and 2004. :-)

I will contact you separately regarding the book. An analysis of the 
difficulties of corrections for multiple comparisons in the GO context 
would be a very valuable addition.

Regards,

Sorin


Sheng Zhong wrote:

>Dear Sorin and Barry,
>
>Thank you for the interesting discussion. 
>
>Sorin: I have found your paper very interesting and refreshing to read. If
>you allow, I would like to add it onto GoSurfer's website as a reference.
>
>I like your point about the heavily correlated GO structure that complicates
>the multiple hypothesis testing issue. Because of this issue, no standard
>FDR calculation is valid. We also had an article that extensively discussed
>this issue and proposed a treatment that makes valid FDR estimate for every
>GO term. Here is a link to this paper:
>http://www.stanford.edu/group/wonglab/doc/Zhong_S_GoSurfer2.pdf
>
>I am happy to contribute any materials you need for the book chapter.
>
>Best regards,
>Sheng
>
>********************
>Sheng Zhong
>Assistant Professor
> 
>Dept of Bioengineering & Dept of Statistics
>http://bioinfor.bioen.uiuc.edu
>********************
> 
>
>-----Original Message-----
>From: owner-gofriends at genome.stanford.edu
>[mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Sorin Draghici
>Sent: Wednesday, August 03, 2005 3:49 PM
>To: Barry Zeeberg
>Cc: go-friends at genome.stanford.edu; claude.pasquier at gmail.com; John N.
>Weinstein
>Subject: Re: A couple comments on
>http://bioinformatics.oxfordjournals.org/cgi/reprint/bti565v1
>
>Barry,
>
>Thank you for your email. The paper dicusses the tools as they were 8-9 
>months ago, when we did this work. As you know, publishing paper 
>involves a certain time lag: submission, review, address any comments, 
>etc. The publisher does not allow further modifications of the paper at 
>this time but we have noted your comments and corrections and I will 
>include them in any future paper on this topic. For the time being, I am 
>currently working on a book on this topic to be published by Chapman and 
>Hall/CRC Press. The book is focused on tools for ontological analysis. I 
>would use this opportunity to inviite you and your collaborators (John 
>Weinstein, etc) to contribute a chapter about GO Miner and other related 
>tools you might have developed in this area. This would give you a first 
>hand opportunity to present the latest and greatest capabilities of your 
>tools. If you would like to contribute with this chapter, please let me 
>know and I will give you more details about it.
>
>Best regards,
>
>Sorin
>
>
>Barry Zeeberg wrote:
>
>  
>
>>Hi Sorin,
>>
>>I just now had a chance to glance through your review, and I noticed a few
>>items related to GoMiner that should be corrected in an erratum. This is
>>    
>>
>not
>  
>
>>exhaustive, as I have only had about one minute to peruse the literature.
>>
>>I will first note that your paper represents an important and ambitious
>>attempt to provide orientation to users in this field. It is inevitable
>>    
>>
>that
>  
>
>>some inaccuracies will creep in. Perhaps you could host  a web  site where
>>authors of the cited papers can correct inaccuracies - maybe even come out
>>with a second edition of the paper that contains all of the corrections?
>>
>>(1) GoMiner is a java application, and is therefore platform-independent,
>>not restricted to Windows only. I have run it on mac os x (Unix) and
>>    
>>
>Solaris
>  
>
>>a _lot_ of times.
>>
>>(2) The timing comparison should be done  using a local  database, since
>>hitting on our database from a remote site will depend on network  traffic
>>etc. I did not read carefully enough to know if you did correctly use a
>>local database that was properly  installed. The presentation was a little
>>ambiguous, in that GoMiner requires a total and a changed gene file as
>>input. It is not clear if the number  of genes on the x axis refers to the
>>total or to the changed gene file? In fact, you only go up to 1000 genes
>>    
>>
>max
>  
>
>>- this is silly, since we routinely analyze 10,000 - 20,000 genes in the
>>total gene file (representing all  of the genes on  a microarray). Assuming
>>a changed genes file of around 400 or 500 genes, and using a local
>>    
>>
>database,
>  
>
>>the analysis is done in around the 350 seconds that your graph implies for
>>1000 genes.
>>
>>(3) GoMiner supports all GO identifiers, as well as HUGO names. HUGO names
>>are not supported by GO database, but we have a freely-available
>>    
>>
>enhancement
>  
>
>>program to post modify the native GO database.
>>
>>(4) Your statement about Onto-Express being the only application that
>>collapses (assigning descendant  genes to parent) is wrong. GoMiner does
>>this also.
>>
>>(5) You state that GoMiner uses a local database server. The context of the
>>statement strongly suggests that there is no alternative. In fact, GoMiner
>>can use either a local database server or our database server, not to
>>mention any other accessible build of the GO database hosted anywhere.
>>
>>[WARNING: the following contains  some philosophizing and self-serving
>>    
>>
>stuff
>  
>
>>that is not mandatory reading,and the casual reader might want to skip]
>>
>>You might have considered a comparison of the ability of the user to
>>hyperlink out from the tool to find more information about the genes or
>>categories of interest. For instance, GoMiner allows access to biocarta and
>>kegg pathway maps, genecards, NCBI Entrez, NCBI 3D structures, etc. There
>>    
>>
>is
>  
>
>>always a danger in a review of this type for the author to focus on
>>    
>>
>features
>  
>
>>in which her or his tool excel. This is particularly true since each person
>>will have a somewhat different view of what is important, and this
>>    
>>
>viewpoint
>  
>
>>will  coincide perfectly only for that author doing the review and her or
>>his own tool. I would certainly not claim for myself sufficient objectivity
>>to value a  different  point of view to the same extent that I value my
>>    
>>
>own.
>  
>
>>As an admittedly self-serving bit of advertising for which I apologize in
>>advance, I  will mention that there is a recent  paper on High-Throughput
>>GoMiner
>>( http://discover.nci.nih.gov/gominer/htgm.jsp ).
>>This is a web based  application and therefore is platform independent.
>>Among other things, it permits _integrative_ analysis of multiple
>>    
>>
>microarray
>  
>
>>(or any other type of high throughput experiment), it implements a multiple
>>comparisons correction, it provides visual information on the transcription
>>factor binding  sites in the genes and categories, and it provides
>>    
>>
>clustered
>  
>
>>image map (CIM) visualizations of the relationships between interesting
>>categories, genes, and experiments.
>>
>>Finally, since the time that GoMiner was evaluated for the review article,
>>it has been enhanced enormously by virtue of being a pilot project in the
>>caBIG initiative. In  particular,  it is fully integrated at the front end
>>with data deposited in  caWorkbench,  and at the back end with VennMaster.
>>
>>Regards,
>>Barry
>>
>>
>> 
>>
>>    
>>
>
>  
>

-- 
Sorin Draghici, Ph.D. 


Director of the Bioinformatics Core, Karmanos Cancer Institute

Associate Professor		Tel: (313) 577-5484
Dept. of Computer Science	Fax: (313) 577-6868
Wayne State University
5143 Cass Ave, Room 431 State Hall, 
Detroit, MI, 48202
WWW: http://vortex.cs.wayne.edu/Sorin/ (personal)
WWW: http://vortex.cs.wayne.edu/Projects.html (lab)


Check out my recent book: Data Analysis Tools for Microarrays:
http://www.crcpress.com/shopping_cart/products/product_detail.asp?sku=C3154&parent_id=&pc=


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