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A couple comments on http://bioinformatics.oxfordjournals.org/cgi/reprint/bti565v1

Joaquin Dopazo jdopazo at ochoa.fib.es
Fri Aug 5 07:25:36 PDT 2005


Dear Sorin and Barry,

Let me join to the discussion with a couple of comments on the paper and a
piece of information, but firstly, I'd like to express my congratulations
for this nice paper. We really needed a review like this in the field.

Regarding FatiGO let me point out that the statistical model we use (table
2) is a Fisher's exact test (despite we show a graphical output with the
differences in percentages, which we think is a intuitive manner of
displaying the differences). Also, in the case of IDs, we support much more
gene IDs, that quited in table 1.

Anyway, we have recently published a couple of papers on related matters.
One of them:
Al-Shahrour, F., Diaz-Uriarte, R. & Dopazo, J. Discovering molecular
functions significantly related to phenotypes by combining gene expression
data and biological information. Bioinformatics. 2005;21: 2988-2993.
http://bioinformatics.oxfordjournals.org/cgi/content/full/bti457
is a way of using GO (and virtually any other type of information) for
finding bloks of genes differentially expressed. It is similar to GSEA
(Mootha, 2003 Nat. Genet., 34, 267^Ö273), but seems to be more sensitive.

And the other one:
Vaquerizas, J.M.,Conde, L., Yankilevich, P., Cabezon, A., Minguez, P.,
Diaz-Uriarte, R., Al-Shahrour, F., Herrero, J & Dopazo, J. Gepas an
experiment-oriented pipeline for the analysis of microarray gene expression
data. Nucleic Acids Research 2005. 33 (Web Server issue):W616-W620
http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_2/W616

The paper is a description of our suite babelomics for functional annotation
of microarray experiments. It includes tests for GO (FatiGO) and more
information such as pathways, interpro motifs, transcription factor binding
sites, pre-tabulated expression in tissues, etc.

As other colleagues, I would be also happy to contribute with any
information or materials you need for the book.

Best regards

Joaquin


--------------------------------------
Joaquin Dopazo
Bioinformatics Department
Centro de Investigacion Principe Felipe
Avd. Autopista del Saler 16,
46013 Valencia
Spain

Tf:  +34 963289680
Fax: +34 963289801
http://bioinfo.cipf.es


-----Mensaje original-----
De: owner-gofriends at genome.stanford.edu
[mailto:owner-gofriends at genome.stanford.edu]En nombre de Sorin Draghici
Enviado el: jueves, 04 de agosto de 2005 0:49
Para: Barry Zeeberg
CC: go-friends at genome.stanford.edu; claude.pasquier at gmail.com; John N.
Weinstein
Asunto: 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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