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A couple comments on

Joaquin Dopazo jdopazo at
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.
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

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

Tf:  +34 963289680
Fax: +34 963289801

-----Mensaje original-----
De: owner-gofriends at
[mailto:owner-gofriends at]En nombre de Sorin Draghici
Enviado el: jueves, 04 de agosto de 2005 0:49
Para: Barry Zeeberg
CC: go-friends at; claude.pasquier at; John N.
Asunto: Re: A couple comments on


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,


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
>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
>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
>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
>- 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
>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
>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
>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
>always a danger in a review of this type for the author to focus on
>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
>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
>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
>( ).
>This is a web based  application and therefore is platform independent.
>Among other things, it permits _integrative_ analysis of multiple
>(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
>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.

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: (personal)
WWW: (lab)

Check out my recent book: Data Analysis Tools for Microarrays:

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