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

Barry Zeeberg zeebergb at mail.nih.gov
Mon Aug 1 15:37:32 PDT 2005


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

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