The Stanford Microarray Database: Nucleic Acids Research, 2001, Vol. 29, No. 1 © 2001 Oxford University Press
The Stanford Microarray Database: Nucleic Acids Research, 2001, Vol. 29, No. 1 © 2001 Oxford University Press
The Stanford Microarray Database: Nucleic Acids Research, 2001, Vol. 29, No. 1 © 2001 Oxford University Press
ABSTRACT
The Stanford Microarray Database (SMD) stores raw
and normalized data from microarray experiments,
and provides web interfaces for researchers to
retrieve, analyze and visualize their data. The two
immediate goals for SMD are to serve as a storage
site for microarray data from ongoing research at
Stanford University, and to facilitate the public
dissemination of that data once published, or released
by the researcher. Of paramount importance is the
connection of microarray data with the biological data
that pertains to the DNA deposited on the microarray
(genes, clones etc.). SMD makes use of many public
resources to connect expression information to the
relevant biology, including SGD [Ball,C.A.,
Dolinski,K., Dwight,S.S., Harris,M.A., Issel-Tarver,L.,
Kasarskis,A., Scafe,C.R., Sherlock,G., Binkley,G.,
Jin,H. et al. (2000) Nucleic Acids Res., 28, 7780],
YPD and WormPD [Costanzo,M.C., Hogan,J.D.,
Cusick,M.E., Davis,B.P., Fancher,A.M., Hodges,P.E.,
Kondu,P., Lengieza,C., Lew-Smith,J.E., Lingner,C. et
al. (2000) Nucleic Acids Res., 28, 7376], Unigene
[Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D.,
Madden,T.L., Schuler,G.D., Tatusova,T.A. and
Rapp,B.A. (2000) Nucleic Acids Res., 28, 1014], dbEST
[Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993)
Nature Genet., 4, 332333] and SWISS-PROT
[Bairoch,A. and Apweiler,R. (2000) Nucleic Acids
Res., 28, 4548] and can be accessed at http://
genome-www.stanford.edu/microarray.
INTRODUCTION
Microarray experiments are routinely performed to examine
gene expression (1) or DNA copy number (2) on a genomic
scale. Typically many thousands of DNA samples are arrayed
on a glass slide, and labeled cDNA or genomic DNA from
control and experimental samples are competitively hybridized
to the array. Images of the slide are then acquired and processed to
produce a data file that contains dozens of values per spot for
several thousand spots. Although the salient information for
each spot is the ratio between the experimental and control
*To whom correspondence should be addressed. Tel: +1 650 498 6012; Fax: +1 650 723 7016; Email: [email protected]
153
154
The enormous quantity of data produced by microarray experiments also poses a challenge for the public dissemination of
the results. Many current publications of microarray results
require supplemental web pages in order to fully release the
data to interested researchers. Furthermore it is in the best
interest of the scientific community at large that the data and
tools are available to all. Therefore SMD is endeavoring to
provide a public interface for data release to the biological
community. The aim is that upon publication, or at the experiment
owners discretion, data will be made world-viewable. Published
data will be organized into curated datasets that can be either
analyzed online or downloaded. The scientific community will
be able to search and analyze experiments by their criterion of
interest, whether it is by organism, by publication, or by category
of experiment. In addition, in collaboration with the Arabidopsis
Functional Genomics Consortium (http://afgc.stanford.edu/),
results from plant microarrays are provided. SMD will not
however act as a pubic repository for data, and instead will
make all of its source code available to enable other institutions
to set up their own microarray databases using SMDs model.
SMD will be supported as long as the microarray community at
Stanford University supports and uses it.
THE FUTURE OF SMD
Once SMD has met its immediate goals of providing a database that can be used by both local and public researchers to
Figure 2. Hierarchical cluster. A portion of a hierarchical cluster, which can be easily navigated, is shown. Red indicates up-regulation in the experimental sample,
and green indicates down-regulation in the experimental sample, with respect to the control. The intensity of the color indicates the magnitude of up- or downregulation (see 6).
3.
4.
5.
6.
7.
8.
REFERENCES
9.
1. Schena,M., Shalon,D., Davis,R.W. and Brown,P.O. (1995) Quantitative
monitoring of gene expression patterns with a complementary DNA
microarray. Science, 270, 467470.
2. Pollack,J.R., Perou,C.M., Alizadeh,A.A., Eisen,M.B.,
Pergamenschikov,A., Williams,C.F., Jeffrey,S.S., Botstein,D. and
10.
11.
155