Microarray (Genome Chip)
Monitoring the Genome on a Chip
1998-2002 by Leming
to the DNA Microarray (Genome Chip) Web site! This simple, printer-friendly
site has been created and maintained
by Leming Shi, Ph.D.
You'll find the basics on DNA microarray technology
and a list of academic and industrial links related to this
exciting new technology. Your comments, corrections, and suggestions are
Please help me make this site more useful to you and many other visitors.
Last updated on January 7, 2002.
This Web site has NO association with Affymetrix,
Inc. or its GeneChip®
|This site was featured
DNA Microarray - A technology that is reshaping
It is widely believed that thousands of genes and their
products (i.e., RNA and proteins) in a given living organism function in
a complicated and orchestrated way that creates the mystery of life. However,
traditional methods in molecular biology generally work on a "one gene
in one experiment" basis, which means that the throughput is very limited
and the "whole picture" of gene function is hard to obtain. In the past
several years, a new technology, called DNA microarray, has attracted tremendous
interests among biologists. This technology promises to monitor the whole
genome on a single chip so that researchers can have a better picture of
the interactions among thousands of genes simultaneously.
Terminologies that have been used in the literature to
describe this technology include, but not limited to: biochip, DNA chip,
DNA microarray, and gene array. Affymetrix,
Inc. owns a registered trademark, GeneChip®,
which refers to its high density, oligonucleotide-based DNA arrays. However,
in some articles appeared in professional journals, popular magazines,
and the WWW the term "gene chip(s)" has been used as a general terminology
that refers to the microarray technology. Affymetrix strongly opposes such
usage of the term "gene chip(s)". More recently, I prefer the term "genome
chip", indicating that this technology is meant to monitor the whole genome
on a single chip. GenomeChip would also include the increasingly important
and feasible protein chip technology.
Base-pairing (i.e., A-T and G-C for DNA; A-U and G-C for
RNA) or hybridization is the underlining principle of DNA microarray.
An array is an orderly arrangement of samples. It provides
a medium for matching known and unknown DNA samples based on base-pairing
rules and automating the process of identifying the unknowns. An array
experiment can make use of common assay systems such as microplates or
standard blotting membranes, and can be created by hand or make use of
robotics to deposit the sample. In general, arrays are described as macroarrays
or microarrays, the difference being the size of the sample spots.
Macroarrays contain sample spot sizes of about 300 microns or larger and
can be easily imaged by existing gel and blot scanners. The sample spot
sizes in microarray are typically less than 200 microns in diameter and
these arrays usually contains thousands of spots. Microarrays require specialized
robotics and imaging equipment that generally are not commercially available
as a complete system.
DNA microarray, or DNA chips are fabricated by high-speed
robotics, generally on glass but sometimes on nylon substrates, for which
probes* with known identity are used to determine complementary binding,
thus allowing massively parallel gene expression and gene discovery studies.
An experiment with a single DNA chip can provide researchers information
on thousands of genes simultaneously - a dramatic increase in throughput.
(*Note: In the literature there exist at least two confusing nomenclature
systems for referring to hybridization partners. Both use common terms:
"probes" and "targets". According to the nomenclature
recommended by B. Phimister of
Genetics, a "probe" is the tethered nucleic acid with known sequence,
whereas a "target" is the free nucleic acid sample whose identity/abundance
is being detected. This site follows that recommendation. See Nature
Genetics volume 21 supplement
pp 1 - 60, 1999, which is freely accessable.
There are two major application forms for the DNA microarray
technology: 1) Identification of sequence (gene / gene mutation); and 2)
Determination of expression level (abundance) of genes.
There are two variants* of the DNA microarray technology,
in terms of the property of arrayed DNA sequence with known identity:
Format I: probe cDNA (500~5,000 bases long) is
immobilized to a solid surface such as glass using robot spotting and exposed
to a set of targets either separately or in a mixture. This method, "traditionally"
called DNA microarray, is widely considered as developed at Stanford University.
A recent article by R. Ekins and F.W. Chu (Microarrays: their origins and
applications. Trends in Biotechnology, 1999, 17, 217-218)
seems to provide some generally forgotten facts.
The microarray (DNA chip) technology is having a significant
impact on genomics study. Many fields, including drug discovery and toxicological
research, will certainly benefit from the use of DNA microarray technology.
View an example of the microarray
Format II: an array of oligonucleotide (20~80-mer
oligos) or peptide nucleic acid (PNA) probes is synthesized either in
situ (on-chip) or by conventional synthesis followed by on-chip immobilization.
The array is exposed to labeled sample DNA, hybridized, and the identity/abundance
of complementary sequences are determined. This method, "historically"
called DNA chips, was developed at Affymetrix,
Inc. , which sells its photolithographically fabricated products under
trademark. Many companies are manufacturing oligonucleotide based chips
using alternative in-situ synthesis or depositioning technologies.
In the preparation of this Web site, "DNA microarray(s)"
and "DNA chip(s)" are used interchangeably. But viewers should aware this
* In addition, microfluidics-based
chip or laboratory-on-a-chip
systems are also listed in this Web site.
For a very well-written introduction on the steps involved
in a microarray experiment, visit Jeremy Buhler's Anatomy
of a Comparative Gene Expression Study
An excellent collection of Genomics
Glossaries (including a Microarrays
Glossary) is being maintained by Mary Chitty of Cambridge Healthtech
Design of a DNA Microarray
There are several steps in the design and implementation
of a DNA microarray experiment. Many strategies have been investigated
at each of these steps. 1) DNA types; 2) Chip fabrication; 3) Sample preparation;
4) Assay; 5) Readout; and 6) Software (informatics)
Table 1. Steps in the design and implementation of a DNA
There are so many options and combinations, as can been seen
from the number of companies involved in this business. It seems too early
to judge who will be the winner(s) in this game. The forecast is further
complicated by recent fights among companies on intellectual property issues.
1) Probe (cDNA/oligo with known identity)
2) Chip fabrication
(Putting probes on the chip)
3) Target (fluorecently labeled sample)
(whole organism on a chip?)
|Photolithography, pipette, drop-touch, piezoelectric
(ink-jet), electric, ...
|Hybridization, long, short, ligase, base addition, electric,
MS, electrophoresis, fluocytometry, PCR-DIRECT, TaqMan, ...
||Fluorescence, probeless (conductance, MS, electrophoresis),
||Robotics control, Image processing, DBMS, WWW, bioinformatics,
data mining and visualization
Applications of DNA Microarray
(Many, many applications, to be listed)
(Many, many applications, to be listed).
Drug discovery: Pharmacogenomics
devices (Chemical & Engineering News, February 22, 1999,
77(8):27-36; password required) fall in this category. Although they are
not the "traditional" gene chip or microarray, I decided to list related
links at this site because of their close connection and integration to
the gene chip (microarray) technology.
Why some drugs work better in some patients than in others?
And why some drugs may even be highly toxic to certain patients? My favorite
definition (modified): Pharmacogenomics is the hybridization of
functional genomics and molecular pharmacology. The goal of pharmacogenomics
is to find correlations between therapeutic responses to drugs and the
genetic profiles of patients.
Toxicological research: Toxicogenomics
Have you seen anybody using this terminology? Now let's
try to give it a definition: Toxicogenomics is the hybridization
of functional genomics and molecular toxicology. The goal of toxicogenomics
is to find correlations between toxic responses to toxicants and changes
in the genetic profiles of the objects exposed to such toxicants. First
Preclinical Toxicity Application (Toxicology EXPRESS™ database using
Gene Logic's Flow-thru Chip™ technology) between Wyeth-Ayerst Research
and Gene Logic
on DNA Microarray Technology
An interesting article: Nuwaysir, E.F., Bittner, M.,
Trent, J., Barrett, J.C., and Afshari, C.A. Microarray and Toxicology:
The Advent of Toxicogenomics. Molecular Carcinogenesis, 24:153-159(1999).
NIEHS sponsored a meeting on the application of DNA microarray
in toxicology (EHP 1999).
NIEHS established the National Center for Toxicogenomics
(NCT) in June 2000.
See also Andreas
Matern's home page on DNA Microarrays.
Jenkins RE, Pennington SR. Arrays for protein expression
profiling: towards a viable alternative to two-dimensional gel electrophoresis?
Proteomics. 2001 Jan;1(1):13-29.
D. D. Shoemaker, E. E. Schadt, C. D. Armour, Y. D., He, P.
Garrett-Engele, P. D. McDonagh, P. M. Loer ..., Experimental annotation
of the human genome using microarray technology, Nature Volume
409 Number 6822 Page 922 - 927 (2001)
Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ,
Assessment of the sensitivity and specificity of oligonucleotide (50mer)
microarrays. Nucleic Acids Res 2000 Nov 15;28(22):4552-7.
G. MacBeath and S.L. Schreiber, Printing Proteins as Microarrays
for High-Throughput Function Determination, Science 2000 September
8; 289(5485): p. 1760-1763. Abstract
(New! Protein chip)
Taton TA, Mirkin CA, Letsinger RL.[Northwestern U.] Scanometric
DNA array detection with nanoparticle probes. Science.
2000 Sep 8; 289(5485):1757-60. Seem to offer great selectivity and
Jörg Reichert et al., Chip-Based Optical Detection of
DNA Hybridization by Means of Nanobead Labeling, Anal. Chem.,
72 (24), 6025 -6029, 2000. Abstract
Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley
R, Jones SJ, Davis EB, Scherer S, Ward S, Kim SK [Stanford] A global profile
of germline gene expression in C. elegans. Mol Cell 2000
Marx J. DNA Arrays Reveal Cancer in Its Many Forms. Science2000
September 8; 289: 1670-1672. (in News Focus)
DJ Lockhart and EA Winzeler. Genomics, gene expression and
DNA arrays. Nature, 2000, 405(6788):827-836.
Cortese JD, The Array of Today: Biomolecule arrays become
the 21st century's test tube, The Scientist 14:25, Sep.
4, 2000 URL
Cortese JD, Array of Options: Instrumentation to exploint
the DNA microarray explosion, The Scientist 14:26, May.
29, 2000 URL
Fritz J, Baller MK, Lang HP, Rothuizen H, Vettiger P, Meyer
E, Guntherodt H, Gerber C, Gimzewski JK. Translating biomolecular recognition
into nanomechanics. Science. 2000 Apr 14;288(5464):316-8.
Mark Schena (Ed.), Microarray
Biochip Technology, $49.95, Eaton Publishing Company, Distributed by
TeleChem / arrayit.com
Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L,
Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville
EA, Pommier Y, Botstein D, Brown PO, Weinstein JN. A gene expression database
for the molecular pharmacology of cancer. Nat Genet. 2000
[Authors' Web site]
Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P,
Iyer V, Jeffrey SS, Van De Rijn M, Waltham M, Pergamenschikov A, Lee JC,
Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO.
Systematic variation in gene expression patterns in human cancer cell lines.
Genet. 2000 Mar;24(3):227-35. [Medline]
[Authors' Web site]
Walt DR. Bead-based
Fiber-Optic Arrays. Science, 2000 January 21; 287: 451-452.
Afshari CA, Nuwaysir EF, Barrett JC [NIEHS] Application of
complementary DNA microarray technology to carcinogen identification, toxicology,
and drug safety evaluation. Cancer Res 1999 Oct 1;59(19):4759-60
Gwynne P. and Page G. Microarray
analysis: the next revolution in molecular biology. Science,
August 6. (special advertising supplement; has a list of microarray-related
Baldwin D, Crane V, Rice D. A
comparison of gel-based, nylon filter and microarray techniques to detect
differential RNA expression in plants. Curr Opin Plant Biol1999
Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov
A, Williams CF, Jeffrey SS, Botstein D, Brown PO [Stanford] Genome-wide
analysis of DNA copy-number changes using cDNA microarrays. Nat
Genet 1999 Sep;23(1):41-6
Khan J, Saal LH, Bittner ML, Chen Y, Trent JM, Meltzer PS.
profiling in cancer using cDNA microarrays. Electrophoresis 1999
Gerhold D, Rushmore T, Caskey CT [Merck]. DNA
chips: promising toys have become powerful tools. Trends Biochem
Sci 1999 May;24(5):168-73
Ekins R. and Chu F.W. Microarrays: their origins and applications.
in Biotechnology, 1999, 17, 217-218.
Nuwaysir, E.F., Bittner, M., Trent, J., Barrett, J.C., and
Afshari, C.A. Microarray
and Toxicology: The Advent of Toxicogenomics. Molecular Carcinogenesis,
Sinclair, B. Everything's
Great When It Sits on a Chip - A bright future for DNA arrays, The
Scientist, 1999 May 24, 13(11), 18-20.
published a special issue (January 1999 Supplement), The
Chipping Forecast. It's a collection of more than 10
reviews (60 pages) on different aspects of microarray analysis. All
the reviews are freely
Technologies to Markets, 2nd Edition, (IBC's
D&MD Report , March 1999, 200+ Pages, 25+ Exhibits, 20+ Companies
Schena, M. and Davis, R.W. Genes, Genomes and Chips. In DNA
Microarrays: A Practical Approach (ed. M. Schena), Oxford University
Press, Oxford, UK, 1999.
Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts
CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE Jr, Hartwell LH,
Brown PO, Friend SH [Rosetta/Stanford]. Drug target validation and identification
of secondary drug target effects using DNA microarrays. Nat Med.
(convincing results on the utility of microarray technology for drug target
validation and identification.)
Wang DG, Fan JB, ..., Lander ES, et al [MIT] Large-scale
identification, mapping, and genotyping of single-nucleotide polymorphisms
in the human genome. Science 1998 May 15;280(5366):1077-82
Schena, M. and R.W. Davis. Parallel Analysis with Biological
Chips. in PCR Methods Manual (eds. M. Innis, D. Gelfand, J. Sninsky), Academic
Press, San Diego, 1998. (Sorry, I haven't seen it yet.)
Lemieux, B., Aharoni, A., and M. Schena. Overview of DNA
Chip Technology. Molecular Breeding 1998, 4, 277-289.
Schena, M., Heller, R.A., Theriault, T.P., Konrad, K., Lachenmeier,
E., and Davis, R.W. Microarrays: biotechnology's discovery platform for
functional genomics. Trends in Biotechnology 1998, 16, 301-306.
Service, R.F. Microchip arrays put DNA on the spot. Science
Service, R.F. Coming soon: the pocket DNA sequencer. Science
Kricka, L. Revolution on a Square Centimeter. Nature Biotechnology
Housman, D.; Ledley, F. Why pharmacogenomics? Why now? Nature
Biotechnology 1998, 16(6), 492-493.
Ramsay, G. DNA
chips - states-of-the-art. Nature Biotechnology 1998,
Marshall, A.; Hodgson, J. DNA
chips - an array of possibilities. Nature Biotechnology 1998,
Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml
P, Leighton S, Torhorst J, Mihatsch MJ, Sauter G, Kallioniemi OP. Tissue
microarrays for high-throughput molecular profiling of tumor specimens.
Nat Med 1998 Jul;4(7):844-847
Blanchard, A.P. (1998) Synthetic DNA Arrays; in Genetic
Engineering, Vol. 20, pp. 111-123, edited by J.K. Setlow, Plenum Press,
Proudnikov D, Timofeev E, Mirzabekov A [Argonne]. Immobilization
of DNA in polyacrylamide gel for the manufacture of DNA and DNA-oligonucleotide
microchips. Anal Biochem 1998 May 15;259(1):34-41
Chen JJ, Wu R, Yang PC, Huang JY, Sher YP, Han MH, Kao WC,
Lee PJ, Chiu TF, Chang F, Chu YW, Wu CW, Peck K Profiling expression patterns
and isolating differentially expressed genes by cDNA microarray system
detection. Genomics 1998 Aug 1;51(3):313-24.
Wallace, R. W. DNA
on a chip - serving up the genome for diagnostics and research. Molecular
Medicine Today 1997, 3, 384-389.
Covacci, A.; Kennedy, G. C.; Cormack, B.; Rappuoli, R.; Falkow,
S. From microbial genomics to meta-genomics. Drug Development Research
Forozan, F.; Karhu, R.; Kononen, J.; Kallioniemi, A.; Kallioniemi,
O. P. Genome
screening by comparative genomic hybridization. Trends in Genetics
Sapolsky, Ronald J.; Winzeler, Elizabeth A. The
Functional Analysis Of Genomes: Recent Research In The Laboratory Of Dr.
Ronald Davis (at Stanford University)
Blanchard, A.P. & L. Hood. Sequence to array:
probing the genome's secrets. Nature Biotechnology 14:1649, 1996
Blanchard, A.P., R.J.Kaiser, L.E.Hood. High-Density
Oligonucleotide Arrays. Biosensors & Bioelectronics 11:687-690, 1996
DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray
M, Chen Y, Su YA, Trent JM [Stanford and NIH] Use
of a cDNA microarray to analyse gene expression patterns in human cancer.
Genet 1996 Dec;14(4):457-60
Shalon D, Smith SJ, Brown PO [Stanford] A DNA microarray
system for analyzing complex DNA samples using two-color fluorescent probe
hybridization. Genome Res 1996 Jul;6(7):639-45
Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW
[Stanford] Parallel human genome analysis: microarray-based expression
monitoring of 1000 genes. Proc Natl Acad Sci U S A 1996 Oct
Schena M, Shalon D, Davis RW, Brown PO [Stanford] Quantitative
monitoring of gene expression patterns with a complementary DNA microarray.
Industry Links (Companies
are listed alphabetically.)
Many academic organizations have set up their mciroarray
core facilities in order to make this technology accessible to their
reserchers. Dr. Wentian Li of Rockefeller University maintains a
list of such core facilities.
DNA Microarray (Genome
Chip) homepage (this site, created by Dr. Leming Shi), is a good starting
point and contains a lot of useful links and background information. This
site was reviewed by
Science magazine maintains an excellent collection
of information on functional
Dr. Ruth Alscher (email@example.com) at Virginia Tech maintains
an excellent Web site GRID
IT on DNA Microarrays (http://www.bsi.vt.edu/ralscher/gridit).
mailing list (maintained by Chandi
Griffin at San Francisco General Hospital/UCSF). To subscribe, send
a one line e-mail message to firstname.lastname@example.org;
the single line message should be: subscribe Gene-Arrays your-first-name
your-last-name. This is a very good place to ask all kinds of questions
regarding gene chips and DNA microarrays. To post a question to the whole
mailing list, send email to http://www.gene-chips.com/GENE-ARRAYS@ITSSRV1.UCSF.EDU.
You may leave the list at any time by sending a "SIGNOFF GENE-ARRAYS" command
Mailing List To subscribe send the word "subscribe" to mailto://email@example.com
Tim Tranbarger maintains the Plant-Array
Website in the context of the WWW Virtual Library ( http://www.w3.org/vl/).
A microarrays newsgroup was recently made available at http://www.egroups.com/group/microarray/
(maintained by Philippe Marc).
The Association of Biomolecular Resource Facilities (ABRF)'s
Microarray Research Group (MARG)
conducted a survey on the current status of the microarray technology.
The results is presented in a poster:
"THE STATE OF THE ART OF MICROARRAY ANALYSIS: A PROFILE OF MICROARRAY LABORATORIES."
Site of Nature Genetics
Laureate Martin L. Perl's group at the Stanford
Linear Accelerator Center (SLAC) is investigating if their new drop-on-demand
inkjet technology originally designed for the searching of certain hypothetical
types of elementary particles would be of use in the production of
Stanford University's Dr.
Patrick Brown, one of the major players in this field. This group has
a complete guide for researchers to build
their own microarrayer, at a fraction of the price of commercial products
Microarray Protocols of Dr. Mark Schena: very detailed and useful information
on performing DNA microarray experiments.
Mark Schena Home Page
ATP Awards 1998: Tools for DNA Diagnostics (7 of the 29 proposals were
awarded) Check project manager Dr. Stanley Abramowitz's overview
talk on this field
Genome Anatomy Project) at the National Cancer Institute (NCI),
Project at the National Human Genome Research Institute (NHGRI),
cDNA Microarray Center: Human ToxChip v 1.0, Human Discovery Chip,
Yeast Chip, Rat Chip, Xenopus Chip v 1.0, and Mouse Chip.
Dr. John N. Weinstein
at the National Cancer Institute (NCI)
developed an "information-intensive"
anticancer drug discovery approach that integrates chemical structure information
and anticancer activity patterns of >70,000 screened compounds with gene
expression (microarray) data of the 60 human cancer cell lines
Dr. Alan Robinson's
web resource on Gene
Expression and Microarray Technologies, at EBI. (highly recommended)
links to public sources of expression data, informatics, analysis tools,
Matern's home page on DNA Microarrays
and "DNA chips" site
of a Comparative Gene Expression Study (by Jeremy
Buhle). It's a very nice description of the microarray technology,
also includes a Glossary
of Microarray-related Biotechnology Terms
for Biomedical Research/MIT Center for Genome Research
Geoffrey Childs, Functional
Genomics at AECOM, Department of Molecular Genetics, Albert Einstein
College of Medicine
at Harvard University (Dr. George M. Church, a lot of very useful links)
Human Genome Project
Information at the Oak Ridge National
Laboratory, U.S. Department of Energy
National Human Genome Research Institute (NHGRI)
is developing "Tissue
Chip" to Illuminate the Cancer Development Process. NIH Clinical
Study: 97-C-0178: Fludarabine Treatment of Chronic Lymphocytic Leukemia:
cDNA Microarray Gene Expression Analysis, and Preclinical Bone Marrow Transplant/Immunotherapy
Garner Lab at UTSW -
Microarray Technology to identify genes controlling spermatogenesis,
Sam Ward at the University of Arizona
Lab at The Children's Hospital of Philadelphia
focuses on the development of Direct Identical-by-Descent (IBD) Mapping,
which is a DNA microarray-based mapping technique that allows isolation
and mapping of DNA fragments shared IBD between individuals.
University of Washington, Dr.
Lee Hood, Java-based
Array Image Spot Finding and Quantification Software (CrazyQuant)
Bernd Weisshaar's listing of DNA microarray links (plants), Max-Planck-Institut
Dr. Landers' Group
at the University of Pittsburgh is developing microcolumn technology for
clinical diagnostics. This capillary-based Integrated Diagnostic (ID) Chip
may have great potential in clinical diagnostics.
Claude Jacq's group at ENS, France. They also maintain a discussion
homepage at the Chemical Industry Institute
of Toxicology (CIIT): discusses how the DNA microarray technology is
impacting toxicological research.
Dr. Kent Vrana's Gene
Expression Technology Group at the Wake Forest University School of
The Vanderbilt University Microarray
Core Facility (microarrays.com) offers microarray-based products and
Toxicology Unit DNA Microarray Pages maintained by Dr Timothy W. Gant.
MicroArrays site provides detailed information on the use of nylon
microarrays (allowing expression profiling with small amounts of unamplified
RNA) and a number of useful utilities for choosing and checking IMAGE clones
representing given genes. contact: firstname.lastname@example.org
Genomics Consortium (AFGC) at Stanford University, funded by NSF:
microarrays, knockouts, and plant-specific genes.
Eiichiro Ichiishi of Kyoto Prefectural Univ. of Medicine maintains
a Web site on DNA chip technology (in Japanese).
C. Pirrung at Duke University is developing novel methods to cleave
DNA strands into the shorter fragments for DNA chip analysis and DNA
platform©: DNA-chips and microarrays in the Netherlands, maintained
at the Department of Human and Clinical Genetics, Leiden University Medical
Microarray Centre at The Ontario Cancer Institute.
Links to DNA
Microarray protocols , maintained by Longcheng Li at UCSF
Research & Development Center, Tsinghua Univeristy, Beijing, China.
Director: Dr. Jing Cheng.
Natl. Lab. of Molecular
and Biomolecular Elecctronics, Southeast Univ., Nanjing, China.
at Karolinska Institutet.
Karolinska Institute cDNA Micro-Array Core Facility
Dr. Gerhard M. Kreshach maintains a list of more than 1000
links to to Life Science News, Resources & Databases, including DNA,
Oligonucleotide, and Protein Arrays
yeast functional genomics group at The Sanger Centre headed by Dr.
Microarray Project at Rockefeller Univ., includes protocols, software,
The U.S. Environmental Protection Agency Microarray Consortium
The Center for Bioelectronics,
Biosensors and Biochips at Virgnia Commonwealth University and the
Medical Colleage of Virginia Health System focuses on next generation microarrays,
integrated molecular electronic devices using biologically active molecules
St. George's Hospital Medical School's microarray facility
on Bacterial Microarrays.
Human Genetics DNA Microarray Core Facility
Weill Medical College DNA Microarray Core Facility (Dr.
Jenny Z. Xiang)
of Medicine Microarray Core Facility
Links to the Genetic World
for Genomic Technology and Informatics, Scotland University of Edinburgh.
Prof. Andreas Manz
of the Imperial College, UK, developed a novel concept for Miniaturized
Total Analysis Systems (u-TAS): sampling, any sample pretreatment, separation,
and detection steps are all performed in an integrated microsystem.
Weller's group works on protein chips.
Stahl's group at the Univ. of Washington is working on the Phylochip
project: developing 16S rRNA-based microchips for determinative, phylogenetic
and environmental studies.
Table 2. The main features of some hybridization
microarray formats currently available*
ACLARA BioSciences, Inc.,
(used to be called Soane Biosciences) Hayward, California (Plastic chips
and microfluidic systems based on "Lab-On-A-Chip" microfluidics US Patent
and device for moving molecules by the application of a plurality of electrical
NIST ATP Award in "Tools for DNA Diagnostics" for Project: Multiplexed
Sample Preparation Microsystem for DNA Diagnostics
Advanced Array Technology
S.A. (Belgium), BIO-CD™:
compact disc platform for DNA detection
Santa Clara, California (The technology leader; manufactures the widely
including HIV, p450, p53, Rat Toxicology U34 arrays, etc.)
Agilent Technologies, Inc.
(Palo Alto, California), a subsidiary of Hewlett-Packard Company, plans
to expand its presence in the life science market through the introduction
of a new DNA microarray
program. It uses inkjet printing technology to manufacture its oligo-based
DNA microarrays. Licensed from Ed Southern/OGT. LabChip™-based DNA and
Alexion Pharmaceuticals Inc., New Haven, Connecticut
Innotech Corp., San Leandro, CA. Alpha Innotech provides innovation
bioinformatic imaging solutions for genetic discovery designed to
acquire, manage, and analyze fluorescence, chemiluminescence, or colorimetric
microarray slides, plates, gels, blots, or films.
Inc., Woburn, Massachusetts (full length cDNA FLEX™ and MicroFLEX library
construction; High Throughput Gene Expression Profiling; High Throughput
DNA Sequencing; Bioinformatics)
Applied Precision, Inc.,
Issaquah, Washington. ArrayWoRx is a wide field light source based microarray
scanner, combines limitless wavelength possibilities with automation and
image processing software.
Estonia. Arrayed Primer Extension (APEX)
and Asper ChipReader
AVIVA Biosciences Corp.,
San Diego, CA. Dedicated to the application of breakthrough multiple-force
biochip technology for genomics and proteomics. The company is developing
an integrated sample-to-result AVIChip™ system with an emphasis on biological
sample preparation and chip-based molecular manipulation. The AVIChip™
system will separate and transport a variety of mRNA, or other molecules
from crude biological samples and simultaneously perform a wide range of
biological and biochemical analyses. AVIVA's technology allows fast, accurate,
automated, and high-throughput biological analysis on integrated biochip
systems and provides novel approaches to both drug development and clinical
Axon Instruments, Inc.,
Foster City, California (GenePix
4000 Integrated Microarray Scanner and Analysis Software, simultaneously
scans microarray slides at two wavelengths using a dual laser scanning
system, displays images from two wavelengths and a ratio image as they
are acquired in real time; US$50,000)
La Jolla, California: Wins
NIST ATP Award in "Tools for DNA Diagnostics" Project: Liquid
Array Technology Development
Silver Spring, MD. Tissue array technology for high-throughput analysis
of tissue specimens.
BioArray Solutions, LLC,
Piscataway, NJ. Light-controlled Electrokinetic Assembly of Particles near
Surfaces (LEAPS), enables computer controlled assembly of beads and
cells into planar arrays within a miniaturized, enclosed fluid compartment
on the surface of a semiconductor wafer.
Cohasset, MA. Provides consulting services to the microarraying community
in the area of optics and instrumentation
Los Angeles, California (ImaGene™,
special image processing and data extraction software; CloneTracker: Databases
clones, plates, and slides, and offers array design tool and interfaces
to arrayers; GeneSight: Powerful expression analysis software which features
statistical methods as well a visualization tools.
Inc., (MACROscope™ for reading genetic microarrays, in collaboration
with Canadian Genetic Microarray Consortium)
bioMerieux, in vitro
Comberton, Cambridge, UK (MicroGrid, for arraying oligonucleotides
or cDNA clones on glass slides and plastic chips)
Brax, Cambridge, UK
Cadus Pharmaceutical Corp.,
Tarrytown, New York (yeast living chip)
Corp., Palo Alto, California: LabChips™ based on microfluidics. Awarded
$2 million contract by NIST to develop high-throughput DNA diagnostic platform.
Laboratory LabChip™ DNA Diagnostics System
Corp., Beijing, China. Co-founded on 30th September 2000 by Tsinghua
University, Huazhong University of Science and Technology, Chinese
Academy of Medical Sciences and Academy of Military Medical Sciences. The
registered capital for Capital Biochip is RMB $390 million with RMB
$240 million contributed by the four institutional founding members and
RMB $150 million from international venture capital firms. (Note: 1 US
dollar = ~8.2 RMB). It is backed by funds from the Chinese governmental
agencies to developed and commercialize various biochip technologies.
It is recruiting
qualified researchers from the world.
Inc., Irvine, CA. PixSys
PA Series: for Automated liquid handling system for creating high-density
arrays for genomics research. Scan
Array 3000: A Fluorescent Imaging System for microarray biochips.
Celera, Rockville, Maryland
(Everyone knows this company!)
Pittsburgh, Pennsylvania (ArrayScan™, cell-based "High Content Screening"
(HCS) for drug discovery)
Clinical Micro Sensors,
Inc., Pasadena, California. Now part of Motorola. DNA microchip-based
medical diagnostics; detection of directly detect DNA via electron transfer.
NIST ATP Award in "Tools for DNA Diagnostics" Project: DNA
Diagnostics for the Point of Care Using Electronic Nucleic Acid Detection
Clondiag Chip Technologies,
Jena, Germany. Working on generation and application of DNA microarrays.
Current products: Iconoclust (imaging tool), Partisan ArrayLIMS (LIMS for
AtlasTM human cDNA
array (nylon-membrane based)
drug discovery platform for identifying drug targets based on the analysis
of EST (Expressed Sequence Tag) and genomic databases, expression results
from chips and proteomics, and polymorphism detection and qualification;
DNA chip design and analysis. LabOnWeb.com
Corning Science Products
Division, Acton, MA provides the (Corning Microarray Technology) CMT-GAPS
amino silane coated slides and CMT-Hybridization
Corvas International, Inc.,
(2D gel, proteomics)
Cruachem Ltd, U.K.
manufactures the phosphoramidite building blocks for the synthesis of DNA.
Its expertise in DNA technology provides an efficient service for the supply
of DNA oligonucleotides. Cruachem Ltd is enthusiastically looking for partners
with which to collaborate in the area of DNA chip technology.
CuraGen Corp., New
Haven, Connecticut. GeneCalling™ and Quantitative Expression Analysis
(QEA™), CuraMode, CuraTox
diaDexus, LLC, Santa
Clara, California. joint venture between SmithKline
Beecham Corp. and Incyte Pharmaceuticals,
Inc.. Specialized in using microarray technology for molecular diagnostics
Biotech, Inc, Vista, CA and Copenhagen, Denmark. discoveryARRAY
slides (over 2400 expressed cDNA fragments); will soon offer over 40,000
arrayed mouse and human genes; GEE-NOME
offers complete "made to order" high density DNA microarray synthesis and
analysis services. Prices, availability, and turnaround time seem impressive.
Erie Scientific Company,
Portsmouth, NH, manufactures microslides for microarrays.
Belgium. Sells yeast and Bacillus subtilis genomic membranes.
Inc., RTP, NC., was formed to provide GeneChip processing and gene
expression analysis using Affymetrix GeneChip microarrays.
Trust, Inc., Deerfield, IL. Acting as a third-party intermediary among
researchers, health care providers and patients. Its goal is to build a
comprehensive, high-security, independent "genetic bank".
Gene Logic, Inc.,
Columbia, Maryland (Flow-thru
ChipTM: has hundreds
of thousands of discrete microscopic channels that pass completely through
it. Probe molecules are attached to the inner surface of these channels,
and target molecules flow through the channels, coming into close proximity
to the probes. This proximity facilitates hybridization. READS™,
Restriction Enzyme Analysis of Differentially-expressed Sequences, for
capturing and analyzing the overall gene expression profile of a given
cell or tissue type to identify drug targets).
Geneka Biotechnology Inc.,
Montreal, Canada. Oligonucleotide-based microarray slide, the P.R.O.M.
(Proteomic Regulatory Oligonucleotide Microarray). 35-45-mers.
Instrumentation Services, Inc., Menlo Park, California (OmniGrid, glass
slides or nylon membranes, similar to Dr. Pat Brown's)
General Scanning Inc.,
Watertown, Massachusetts (laser scanning and micropositioning, manufactures
MicroArray Biochip Scanning System: ScanArrayTM).
Now called GSI
The Genetics Profiling Company
New Jersey. Provides fluorescently-labeled kits for gene
expression arrays. (uses highly branched nucleic acids - dendrimer
Analysis Technology Consortium (GATC)
Inc., Woburn, Massachusetts (instrumentation for DNA microarray-based
analysis) Acquired by Affymetrix.
Genetix Ltd., Christchurch,
Dorset, UK (Q-Bot, Q-Pix)
Corp, San Diego, CA. Developed an ultra-sensitive signal generation
and detection platform technology based on Resonance Light Scattering (RLS)
for the simple and efficient detection, measurement and analysis of biological
Genome Systems Inc.,
St. Louis, MO, a wholly owned subsidiary of Incyte Pharmaceuticals, Inc.,
Gene Discovery Array
The Woodlands, Texas (Bioscanner™, GeneView®, Universal Arrays™, Risk-Tox)
Ann Arbor, Michigan (Flexys™ modular robotic system, GeneTAC™ and Genomic
Integrator™ array analysis products automates the imaging and analysis
of gene microarrays.)
GENPAK Inc, Stony
Brook, NY. genpakARRAY
21 robotic microarrayer system and genSTATION
3XL manual microarrayer system.
GENSET, Paris, France
(specialized in pharmacogenomics)
Genemed Synthesis Inc.,
South San Francisco, CA. Supplies oligos.
print and electronic provider of news and information on the business and
technology of genomics and bioinformatics worldwide.
GeSiM, Germany. The Nano-Plotter
is based on piezoelectric pipetting principle.
Genzyme Molecular Oncology
Serial Analysis of Gene Expression)
GeneArray Scanner (used by Affymetrix and others)
, Millbury, MA. Hypromatrix AntibodyArray TM is designed to detect protein-protein
interactions, post-translational modification and protein expression.
Hyseq Inc., Sunnyvale,
By Hybridization. HyX platform and Gene Discovery, HyGnostics, and
Illumina, Inc., San
Diego, California. utilizes fiber optics, microfabrication, and advanced
information processing to create arrays where 250,000 discrete sensors
fit on a probe the diameter of the head of a pin.
Consortium: "Sharing resources to achieve a common goal - the discovery
of all genes"
Incyte Genomics, Inc.,
Palo Alto, California (GEM
array, LifeSeq® Database with estimated 100,000 genes, and
Huntsville, AL. Produces DermArray DNA microarrays for dermatologic research.
JMAR's Precision Systems,
Inc., Chatsworth, CA. Designer and manufacturer of UV exposure and
mask aligner systems specifically designed for bio-chip manufacturers.
Also produces custom micropositioning systems for micro-spotting equipment
and high resolution dimensional metrology and defect inspection systems
for quality assurance of bio-chips and DNA microarrays.
provides focused information on all Lab-on-a-Chip technologies. It includes
published papers, news, events, new products, suppliers, research links,
jobs and discussion forums.
Ltd., North Yorkshire, TS9 5JY, UK (HDMS: Labman High-Density Microarray
Stamford, Connecticut (Lifecodes MicroArray System: LMAS)
Lynx , Megasort™
is a bead-based process providing differential DNA analysis.
Medway SA, Mezzovico,
Switzerland. MEDWAY designs, develops, manufactures and commercialises
medical devices for diagnostics, robotic systems, optical instruments,
fluorescent molecular markers, sieving microchips. Offers GMO testing.
Mergen Ltd., San
Leandro, CA. ExpressChip™
oligonucleotide microarray. Offers a full range of services.
Gaithersburg, MD. The 4D Array utilizes a patented flow through design
that optimizes the surface area to volume ratio, has shorter hybridization
times, provides larger binding/signal capacity, and is more readily automated
than flat biochips.
Micralyne Inc., (formerly
Alberta Microelectronic Corp.) Edmonton, Alberta, Canada. Fabricates
micromachined glass, silicon and thin film components for use in microfluidics.
Inc., Plano, TX. manufactures piezoelectric drop-on-demand ink-jet
printing technology for
Redmond, Washington. microfluidics based systems for application to clinical
laboratory diagnostics: Microcytometer™, H-Filter™, T-Sensor™, and O.R.C.A.
Inc., Sunnyvale, California (Storm®
Molecular Tool, Inc.,
Baltimore, Maryland. Genetic Bit Analysis, GBA®, Genomatic™.
Acquired by Orchid Biocomputer
on September 14, 1998.
Mosaic Technologies, Inc.,
Waltham, MA. EZ-RAYSTM
activated slide kits for DNA microarrays.
BioChip Systems. Licensed a 3-D gel pad technology from Argonne
Nanolytics is developing
Custom Array Synthesis Technology
Nanogen, San Diego,
California (Electronic Addressing, Concentration, and Hybridization)
NEN Life Science Products,
Boston, MA (MICROMAX™
Human cDNA Microarray System I for differential gene expression analysis)
Oncormed Inc., (acquired
by Gene Logic in July, 1998) characterizes
genes to establish their clinical relevancy and provides molecular profiling
of patients for pharmacogenomic and therapeutic purposes
Operon Technologies, Inc.,
Alameda, CA. Low density (320 or 370 genes, 70-mers) OpArraysTM
Orchid BioSciences, Inc.,
Princeton, New Jersey (a Sarnoff
company) microfluidic chips; applying microfabrication processes in glass,
silicon, and other materials to create three dimensional structures.
Contained within these devices are small capillary channels less than a
millimeter wide. Wins
NIST ATP Award in "Tools for DNA Diagnostics" Project: Polymerase
Signaling Assay for DNA Variation Detection on Universal Processor Arrays
It also has a Web site on single nucleotide polymorphisms (SNPs).
OriGene Technologies Inc.,
Rockville, MD. Offers SmartArray™
chips (Huamn), including nuclear hormone receptors, homeobox/b-zip/HLH
transciption factors, tissue-specific/inducible transcription factors ,
and phosphotyrosine Kinases.
Oxford Gene Technology Ltd
(Ed Southern) Oligo-based microarray
Company, Meriden, Connecticut. (BioChip
PamGene B.V., The Netherlands.
flow-through technology for microarray.
PE Applied Biosystems, Wins
NIST ATP Award in "Tools for DNA Diagnostics" for project: Integrated,
Micro-Sample Preparation System for Genetic Analysis
Monmouth Junction (near Princeton), NJ. Developer of microtransponder-based
technology for DNA diagnostic assays. Wins
NIST ATP Award in "Tools for DNA Diagnostics" for project: Multiplex
DNA Diagnostic Assay Based on Microtransponders
Phase-1 Molecular Toxicology,
Inc., Santa Fe, New Mexico. Molecular and high throughput toxicology
using gene chips (Licensed from Xenometrix)
Proligo LLC, Boulder,
CO. Nucleic acid supplier.
Palo Alto, California (Surface tension array on glass substrate; "Printing"
reagents using drop-on-demand technology)
Minneapolis, M. Cytokine
Expression Array allows one to determine the RNA level for approximately
400 cytokines and related factors in one standard hybridization experiment.
(charged nylon membrane)
Medfield, Massachusetts. Custom DNA, RNA, PNA, and Protein MicroArray
RELAB AG, Germany, is
developing BioChip arrays for diagnostic applications (oncology). The GeneStick
platform with arrays on plastic sticks and a new chemiluminescence imager.
Research Genetics, Huntsville,
Inc., Carlsbad, CA. Its RoboArrayer
is integrated with a vision system to allow for real-time quantification
of spot size and spot volume during the printing process.
Rosetta Inpharmatics, Kirkland,
DNA oligonucleotides microarrays (in-situ synthesized on a glass support
via ink-jet printing process); Resolver™
Expression Data Analysis System.
Durham, NC. Offers ArrayWorksTM,
a complete line of custom microarray services, for the production, processing,
and analysis of microarrays, using PixSysTM
arrayers from Cartesian Technologies.
It also provides customized ArrayEngineTM
(merged with Arris Pharmaceutical to become AxyS
Pharmaceuticals), La Jolla, California
Germany, and San Diego, California (DNA MassArray, BiomassPROBE, Biomass
SIZE, BiomassSEQUENCE, BiomassSCAN, BiomassINDEX, and SpectroChip)
The Woodlands, Texas (Panorama™E.
coli Gene Arrays, 4,290 genes per array)
Bethesda, MD. Their gene expression array (GEArray™
) systems (Human and mouse) are designed for pathway-specific gene expression
profiling. Also offers ChoiceGEArray to meet customer's specific
Eden Prairie, Minnesota. Manufactures 3D-LinkTM
activated slides for the production of microarrays. Uses amine-modified
DNA to hybridize on the surface of the slide.
Synteni, Inc., Fremont,
California (acquired by Incyte Pharmaceuticals,
Inc. in January 1998) (UniGEM™
Gene Expression Microarray)
The German Cancer Institute, Heidelberg, Germany
Sunnyvale, California (offers whole system parts: ChipMaker, SmartChips,
Hybridization Cassette, ScanArray 3000, ImaGene Quantification Software,
and Super Microarray
Third Wave Technologies, Inc.,
Madison, WI. Develops and commercializes simple, low-cost nucleic acid
platform technologies to fundamentally alter disease discovery, diagnosis
and treatment. Invader®
assay and CFLP®
for expression study of protein and in situ screening of mRNA.
Inc., San Diego, CA. Supplies inexpensive replicators
($3000 or so) that will make macroarrays on membranes, or microarrays on
Virtek Vision International
Inc. (Ontario, Canada) ChipReader™
is a high-sensitivity laser confocal system for rapid imaging of the DNA
Vysis, Inc., Downers
Grove, Illinois (CGH-Comparative Genomic Hybridization; The GenoSensor
Microarray System includes genomic microarrays, reagents, instrumentation
and analysis software.)
Triangle Park, North Carolina, has developed a multiplexed, microplate-based
electrochemical detection system for high-throughput screening of compounds
for their effects on gene expression. Based on measurement of the
oxidation of guanine on an electrode.
Xenometrix, Inc., Boulder,
CO (Gene Profile Assay and bioinformatics for gene induction profile analysis;
a demo is available)
XENOPORE Corp., Hawthorne,
NJ. Manufacturer of coated microscope slides, including silanated,
silylated, epoxy, streptavidin, nickel chelate, and many other surfaces.
* to be updated... Modified from Marshall, A.; Hodgson,
J. DNA chips - an array of possibilities. Nature Biotechnology1998,
Santa Clara, California
| In situ (on-chip) photolithographic synthesis
of ~20-25-mer oligos onto silicon wafers, which are diced into 1.25 cm2or
5.25 cm2 chips
||10,000-260,000 oligo features probed with labeled 30-40
nucleotide fragments of sample cDNA or antisense RNA
||Expression profiling, polymorphism analysis, and diagnostics
|Brax, Cambridge, UK
||Short synthetic oligo, synthesized off-chip
||1000 oligos on a "universal chip" probed with tagged
||Diagnostics, expression profiling, novel gene identification
|Gene Logic, Inc.,
The Woodlands, Texas
|GENSET, Paris, France
|Hyseq Inc., Sunnyvale,
||500-2000 nt DNA samples printed onto 0.6 cm2
(HyGnostics) or ~18 cm2 (Gene Discovery) membranes
Fabricated 5-mer oligos printed as 1,15 cm2
arrays onto glass (HyChip)
|64 sample cDNA spots probed with 8,000 7-mer oligos (HyGnostics)
or <=55,000 sample cDNA spots probed with 300 7-mer oligo (Gene Discovery)
Universal 1024 oligo spots probed 10 kb sample cDNAs,
labeled 5-mer oligo, and ligase
|Expression profiling, novel gene identification, and
large-scale sequencing (Gene Discovery array), polymorphism analysis and
diagnostics (HyGnostics/HyChip arrays), and large-sample sequencing (HyChip
Inc., Palo Alto, California
||Piezoelectric printing for spotting PCR fragments and
on-chip synthesis of oligos
||<=1000 (eventually 10,000) oligo/PCR fragment spots
probed with labeled RNA
||Fluorescence and radioisotope
||Expression profiling, polymorphism analysis, and diagnostics
Inc., Sunnyvale, California
|500-5000 nt cDNAs printed by pen onto ~10 cm2
on glass slide
||~10,000 cDNA spots probed with 200-400 nt labeled sample
||Expression profiling and novel gene identification
|Nanogen, San Diego,
||Prefabricated ~20-mer oligos, captured onto electroactive
spots on silicon wafers, which are diced into <=1 cm2 chips
||25, 64, 400 (and eventually 10,000) oligo spots polarized
to enhance hybridization to 200-400 nt labeled sample cDNAs
||Diagnostics and short tandem repeat identification
Palo Alto, California
||On-chip synthesis of 40-50-mer oligos onto 9 cm2
glass chip via printing to a surface-tension array
||<=8,000 oligo spots probed with 200-400 nt labeled
sample nucleic acids
||Expression profiling and polymorphism analysis
Germany, and San Diego, California
|Off-set printing of array; around 20-25-mer oligos
||250 locations per SpectroChip interrogated by laser desorbtion
and mass spectrometry
||Novel gene identification, candidate gene validation,
diagnostics, and mapping
Fremont, California (acquired by Incyte
||500-5,000 nt cDNAs printed by tip onto ~4 cm2
||<=10,000 cDNA spots probed with 200-400 nt labeled
||Expression profiling and novel gene identification
|The German Cancer Institute, Heidelberg, Germany
||Prototypic PNA macrochip with on-chip synthesis of probes
using f-moc or t-moc chemistry
||Around 1,000 spots on a 8 x 12 cm chip
||Expression profiling and diagnostics
Data Mining: Making Sense of Gene Expression
Schema of Array Databases and On-line Tools:
"House Keeping Genes": http://www.hugeindex.org/;
Khan et al, Cancer Research 58, Nov. 1998, p.5009-5013
A comprehensive list of is gene expression database
and analysis tools is available at NCGR's GeneX
Microarray Gene Expression Database (MGED)
Group, was formed to facilitate the adoption of standards for DNA-array
experiment annotation and data representation, as well as the introduction
of standard experimental controls and data normalisation methods.
databases on the WWW (by Bernard MARTIN and Philippe MARC)
NCBI's Gene Expression
Omnibus (GEO) public gene expression repository in development - contact
Alex Lash - email@example.com
at the National Human Genome Research
at the National Cancer Institute's is in the final stages of reviewing/implementing
a complete, robust schema.
of George Church Lab's at Harvard Medical School: a relational database
containing yeast RNA expression data. As of July, 1999 it contains 17.5
million pieces of information loaded from 11 published and in-house expression
(Microarray Analysis Tool) at Albert Einstein College of Medicine: based
on Java, JDBC, and Sybase SQL.
consortium's published schema
a Collaborative Internet Database and Toolset for Gene Expression Data
at the National Center for Genome Resources.
of Silicon Genetics is a public web database that allows scientists to
freely distribute and visualize gene expression data (text and image) from
microarrays, Affymetrix chips, and related technologies. It can also dynamically
generate several graphs from the data being viewed, such as: scatter plots,
trees, overlays, ordered lists, line graphs, or physical position graphs.
It is designed to store annotations and interpretations on finished experiments,
and can access data from SQL databases like GATC or even from flat text
The Arabidopsis Functional Genomics Consortium (AFGC)'s Arabidopsis
cDNA Microarray Results
being developed at the European Bioinformatics Institute, will be a public
array-based gene expression data repository. An international meeting on
Gene Expression Databases, November 14-15, 1999.
Dr. John Weinstein's
Genomics and Bioinformatics Group at the NCI has made some microarray data
and tools available online.
Lemkin at the NCI developed a Java applet, MicroArray Explorer (MAExplorer),
which is currently being used in the Mammary
Genome Anatomy Program
Dr. Leif Peterson's CLUSFAVOR:
Large-sample Microarray-based Gene Expression Profiles Using Principal
Public Gene Expression Resource, Alex E. Lash et al., Genome Res. 2000
July 1; 10(7): p. 1051-1060
Java program for analyzing microarray data. SOM and PCA implemented, by
at the EBI
Articles on Microarray Datamining:
Maths, Belgium. GenExplore™
: 2-way cluster analysis, principal component analysis, discriminant
analysis, self-organizing maps.
Los Angeles, California (ImaGene™,
special image processing and data extraction software, powered by MatLab®;
hierarchical clustering, artificial neural network (SOM?), principal component
time series; AutoGene™;
Cose, France. XDotsReader
GeneData AG (Basel,
Switzerland), analysis of genomics and proteomics data: GeneData WorkBench,
Network Inference from Large-Scale Gene Expression Data (Patrik D'haeseleer,
University of New Mexico).
Gene Network Sciences,
Ithaca, NY 14850. Accelerates the drug discovery process by creating dynamic
computer models of living cells. BioMine for microarray data analysis.
Recognition web site at MIT's Whitehead
Genome Center. Focuses on computational methodologies for the analysis
and interpretation of large-scale expression data sets generated by DNA
Inc., St. Catharines, Ontario, Canada. The company writes software,
develops detection technologies, and integrates systems for image analysis.
Its PC-based ArrayVisionTMsystem
has been widely used for rapid and automated analysis of genome arrays.
a new software for analyzing gene expression data. arraySCOUT™ is able
to link all expression data to internal and external biological databases
via SRS. This link provides information on the function, structure
and metabolic pathways of genes from up to 400 databases. arrayTAG - cDNA
collections specifically tailored to chip technology; arrayBASE - cDNA
annotations in a comprehensive database.
Molecular Applications Group,
Palo Alto, CA. Stingray™
is integrated software and database products for gene expression, gene
function, and gene sequence analysis from microarray data. It is integrated
with and dependent upon the use of Affymetrix's GeneChip®
system and its Expression Data Mining Tool (EDMT) software. [Its ownership
of and rights to Stingray™ were sold to Affymetrix in December, 1999.]
No longer a corporate entity.
Partek, Inc., St. Peters,
Missouri. Provider of pattern recognition and data visualization software
for science and engineering. Its Partek
Pro 2000 system has been used by companies to analyze microarray gene
Rosetta Inpharmatics, Kirkland,
Expression Data Analysis System.
, Fairfax, VA. Its MicroArray
Suite enables researchers to acquire, visualize, process, and analyze
gene expression microarray data. Developed by scientists at the NIH's National
Human Genome Research Institute.
workbench for analyzing experiments based upon genomic expression experiments.
Spotfire, Inc., Cambridge,
Massachusetts. Offers advanced data visualization capabilities including
the ability to perform gene cluster analysis and metabolic pathway mapping.
The Spotfire Array Explorer is particularly attractive to experimentalists
performing microarray analysis.
L.P., Silver Spring, MD: Array-Pro(R).
developed by Stanford University
Synomics Ltd., Cambridge,
TIGR (The Institute for
Genome Research) offers software
tools (free for academic institutions) for array analysis.
Speed's Microarray Data Analysis Group Page: very good resource on
statistics aspects of microarray data [Berkeley]
Improves MicroArray Data Analysis, Visualization, and Management
International, Palo Alto, CA. Array
Designer - designs PCR primers and oligonucleotide probes for microarrays
OmniViz, Inc., Columbus,
OH, a subsidiary of Battelle.
Provides information visualization and data mining solutions for life and
chemical sciences. Product: OmniViz
ViaLogy Corp., utilizes
quantum interferometric computing to analyze biochips
Xpogen Inc., Cambridge,
MA. Web-based tools for organizing, sharing, analyzing, and interpreting
gene expression microarray data and associated annotation. "relevance
Wentian Li of Rockefeller University maintains a
list of papers on data analysis: http://linkage.rockefeller.edu/wli/microarray/
The International Society for Computational Biology (ISCB).
models for microarrays and DNA expression at Stanford University
[University of New Mexico]: Gene
Network Inference from Large-Scale Gene Expression good discussions
and a list of articles. [with Incyte, NIH]
Michael P. S. Brown, William Noble Grundy, David Lin,
Nello Cristianini, Charles Sugnet, Terrence S. Furey, Manuel Ares, Jr.,
David Haussler [UCSC]. Knowledge-based Analysis of Microarray Gene Expression
Data Using Support
Vector Machines. (SVMs are considered a supervised computer learning
on Biocomputing 2000
Symposium on Biocomputing 1999
The Nature of GED (Gene Expression data); Experimental
Variables (Dimensionality); Quality (Reproducibility) of GED; Extracting
Signal from Noise; Statistical Approach; Artificial Intelligence-Based
Approach; Interpretation of Results; Publicly Available GED (GEO, EBI,
Protein Chips (Protein
The idea of protein microarray is not new. In fact,
the basics and theoretical considerations of protein microarrays were done
in the 1980's by Roger Ekins and coleagues. See, e.g., Ekins R.P., J
Pharm Biomed Anal 1989. 7: 155; Ekins R.P. and Chu F.W., Clin Chem
1991. 37: 1955; Ekins R.P. and Chu F.W, Trends in Biotechnology,
The are two main objectives for proteomic research: 1.
quantification of all the proteins expressed in a cell; 2. functional study
of thousands of proteins in parallel. For quantification purpose,
the standard method is 2D gel separation followed by MS identification.
For protein function study, microarray-based assays are being used to study
protein-protein and protein-ligand interations.
Gavin MacBeath and Stuart L. Schreiber of Harvard University just published
a paper on protein microarray - more than 10,000 protein spots were
printed on a glass slide. The chip was used to identify protein-protein
and protein-drug interactions. I believe it's a truly breakthrough
for proteomics and for drug discovery. G. MacBeath and S.L. Schreiber,
Printing Proteins as Microarrays for High-Throughput Function Determination,
2000 September 8; 289(5485): p. 1760-1763. Abstract
The question is how to get thousands of pure proteins and keep them in
their natural conformation.
recently finished a strategic report on protein chips: sales of protein
chips are likely to balloon from $45 million in 2000 to almost $500 million
in 2006. Press
MacBeath G. and Schreiber SL, Printing Proteins as Microarrays
for High-Throughput Function Determination, Science 2000 September
8; 289(5485): p. 1760-1763. Abstract
de Wildt RM, Mundy CR, Gorick BD, Tomlinson IM. Antibody
arrays for high-throughput screening of antibody-antigen interactions.
Biotechnol. 2000 Sep;18(9):989-994
Irving RA, Hudson PJ. Proteins emerge from disarray. Nat
Biotechnol., 2000 Sep;18(9):932-933.
Aled M. Edwards, Cheryl H. Arrowsmith, and Bertrand des Pallieres,
Proteomics: New tools for a new era, Modern Drug Discovery,
Sept., 3(7) 34-44.
Kollol Pal, The Keys to chemical genomics, Modern Drug
Discovery, 2000, Sept., 3(7) 46-55.
Joos TO, Schrenk M, Hopfl P, Kroger K, Chowdhury U, Stoll
D, Schorner D, Durr M, Herick K, Rupp S, Sohn K, Hammerle H, A microarray
enzyme-linked immunosorbent assay for autoimmune diagnostics. Electrophoresis,
Walter G, Bussow K, Cahill D, Lueking A, Lehrach H., Protein
arrays for gene expression and molecular interaction screening, Curr
Opin Microbiol. 2000 Jun;3(3):298-302.
Arenkov P.;Kukhtin A.;Gemmell A.;Voloshchuk S.;Chupeeva V.;Mirzabekov
A., Protein Microchips: Use for Immunoassay and Enzymatic Reactions, Analytical
Biochemistry, 2000, 278, 2, 123-131
Emili AQ and Cagney G. Large-scale functional analysis using
peptide or protein arrays. Nat Biotechnol. 2000 Apr;18(4):393-7.
Ge H., UPA,
a universal protein array system for quantitative detection of protein-protein,
protein-DNA, protein-RNA and protein-ligand interactions. Nucleic
Acids Res. 2000 Jan 15;28(2):e3
Lueking A, Horn M, Eickhoff H, Bussow K, Lehrach H, Walter
G [Max Planck] Protein
microarrays for gene expression and antibody screening. Anal.
Biochem. 1999 May 15;270(1):103-111
Zong Q, Schummer M, Hood L, Morris DR. Messenger RNA translation
state: the second dimension of high-throughput expression screening. Proc
Natl Acad Sci U S A 1999 Sep 14;96(19):10632-6.
Mendoza LG, McQuary P, Mongan A, Gangadharan R, Brignac S,
Eggers M. [Genometrix] High-throughput microarray-based enzyme-linked immunosorbent
assay (ELISA). Biotechniques 1999 Oct;27(4):778-80, 782-6, 788. [Medline]
Brett D. Martin,* Bruce P. Gaber, Charles H. Patterson, and
David C. Turner, Direct Protein Microarray Fabrication Using a Hydrogel
Langmuir, 14 (15), 3971 -3975, 1998.
Konrad Büssow at Max-Planck-Institut für Molekulare Genetik
Large Scale Proteomics Corporation, Rockville, MD, a subsidiary
of Large Scale Biology Corporation.
Palo Alto, California. ProteinChip™
Arrays for the investigation of proteins on the femtomole scale directly
from their "native" environments. Based on Surface-Enhanced Laser Desorption/Ionization
and Medical Sciences Institute), a protein array for autoimmune diagnostics.
Ltd., Cambridge, UK. COVET™
protein microarrays (Cloned Open reading frames for the Validation of Experimental
ExPASy (Expert Protein
Analysis System) proteomics server of the Swiss
Institute of Bioinformatics (SIB).
GeneBio (Geneva Bioinformatics
LumiCytes, Inc., Fremont,
CA. SELDI BioChip based molecular profiling platform.
Cambridge Healthtech Institute's conference on Human
Proteome Project, April 2-4, 2001, McLean, VA.
Related Meetings / Workshops
Design GmbH, Heidelberg, Germany. Uses chemical microarrays as screening
tools to enhance the understanding of protein binding specificity, based
on diversity Label-free Detection
Gregory A. Korbel, Gojko Lalic, and Matthew D. Shair*; Reaction
Microarrays: A Method for Rapidly Determining the Enantiomeric Excess
of Thousands of Samples, Journal of the American Chemical Society;
2001; 123(2); 361-362.
Eric LeProust et al., Digital Light-Directed Synthesis. A
Microarray Platform That Permits Rapid Reaction Optimization on a Combinatorial
Basis, J. Comb. Chem., 2 (4), 349 -354, 2000.
Paul J. Hergenrother, Kristopher M. Depew, and Stuart L.
Schreiber*; Small-Molecule Microarrays: Covalent Attachment and
Screening of Alcohol-Containing Small Molecules on Glass Slides, Journal
of the American Chemical Society; 2000; 122(32); 7849-7850
Gavin MacBeath, Angela N. Koehler, and Stuart L. Schreiber*;
Small Molecules as Microarrays and Detecting Protein-Ligand Interactions
en Masse, Journal of the American Chemical Society; 1999;121(34);
IBC 8th Annual Biochip
Technologies Conference - Chips To Hits, October 29 - November 1,
2001, San Diego, CA.
2001: The Microfluidics, Microarrays, and BioMEMS Conference and Exhibition,
27-31, 2001, San Diego, California, USA. Sponsored by the Association
for Laboratory Automation.
6th Annual Drug Discovery Technology 2001, August 13-17, 2001,
Boston, MA, USA
Microarray and Microfluidic Technology Congress, June 5-8, 2001,
Hilton Munich Park, Munich, Germany. (IBC)
Microarray Conference, Seattle WA.
Microarray Survey: 2000-2001. An analysis of data submitted to this
survey will be presented at the ABRF2001
meeting in February 2001
Bioinformatics Strategies for Application of Genomic Tools
to Environmental Health Research, March 5, 2001, National Center
for Toxicogenomics (NCT),
Raleigh, NC, USA. Accompanying
symposium at NCSU.
2001 - Technology Development & Application, March 12 - 13,
2001, Brooklyn, New York, USA.
Technology, March 21-23, 2001 - San Diego, CA. (IBC). Keynote
speaker: Prof. Roger Ekins
3rd MGED: The
Third International Meeting on Microarray Data Standards, Annotations,
Ontologies and Databases, March 29-31, 2001, Stanford University,
Cambridge Healthtech Institute's conference on Human
Proteome Project, April 2-4, 2001, McLean, VA.
15-16, 2001 - Sheraton San Diego Hotel & Marina, San Diego, CA.
Cambridge Healthtech Institute's Third Annual Integrated
Bioinformatics - High-Throughput Interpretation of Pathways and Biology,
24-26, 2001, Zurich, Switzerland.
Cambridge Healthtech Institute's Third Annual Lab-on-a-Chip
and Microarrays for Biomedical and Biotechnical Applications, January
22-24, 2001, Zurich, Switzerland.
CAMDA'00 Conference: Critical
Assessment of Techniques for Microarray Data Mining, December 18-19,
2000, Duke University, Durham, NC,
IBC’s 7th Annual Biochip
Technologies Conference - Chips To Hits, November 6-9, 2000,
IBC's Biomics Congress,
13-16, 2000, Stuttgart, Germany.
International Forum on Biochip Technologies, October 11-14, 2000,
Northwest MicroArray Conference, September 6-8, 2000,
The University of Washington, Seattle, WA.
Workshop: Functional Genomics and Microarray Data Mining, Aug 3-4,
2000, Duke University, Durham, NC.
Throughput Technologies, June 19-21, 2000, Philadelphia, PA.
The Second International
Meeting on Microarray Data Standards, Annotations, Ontologies and Databases,
25 - 27, 2000, Heidelberg, Germany.
The Microfluidics and Microarrays Conference, July 8-12, 2000,
Hyatt Regency Hotel, San Diego, California, USA. Sponsored by the Association
for Laboratory Automation.
Cambridge Healthtech Institute's first annual Lab-Chips
and Microarrays Japan, May 8-9, 2000, Tokyo, Japan.
Cambridge Healthtech Institute's first annual MACRO
RESULTS FROM MICROARRAYS: Establishing Leads for Drug Development,
3-5, 2000, Cambridge, Massachusetts.
Genetix Ltd’s International
Microarray Users Forum, November 16-18 1999, Burley Manor Hotel,
Burley, Hants. UK.
Conference on Small Genomes, November 14-17, 1999, The Doubletree
Hotel, Arlington, Virginia. Sponsored by the U. S. Department of Energy,
The Office of Naval Research, and the National Science Foundation. There
are some talks on DNA microarrays.
Algorithms and Statistical Analysis: Methods and Standards, November
9-12, 1999, Granlibakken at Lake Tahoe, California. This conference
will be totally focused on the internals and methods of the mathematical
and algorithmic side of sequencing and microarray analysis. It is not a
forum for the presentation of new scientific data of a biological nature
that is being generated using sequencing or arrays.
Annual Biochip Technologies Conference: Chips to Hits '99, November
2-5, 1999, Berkeley, California. This event will certainly be another
There is a Microarray
Technology Workshop being held at George Mason University (IB3, The
Institute for Biosciences, Bioinformatics and Biotechnology) at George
Mason University on October 12-15, 1999.
Meeting--Technology, Application and Analysis, September 22 - 25,
1999, Mountain Shadows Marriott Resort Scottsdale, Arizona. Confirmed
speakers include most major players in this field. call BioEdge.Net (phone:
US: +1-800-737-1333; International: +1-402- 996-9185) for information on
of Biomolecular Resource Facilities 1999 Meeting: Bioinformatics and
Biomolecular Technologies: Linking Genomes, Proteomes and Biochemistry
Lab Chips and Microarrays
for Biotechnical Applications, January 1999 Zurich, Switzerland
Annual Conference on Biochip Technologies
IBC's conference on
Toxicology , April 29-30, 1999, The Watergate Hotel, Washington, D.C.
(many talks on DNA microarrays)
on microarray technology (July, 1998) (Not accessible from outside of the
In addition to the numerous inqueries I received on the
technical part of DNA microarray I also received many requests from my
visitors for investment advices. Unfortunately, I am not a financial adviser.
However, I list here some of the stocks
that are related to the DNA microarracy technology in one way or another.
This is FYI only and I shall not be held responsible for your investment
outcome. If you think this site helped you make a good investment decision
you are welcome to make a donation to maintain it and/or send my little
kids some Pokemon toys :)- Good luck!
Shoko Kawamoto, Tadashi Ohnishi, Hiroko Kita, Osamu Chisaka,
and Kousaku Okubo [Osaka/Kyoto]. Expression Profiling by iAFLP: A PCR-Based
Method for Genome-Wide Gene Expression Profiling. Genome Res 1999
Instrument Co., and Argonne National
Laboratory to Develop
Advanced Biochip Technology
DNA Chips to Potato Chips....
Welcome to BioTech
Resources at NCBI:
The Genome Database (GDB)
is a database of human genes, their products and their involvement in diseases.
It offers concise information about the functions of all human genes that
have an approved symbol, as well as selected others. It is especially useful
for those who are searching for information about large sets of genes or
proteins, e.g. for scientists working in functional genomics and proteomics.
two-hybrid system pathways
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler
GD, Tatusova TA, Rapp BA. Database resources of the National Center for
Biotechnology Information, Nucleic Acids Res. 2000 Jan 1;28(1):10-4.
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