|
You are here Biopharmaceutical Glossary Homepage/Search > Technologies> Microarrays > Pharmaceutical Microarray categories Pharmaceutical
Microarray & protein chips categories & taxonomy <%END IF%>
|
Back
to BiopharmaceuticalGlossaries.com
You are here Biopharmaceutical
Glossary
Homepage/Search > Technologies> Microarrays > Pharmaceutical
Microarray
categories Pharmaceutical
Microarray & protein chips categories & taxonomy Technologies
map Finding guide to terms in these glossaries Site
Map Affymetrix GeneChipsTM:
Oligonucleotide arrays in which the oligonucleotides are synthesized
directly on the chip using a photolithography process. antibody
arrays: Protein
technologies arrays: Narrower terms include bead arrays, bead based arrays,
bioarrays, bioelectronic arrays, cDNA arrays, cell arrays, DNA arrays, gene arrays, gene expression arrays,
frozen cell arrays, genome arrays,
high density oligonucleotide arrays, hybridization arrays, microcantilever
arrays, microelectronic arrays, multiplex DNA hybridization arrays,
nanoarrays, oligonucleotide
arrays, oligosaccharide arrays, planar arrays, protein arrays, solution arrays, spotted arrays,
tissue arrays, exon
arrays, filter arrays, macroarrays, small molecule microarrays, suspension arrays,
theme arrays, tiling arrays, transcript
arrays. Related terms: arrayed library.
See also chips, microarrays. bead arrays: These arrays are made up of small beads containing
capture oligonucleotides encoded with fluorescent dye combinations or through
some equivalent means. Relative to conventional two- dimensional microarrays,
the bead arrays have larger surface- to- volume ratios, providing faster hybridization
kinetics, and they also offer much more flexibility and scalability in assay
design. Google = about 241 July 10, 2002;
about 598 Sept. 16, 2003 Narrower/equivalent? term: encoded bead arrays.
bead based arrays:
Arrays in which reactions take place on the surface of
microbeads. These arrays can contain hundreds of thousands to millions of
individual probes, making them perhaps the most promising technology for the
vast number of tests that will be needed for applications such as drug discovery
and for diagnosis and treatment of patients. Google = about 38 July 10, 2002;
about 150 Sept.. 16, 2003 Related
terms
bead arrays; Microarrays : fiber optics.
biochips: An integrated circuit whose electrical and logical
functions are performed by protein molecules appropriately manipulated.
[IUPAC Biotech] Google = about 16,800 July 10, 2002;
about 36,800 Sept. 16, 2003 bioelectronic arrays: See under microelectronic arrays
Google = about 6, Sept.
16, 2003
boutique
arrays: Small scale specialty or 'boutique' array,
where large proportions of the genes on the microarrays are expected to be
highly differentially expressed. DL Wilson et. al New
normalization methods for cDNA microarray data, Bioinformatics. 2003 Jul
22;19(11): 1325-1332
categories -- microarrays :
Numerous types of microarrays are in common
use today, but for our purposes, it suffices to categorize them into three main
groups: spotted cDNA microarrays, spotted oligonucleotide microarrays,
and Affymetrix GeneChips, which are sufficiently unique to warrant their
own grouping. In the spotted- array categories, we include both
traditional arrays produced using contact printing in the style of Pat Brown
(Stanford University), and ones produced using the newer ink- jet
technology pioneered in the laboratory of Lee Hood of the University of Washington and developed
to commercial fruition by Rosetta Inpharmatics and Agilent Technologies.
Current DNA array formats can be categorized
into various groups based on the type of matrix, the probe number and/or density,
the physical size of the array, and the type of target labeling. The general
categories we describe are macroarrays, microarrays, high- density
oligonucleotide arrays (e.g., Affymetrix’s GeneChips), and microelectronic
arrays.
cDNA
arrays
A microscopic, ordered array of nucleic acids, proteins, small
molecules, cells or other substances that enables parallel analysis
of complex biochemical samples. [Mark Schena et al. "Quantitative monitoring
of gene expression patterns with a complementary DNA microarray" Science
270, 467-470 Oct. 20 1995] Google = about 2,610 July 10, 2002;
about 9, 760 Sept. 16, 2003
Related terms: DNA chips, macroarrays; Microarrays: arrayed
library
cDNA microarrays: DNA microarrays
in which the DNA
used for the probe is extracted from cDNA clones, such as those used to
sequence ESTs. Google = about 4,700 July 10, 2002; about 16,800
Sept. 16, 2003
cell biochips, cell chips, cell microarrays:
Cell & tissue technologies
chips: A quartz or silicon substrate, generally either
part of a quartz or silicon wafer, less than 500 um in thickness. “Although the single chip approach is attractive, it is not critical that
all unit operations be performed on the chip. Important operations,
including sample preparation, preliminary reactions, piezoelectric sample
deposition and mass spectrometry frequently can, or must, be done with off- chip devices.
.. Integrating all these components … is perhaps the most
important issue. [F Regnier et al “Chromatography and electrophoresis
on chips” Trends in Biotechnology 17:101 March 1999]
The term chip originally referred to the Affymetrix GeneChip.
In many cases microarray, array,
and chip can be used interchangeably, except when it is important to distinguish
between the spotted and Affymetrix approaches.
chromatin
array: To enable the simultaneous measurement of
the global chromatin accessibility state at the resolution of single genes, we
developed the Chromatin Array technique, in which chromatin is separated by its
condensation state using either the solubility differences of mono- and
oligonucleosomes in specific buffers or controlled DNase I digestion and
selection of the large refractory (condensed) DNA fragments. By probing with a
comparative genomic hybridization style microarray, we can determine the
condensation state of thousands of individual loci and correlate this with
transcriptional activity. MR Weil et. al, Global
survey of chromatin accessibility using DNA microarrays, Genome Research,
14(7): 1374- 1381, July 2004 Google = about 78,
July 12, 2004; about 93 Feb. 28, 2005
DNA arrays: We generally will use the
generic terms "DNA array" or "hybridization array"
when we are referring broadly to all types of arrays. ... Regardless of
nomenclature, each DNA array experiment is conducted in essentially the same
manner (Figure 11). First, an array of gene- specific probes is created
or obtained. (While a growing number of institutions and companies are creating
their own arrays, most research is now conducted with commercially- available
arrays.) Nucleic acids (RNA or DNA) are then isolated from biological samples
(blood or tissue). These nucleic acids are converted into labeled targets
through one of several methods. ... The labeled targets are then incubated
with the solid- state probes, allowing targets to hybridize with probes in a
high- fidelity manner. This hybridization is of the classic A/T and G/C variety.
.. After the incubation, nonhybridized samples are washed away, and measurements
are made of the signal (dye fluorescence or radioactivity) that is produced when
hybridization occurs at particular probe locations Google = about 6520 July 10, 2002;
about 15,600 Sept. 16, 2003; about 19,200 June 21, 2004 DNA chips:
Also referred to as "microarrays."
Non- porous solid supports, such as glass have facilitated miniaturization
and fluorescence based detection. About 10,000 cDNAs can be robotically
spotted onto a microscope slide and hybridized with a double labeled probe,
using protocols pioneered by Pat Brown and colleagues [at Stanford University]
[Eric Lander "Array of hope" Nature Genetics 21 (1s): 3-4 Jan 1999] Google = about 10,700 July 10, 2002;
about 23,000 Sept. 16, 2003; about 26,800 June 21, 2004 Related term hybridization arrays
DNA microarrays:
The most common genomic method used to measure gene
expression levels. DNA microarrays consist of a small solid support (such as a
glass slide, nylon membrane, or silicon wafer) with an ordered array of DNA
fragments attached to it. Other names in the literature include biochips, DNA
chips and gene arrays. CHA Cambridge
Healthtech Advisors, Clinical
Genomics: The Impact of Genomics on Clinical Trials and Medical Practice
report, 2004 Google = about 13,100 July 10, 2002;
about 45,000 Sept. 16, 2003; about 64,300 June 21, 2004 DNA microchip:
A revolutionary new tool used to identify mutations in genes like BRCA1 and
BRCA2. The chip, which consists of a small glass plate encased in plastic, is
manufactured somewhat like a computer microchip. On the surface, each chip
contains thousands of short, synthetic, single- stranded DNA sequences, which
together, add up to the normal gene in question. NHGRI, US "What is a DNA
chip?" "What is it used for? "How does it work?" http://www.genome.gov/10000205
Google = about 938
Sept. 16, 2003
exon arrays:
Used to confirm predicted exons, described in
D.D. Shoemaker et.
al "Experimental
annotation of the human genome using microarray technology" Nature
409, 922-927, 15 Feb. 2001. Related term: tiling arrays Google = about 24 July 10, 2002;
about 45 Sept. 16, 2003
exon array CGH
comparative genome hybridisation: Researchers
from the Wellcome Trust Sanger Institute and colleagues describe a new method
called 'Exon Array CGH' (comparative genome hybridization) to detect loss or
gain of DNA regions across the genome using a DNA 'chip' or array method.
Published in the American
Journal of Human Genetics on Monday April 4, 2005 http://www.sanger.ac.uk/Info/Press/ filter arrays: Filters on which clones or purified cDNAs
have been arrayed at high density to provide targets for reverse- transcribed
probes. [D Bowtell “Options available – from start to finish — for obtaining
expression data by microarray” Nature Genetics 20 (1s): 25- 32 Jan 1999] Google = about 893 July 10, 2002;
about 2,190 Sept. 16, 2003 gene arrays, gene microarrays: See DNA chip, DNA arrays, DNA
microarrays
GeneChip
is an Affymetrix product. Steve Fodor and colleagues
[at Affymetrix] have adapted photo- lithographic
masking techniques
used in semiconductor manufacture to produce arrays with
400,000 distinct oligonucleotides. [Eric Lander "Array of hope" Nature
Genetics 21(1s): 3- 4, Jan 1999]
genome arrays:
The sequencing of complete genomes has made possible
whole genome arrays of bacteria and other organisms. Affymetrix has made E.
coli, yeast and Arabidopsis genome arrays. Used for
the study of gene expression and to determine co- regulated genes. Google = about 211 July 10, 2002; about 791
Sept. 16, 2003; about 1,670 July 23, 2004
genome chip: Technology is meant to monitor the whole genome
on a single chip. GenomeChip would also include the increasingly important
and feasible protein chip technology. [Leming Shi “DNA Microarrays”
1998- 2002] http://www.gene-chips.com/ Google = about 108 July 10, 2002;
about 894 Sept. 16, 2003; about 776 July 23, 2004 Related terms
Microarrays categories: genome arrays, genomic arrays, genomic microarrays.
genomic arrays:
Allow toxicologists to look at cellular behavior in a completely new light. In a sense, recording individual gene responses to
powerful insults such as alkylating agents was akin to studying the effects of poverty by monitoring a person's bank
account - the complete picture is much larger than what is actually being measured. But genomic arrays simultaneously report indicators of multiple dimensions of the
cellular response to stimuli. Now, in addition to gaining insight into basic cellular mechanisms of repair, researchers looking at a variety of
indicators and responses of toxicity may gain some predictive power regarding individual
compounds - and individual humans. Both academic and private laboratories have already begun work on finding genes that induce protection or sensitivity to toxicants in
individual cells and people. [NIEHS News "Arrays cast toxicology in a new
light" Environmental Health Perspectives 09 (1), Jan. 2001] http://ehpnet1.niehs.nih.gov/docs/2001/109-1/niehsnews.html
Google = about 129 July 20, 2002;
about 374 Sept. 16, 2003; about 394 July 23, 2004 Related terms
genome arrays, genome chip, genomic microarrays.
genomic microarrays:
The current methodological approach for the construction of
genomic arrays is dominated by the use of genomic clones (BACs, PACs and
cosmids) as targets for array hybridization. [These are] only the beginning of a
new generation of high - resolution and high - throughput tools for genetic
analysis. KK Mantripragada et. al "Genomic microarrays in the
spotlight, Drug Discovery Today Microarray supplement 9(24): S45-S52, 15 Dec.
2004 Google = about 905 July 10, 2002;
about 517 Sept. 16, 2003; about 4,450 Dec. 13, 2004 Related terms genome arrays, genome chip, genomic arrays.
GPCR
microarrays: The dominance of G protein-coupled
receptors (GPCRs) as a drug target class, coupled with the increased pace of
target identification and expansion of compound libraries, presents a compelling
need to develop technologies to screen multiple GPCRs simultaneously. To address
this need, GPCR microarrays that require the co-immobilization of lipid
molecules and the probe receptors of interest have been fabricated, using
conventional robotic printing technologies. Y. Fang et. al, G
protein-coupled receptor microarrays for drug discovery, Adv Biochem Eng
Biotechnology 83:189- 209, 2003
high density oligonucleotide arrays:
High- density oligonucleotide arrays differ from other formats in
that the probe is generated in situ on the surface of the matrix
as opposed to being generated separately and then spotted on the surface.
Affymetrix has historically led the way in this area through a photolithographic
process similar to methods used in semiconductor fabrication.... this method
involves adding one base at a time to sequentially create oligonucleotides.
Specific oligonucleotides can be placed at specific locations by the use of
protective chemistry and lithographic masks. Because this combinatorial
synthesis approach has a 95% efficiency at each step, synthesis of
oligonucleotides longer than 25 bases is problematic. Because 25-residue
oligonucleotides have limited specificity and binding affinity for gene
expression analysis, mismatches and spurious target- probe binding can take
place. In much of the literature, the term high-density oligonucleotide array
is used as a generic synonym for Affymetrix GeneChip. Google = about 1,290 July 10, 2002;
about 4,210 Sept. 16, 2003 Broader terms
oligonucleotide arrays, oligonucleotide chips,
oligonucleotide microarrays,
microchips.
hybridization arrays: DNA hybridization arrays are currently the most
widely used tools for large- scale analysis of gene expression
and other genomic- level phenomena and patterns. In all DNA array formats, gene-
specific sequences (probes) are immobilized on a solid- state matrix
(nylon membranes, glass microscope slides, silicon/ ceramic chips) and then
queried with nucleic acids from biological samples (targets). In gene
expression studies, for instance, the amount of target that hybridizes to the
gene- specific probe gives a measure of the abundance of that particular
transcript within the sample. . ;;; We generally will use the generic terms
"DNA array" or "hybridization array" when we are
referring broadly to all types of arrays. Google = about 337 July 10, 2002;
about 889 Sept. 16, 2003 Also called hybridization array assays
in situ arrays:
Oligonucleotides are
constructed on the matrix. From the Latin "in situ" in place.
Google = about 28 July 10, 2002;
about 50 Sept. 16, 2003 in situ synthesis:
One further nuance with ink- jet
oligonucleotide microarrays is that it is possible to synthesize the
oligonucleotides on- the- fly directly on the array surface. The process entails
sequentially spraying each spot with the chemicals needed to add the next base
to a growing DNA molecule, washing off the excess, and going on to the next
base. The advantage is flexibility. To change the DNA that will be placed on an
array, you simply give the machine a new list of sequences to synthesize. LabChipR : is a Caliper product.
http://www.caliperls.com/products/labchip-systems/ lab-on-a-chip: The
technology that is used to perform a combination of analysis on a single
miniaturized devise for biological and clinical analysis. Glossary, Nature Reviews
Genetics http://www.nature.com/nrg/journal/v5/n3/glossary/nrg1296_glossary.html Google = about 9,300 July 10, 2002;
about 21,500 Sept. 16, 2003; about 952,000 Apr 9, 2007 macroarrays:
A macroarray is up to 8 x 12 cm with spots of 1 mm or more, and typically
contains hundreds to a few thousand spots. Up to 8 x 12 cm membranes with anywhere from hundreds, to thousands of
genes. ... Macroarrays can be thought of as the most technologically basic form
of hybridization arrays. The idea of macroarrays grew from early
hybridization experiments against cDNA libraries. These arrays consist of
probes spotted onto a solid matrix of nylon, nitrocellulose, or
plastic. Unlike microarrays, macroarrays rely on radioactivity instead of fluorescent
tags for target labeling. Generally, macroarrays contain fewer genes than microarrays
or high- density oligonucleotide arrays, and their density typically
ranges from 200 to 10,000 genes. A wide variety of macroarrays are commercially
available for many different organisms and genes. Macroarrays can also be
constructed in- house through methods similar to those used to create
microarrays. ... , the simplicity of these arrays is a major drawing point.
... given their high sensitivity to small changes in gene expression,
macroarrays are particularly well suited to specialized applications such as gene
expression analysis in small tissue samples
Google = about 865 July 10, 2002;
about 15,700 Sept. 16, 2003 Narrower term: nylon
macroarrays.
microarrays:
Microarrays (in which nucleic acids
representing genes are spotted onto or synthesized on a substrate and then
tested against a sample) gauge mRNA levels - and thus gene expression. With
these tools, many different genes can be studied, enabling expression patterns
to be discerned in, for example, diseased versus normal tissue or in early-
stage
disease tissue versus late- stage disease tissue. Microarrays
has additional definitions and microarray links.
Google = about 95,700 July 10, 2002;
about 276,000 Sept. 16, 2003
microchip analytical
procedures: The preparation and analysis of samples on miniaturized devices.
MeSH 2005 microchips:
A microchip (sometimes just called a "chip") is a
unit of packaged computer circuitry (usually called an integrated
circuit) that is manufactured from a material such as silicon
at a very small scale. Microchips are made for program logic (logic or microprocessor
chips) and for computer memory (memory or RAM
chips). Microchips are also made that include both logic and memory and for
special purposes such as analog-to-digital
conversion, bit slicing, and gateways. [whatis.com] Related terms: Nanoscience
& Miniaturization
microelectronic arrays:
One of the newer formats for
hybridization arrays, are the result of a combination of advances in molecular
biology and semiconductor microfabrication techniques. Instead of being
based on a membrane or a glass- slide platform, these arrays consist of sets of
electrodes covered by a thin layer of agarose coupled with an affinity moiety
(permitting biotin- avidin immobilization of probes). Each microelectrode
is less than 100: M in diameter and is capable of generating a controllable
electric current that can be used to draw probes, samples, and reagents to
specific locations on the chip surface. The limiting factor in the number of
genes these arrays can cover is how many electrodes can be made within the area
of the array.
These arrays, based on semiconductor
microfabrication techniques, are made up of microelectrodes capable of
generating a current that can be used to draw probes, samples, and reagents to
specific locations on the chip. This approach allows faster, more controlled
hybridization. Google = about 77 July 10, 2002
"microelectronic chips = about 506; about 193 Sept. 16,
2003 about 858 Also called microelectronic chips
See also under multiplex DNA
hybridization arrays
microfluidics based chips: These chips, which contain tiny channels in
which the movement of fluids is controlled, allow the integration and
miniaturization of a range of laboratory processes. Because of their small
scale, these devices require much lower quantities of chemicals and test
materials than those used in traditional molecular- biological approaches. multiplex DNA hybridization arrays: We will use the term DNA array
for any matrix containing multiple gene- specific sequences that permits
simultaneous evaluation of hundreds to thousands of individual genes. This term
will include nylon- membrane- based arrays (so- called macroarrays), microscope-
slide- based arrays (microarrays), silica chips with high- density
oligonucleotides constructed in situ (the Affymetrix GeneChip), and
microelectronic arrays (a unique combination of addressable electrodes and gene-
specific fragments). All these formats fall under the description multiplex
DNA hybridization array. However, common usage in the field frequently
refers to all these formats as microarrays. nylon macroarrays:
High density membranes, in which cDNA
colonies or polymerase chain reaction (PCR) products are regularly arranged
with a spot spacing (“pitch”) of 1 to 2 mm have been used for some time
with expression measurements with radioactive complex probes. [Note] There
is a certain tendency by some firms to call their macroarrays “microarrays”.
[S Granjeaud “Expression profiling: DNA arrays in many guises” BioEssays
21: 781-790 Sept 1999] Broader term:
macroarrays
oligo arrays, oligo chips: See oligonucleotide arrays, oligonucleotide chips,
oligonucleotide microarrays
oligonucleotide arrays: Hybridization
of a nucleic acid sample to a very large set of oligonucleotide
probes,
which are attached to a solid support, to determine sequence or to detect
variations … or expression or for gene mapping. [MeSH, 1999 ‘oligonucleotide array
sequence analysis’, Google = about 3,370 July 10, 2002;
about 12,500 Sept. 16, 2003 oligonucleotide chips: See
oligonucleotide
arrays, oligonucleotide microarrays Google = about 294 July 10, 2002;
about 760 Sept. 16, 2003 oligonucleotide microarrays: With oligonucleotide
arrays, the DNA used as the probe is synthesized based on the sequence of
the gene. Since oligonucleotides are shorter than genes, there is considerable
flexibility as to which part of the gene sequence to synthesize, and software is
employed to select good sequences. Google = about 1,120 July 10, 2002;
about 6,330 Sept. 16, 2003 Related term: Affymetrix
GeneChips. planar arrays:
Microarrays with transducers? Does this refer to
the dimensions? Google = about 1240 July 10, 2002;
about 2,490 Sept. 16, 2003
probes- microarrays: See Microarrays RNA biochips: Advanced versions of our prototype RNA biochip can be used to see many different
targets like drugs, toxins and metabolites, as well as both proteins and nucleic acids," he
[Ronald Breaker] says. "We even have a molecular switch that can be triggered indirectly by UV light. In other words, our RNAs fold into intricate 3-D structures that selectively recognize a wide range of
targets, a function that is similar to antibodies. Therefore, advanced RNA biochips should be able to be used to detect almost anything that an RNA can be made to bind."
Yale scientists create RNA biochip" Yale Bulletin and Calendar 29 (26)
April 13, 2001 http://www.yale.edu/opa/v29.n26/story15.html Google = about 21 July 10, 2002;
about 77 Sept. 16, 2003; about 69 Feb. 28, 2005 reverse
microarrays: Deter Stoll et. al, Microarray
Technology: an increasing variety of screening tools for proteomic research,
Drug Discovery Today Microarray supplement 9(24): S10-17, 15 Dec. 2004 SNP chips: Microarrays used for genome wide genotyping of single
nucleotide polymorphisms (SNPs) Google = about 93 July 10, 2002;
about 258 Sept. 16, 2003; about 370 Feb. 28, 2005 Related terms SNPs & other Genetic variations SNP
small molecule microarrays:
By fabricating microarrays of small
molecules (prepared by split- and- pool synthesis), we can screen large libraries
of compounds very efficiently to identify new ligands for (almost) any
protein of interest. Such ligands can then be used to study the biological
role of its protein target by perturbing its function in vivo. [Harvard
Center for Genomic Research, MacBeath Lab, Overview] http://www.cgr.harvard.edu/macbeath/index.html
Google = about 87 July 10, 2002;
about 424 Sept. 16, 2003
solution arrays: Labels, signaling & detection
spotted arrays:
A solid surface (often a
glass microscope slide) onto which spots of DNA, each of which represents a
specific gene, have been placed in a regular,
rectangular pattern. [ More precisely, each spot represents a specific transcript
of a specific gene. ... A spotted microarray is much smaller [than macroarrays]
: 2.5 x 7.5 cm (1" x 3") with spots in the 100 mm range. Google = about 412 July 10, 2002;
about 1,250 Sept. 16, 2003 Related terms: cDNA arrays, spotted microarrays
spotted microarrays:
A solid surface - often
nothing more than a glass microscope slide - onto which spots of DNA, each of
which represents a specific gene, have been placed in a regular, rectangular
pattern. More precisely, each spot represents a specific transcript of a
specific gene. Google = about194 July 10, 2002;
about 699 Sept. 16, 2003 Related terms: cDNA arrays, spotted arrays;
See also microarrays - categories
substrate
chips: Analyse the net proteolytic potential of the
entire functional protease degradome towards a particular substrate without
identifying the active proteases that are involved. This is important
information, as the net cleavage of a particular substrate determines the
biological response. Protease Degradomics: A New Challenge for Proteomics,
Carlos Lopez- Otin & Christopher M. Overall, Nature Reviews Molecular Cell
Biology 3, 509 -519, 2002 http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrm/journal/v3/n7/abs/nrm858_r.html
Related terms: -Omes
& -omics degradome, degradomics
suspension arrays: The maturation of approaches to perform
highly parallel analyses using suspension arrays of microspheres with different
morphospectral features is making flow cytometry an important tool in
protein and genetic analysis. In this paper, we review the development of
suspension array technology (SAT), current applications in protein and genomic
analysis, and the prospects for this platform in a variety of large scale screening
applications. [JP Nolan, FF Mandy, "Suspension array technology: new tools
for gene and protein analysis" Cell Mol Biol (Noisy-le-grand) 47 (7) :
1241- 1256. Nov. 2001] synthetic DNA arrays:
"Synthetic DNA arrays" Alan Blanchard
http://www.abraxas.to/Synthdna.html
theme arrays: Microarrays containing genes
thought to be involved in specific diseases or processes.
tiling arrays:
Used to refine the precise exon structures of genes in a genomic region of
interest, described in D.D. Shoemaker et.
al "Experimental
annotation of the human genome using microarray technology" Nature
409, 922-927, 15 Feb. 2001. Google = about 97 July 10, 2002;
about 194 Sept. 16, 2003 Related term exon arrays.
Cell & tissue technologies flow cytometry
transcript arrays: Uses patterns to interrogate gene function
Google = about 32 July 10, 2002;
about 56 Sept. 16, 2003 ultra high density microarrays: Contain hundred to thousands to millions of
features. Able to run many types of assays, not just DNA hybridization. Related term:
bead based arrays. Broader term density of
microarrays, high density oligonucleotide arrays
universal arrays:
Universal microarray technology
provides a one-size-fits-all solution that is adaptable to studying any
combination of expressed genes. Google = about 87 July 10, 2002;
about 190 Sept. 16, 2003
universal microarrays: The category of universal microarrays
applies to both the two- dimensional and bead categories. Whereas conventional
arrays contain immobilized oligonucleotides that are complementary to the target
SNP sequences, universal microarrays contain sequences complementary to
sequences appended to the SNP- containing sequences. The actual SNP- detecting
hybridization process occurs in the solution phase (providing a speed
advantage). The array (a one- size- fits- all unit) then provides a means to
capture labeled reaction products and localize them on the array for
identification. Google = about 23 July 10, 2002;
about 43 Sept. 16, 2003 viral gene
chip: The viral gene chip they
[researchers led by Joseph DeRisi of the University of California at San
Francisco] created can rapidly identify known viruses and classify new ones
based on their genetic makeup. This was validated in March when the viral chip
contributed to the identification of the cause for severe acute respiratory
syndrome (SARS) as a novel coronavirus. Gene chip for viral discovery, Public
Library of Science 1(2): Nov 2003 http://biology.plosjournals.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0000003 whole genome oligonucleotide arrays: Google = about 60 Jan. 24, 2003;
about 144 Sept. 16, 2003 Bibliography Seeing the complete
repertoire of genes in a genome confronts us with the fact that we know the
biochemical activities and the biological functions of only a tiny fraction of
the genes and proteins that make up a living organism. The discovery of this
genetic "terra incognita" has reminded us how much of the living world
is beyond the frontier, and challenged us to explore this new world.
The torrent of DNA
sequences has not only made a new era of exploration imperative, but also made
it possible: Nucleic acid hybridization provides a simple, direct, way to use
the DNA sequence of a gene as a specific assay reagent to detect and monitor
that gene and its activity. We have therefore developed a convenient tool, a
"DNA microarray", that uses nucleic acid hybridization to monitor
thousands of genes at once. Patrick O. Brown, Research, Dept. of
Biochemistry, Stanford Univ.
How
to look for other unfamiliar terms
IUPAC definitions are reprinted with the permission of
the International Union of Pure and Applied Chemistry.
Evolving Terminology for Emerging Technologies
Comments? Questions?
Revisions? Mary Chitty mchitty@healthtech.com
Last revised March 23, 2012
View a Printer-Friendly Version of this Web Page!
<%END IF%>
Related glossaries include Microarrays
Protein arrays/microarrays are in Protein
technologies Cell and tissue arrays are in Cell
& Tissue Technologies
Google = about 14 Sept. 16, 2003; about 9 Feb. 28, 2005 Related term:
designer microarrays
DNA microarray:
Wikipedia http://en.wikipedia.org/wiki/DNA_microarray
Google = "gene arrays" about
3,490 July 10, 2002; about 15,800 Sept. 16, 2003
Google = "gene microarrays" about 472 July 10,
2002; about 1,540 Sept. 16, 2003
Google = about 7,010 July 10, 2002:
about 19,600 Sept. 16, 2003 Related terms genome
chip, genomic arrays, genomic microarrays.
Wikipedia http://en.wikipedia.org/wiki/Lab-on-a-chip
Viral
discovery and sequence recovery using DNA microarrays, David Wang et. al. PLOS 1
(2): Nov. 2003 http://biology.plosjournals.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0000002
MicroArray Explorer Glossary, NCI, Lab of Experimental & Computational
Biology http://www.lecb.ncifcrf.gov/searchframes.html
About 50 definitions
Microarrays
Gateway, BioMedCentral, http://www.biomedcentral.com/gateways/microarrays
Nature Genetics, “Chipping Forecast” supplement 21 (1s), Jan 1999
http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v21/n1s/index.html
Nature Genetics, "Chipping Forecast II"
supplement 32, 2002 http://www.nature.com/cgi-taf/dynapage.taf?file=/ng/journal/v32/n4s/index.html
Chipping Forecast III,
Nature Genetics, 37 (65): June 2005 http://www.nature.com/ng/journal/v37/n6s/index.html
Profiling Microarrays, Nature Genome Gateway - Post- Genomics http://www.nature.com/genomics/post-genomics/microarrays.html