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Pharmaceutical Microarray & protein chips categories & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions? Mary Chitty 
mchitty@healthtech.com
Last revised November 15, 2007
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Technologies map   Finding guide to terms in these glossaries   Site Map
Related glossaries include Microarrays glossary

Affymetrix GeneChipsTM: Oligonucleotide arrays in which the oligonucleotides are synthesized directly on the chip using a photolithography process. 

antibody microarrays:  While transcriptional profiling provides invaluable insight into biological function on a genome- wide scale, it doesn't offer information on regulation that occurs at the protein level (e.g., degradation, phosphorylation/ dephosphorylation, sub- cellular localization, etc.). We are investigating the possibility of using microarrays of antibodies to study regulation at the protein level. Harvard Center for Genomic Research, MacBeath Lab] http://www.cgr.harvard.edu/macbeath/index.html

Wikipedia  http://en.wikipedia.org/wiki/Antibody_microarray 

Google = about 164 July 10, 2002: about 888 Sept. 16, 2003; about 3,060 Oct. 26, 2004

Related terms: protein arrays   

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 glossary: 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

Google = about 14 Sept. 16, 2003; about 9 Feb. 28, 2005

Related term: designer microarrays

carbohydrate chips: University scientists have described the first chip- based chemical strategy for rapidly screening carbohydrates for biologically useful activity. [Chemical method makes further investigation of carbohydrates possible, Univ. of Chicago Chronicle, 21 (3) April 11, 2002]   http://chronicle.uchicago.edu/020411/biochip.shtml

Google = about 28 July 10, 2002; about 86 Sept. 16, 2003; about 107 July 22, 2004 [but some of these at Atkins related "low carb chips"]

carbohydrate microarrays: Stu Borman, Chemical and Engineering News, Dec. 16, 2002 lists as highlights of 2002  http://pubs.acs.org/cen/coverstory/8050/8050chemhighlights5.html with references to the literature on polysaccharide and glycoconjugate microarrays, monosaccharide chips, natural and synthetic oligosaccharide arrays, and synthetic oligosaccharides in microtiter plate format.

Google = about 176 July 23, 2004

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 glossary: 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 microarrays: Cell assays performed on a microarray.

Google "cell microarrays" = about 91 July 10, 2002; about 426 Sept. 16, 2003; about 653 June 21, 2004

Related terms: tissue array, tissue biochips; Narrower term: Microarray categories frozen cell arrays

cell chips:  The in vitro analysis of cell genomic activity has been revolutionized by a variety of chip technologies. Further important advances can be expected as high resolution analytical approaches are utilized to interrogate chips. [National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999] 

Google = about 1,570 Sept. 16, 2003; about 10,800 June 21, 2004

CellChip TM System: A miniaturized automated platform that performs both High Throughput Screening and High Content Screening on microarrays of selectively localized living cells on chips. [Cellomics, Inc. website] http://www.cellomics.com

CGH Microarrays: Advancement of CGH array applications, April 2006, Boston MA

Related term: PCR glossary comparative genomic hybridization CGH

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.

Narrower terms include Microarrays categories DNA chips, GeneChipR , genome chip, LabChipR, lab- on- a- chip, microelectrophoresis chips, oligo chips, oligonucleotide chips,  protein chips  biochips, CellChipTM System, cell chips,  microchips, microfluidics- based chips, SNP chips, tissue chips, glycochips, lymphochip, pump chips Nanoscience & miniaturization nanochip;  Related terms:  arrays, microarrays.

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 [CHI High Throughput Genomics] report,  2001]

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

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

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] 

Google = about 7,010 July 10, 2002: about 19,600  Sept. 16, 2003

Related terms genome chip, genomic arrays, genomic microarrays.

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. 

glycoarray: A new type of analytical chip that can observe the interactions between sugars and proteins is being developed by us at the Universities of Dundee, East Anglia, Liverpool, Manchester, Oxford and Imperial College, London. UK GLycoarrays Consor5tium      http://www.glycochips.org.uk/our-research.html 

glycoprotein microarrays:  We employ carbohydrate and glycoprotein microarrays to analyze glycan- dependent gp120- protein interactions. In concert with new linking chemistries and synthetic methods, the carbohydrate arrays combine the advantages of microarray technology with the flexibility and precision afforded by organic synthesis. With these microarrays, we individually and competitively determined the binding profiles of five gp120 binding proteins, established the carbohydrate structural requirements for these interactions, and identified a potential strategy for HIV vaccine development. EW Adams et. al., Oligosaccharide and glycoprotein microarrays as tools in HIV glycobiology; glycan- dependent gp120/ protein interactions, Chem Biol. 11(6): 875- 881, June 2004 

Google = about 14, July 23, 2004

Related terms: oligosaccharide chips; Glycosciences glossary

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.

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

low density arrays:  There is currently keen interest in the development of low- density microarrays, useful for processing of 100 or fewer SNPs. Although no products are yet on the market, it is safe to assume that unit prices will fall below $100 and processing times will drop significantly as well. However, low- density arrays must compete with emerging products in the encoded- bead- array category, in which small beads containing capture oligonucleotides are encoded with fluorescent dye combinations or through some equivalent means.  [CHI  SNPs Update report]

See also under density of microarrays. Related term: macroarrays

lymphochip: A specialized DNA microarray, termed the "Lymphochip", that is enriched in genes which are selectively expressed in lymphocytes and genes which regulate lymphocyte function (1). Since the majority of human lymphomas appear to represent malignant transformation of the germinal center B lymphocyte, a cDNA library was created from germinal center B lymphocytes that were purified by flow sorting from human tonsils. [Louis Staudt Lab "Current Projects" NCI, NIH 2001] http://lymphochip.nih.gov/current.html

Related terms: Cancer genomics

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.

microarray probes: See probes- microarrays Microarrays glossary

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 glossary 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 glossary

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: Biomolecules glossary

oligonucleotide array sequence analysis: Microarrays glossary

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.

oligosaccharide arrays: See glycochips, oligosaccharide microarrays

Google = about 15 Sept. 16, 2003; about 27 July 23, 2004

oligosaccharide microarrays: Studies on glycans are indispensable to define complex life systems and cell communities because all living organisms consist of diverse cells, which are covered with an abundance of heterogeneous carbohydrates. Although studies on glycans are extremely difficult because of the lack of basic technologies common to DNAs and proteins, a few new aspects of glycotechnologies have now become realized in the form of 'bio- chips', which include 'oligosaccharide arrays' or 'glyco- chips'. Recently, Fukui et al. developed oligosaccharide microarrays for glycomic analysis of extensive carbohydrate- binding proteins. How and why such glyco- engineering projects have been made in the contexts of both pure and applied sciences is described. J. Hirabayashi, Oligosaccharide microarrays for glycomics, Trends in Biotechnology 21 (4): 141-143, Apr. 2003

Google = about  40  Sept. 16, 2003; about 68 July 23, 2004

Related terms: glycochip, glycoprotein arrays 

peptide arrays:  Steve Fodor and colleagues at Affymax published several articles on these in the early 1990s. 

Google = about 322 July 10, 2002; about 876  Sept. 16, 2003

Related terms protein arrays, protein chips, protein microarrays

phenotype microarrays:

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 glossary

protein arrays: Microarrays glossary

protein chips:  The protein chip is not going to replace certain discovery methods (such as 2D gel electrophoresis), which are very good at identifying novel proteins in a complex mixture. Perhaps the greatest limitation of methods based on electrophoresis is that they are relatively expensive to perform in terms of the cost per data point, and can be quite laborious. The trend, however, may continue toward reduced costs and ease of use. Another limitation of conventional proteomic methods is that they may not be versatile enough to rapidly gather biological information - changes in protein expression, protein- protein interactions, response to various conditions.

Some chips can operate with both nucleic acids and proteins. Analogous to DNA chips, these are used for studying protein expression or protein- protein interactions, but are at an earlier stage of development. 

Google = about 3090 July 10, 2002; about 8,640  Sept. 16, 2003; about 19,000 Feb. 28, 2005

Related terms antibody arrays, protein arrays, protein microarrays; Narrower terms high- density protein microarrays, protein- protein interaction chips,  proteome chip

protein microarrays:  In conjunction with high throughput expression and purification of recombinant proteins, we can prepare microarrays of functionally active proteins on glass slides. These arrays can then be used to identify protein- protein interactions, to identify the substrates of protein kinases, or to identify the targets of biologically active small molecules. [Harvard Center for Genomic Research, MacBeath Lab, Overview]  http://www.cgr.harvard.edu/macbeath/index.html

Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2001 Jan 22; 2(2): RESEARCH 0004.1-0004.13. 

Protein microarrays will permit researchers to scan thousands of proteins in a variety of proteomic experiments, including differential expression, response to drugs, protein- protein interactions and identification of disease biomarkers. So far, they have proven to be very quantitative and, by virtue of their addressable arrays, much easier to compare results between experiments than 2D gels. Commercialization of protein arrays also promises rapid development toward real applications in clinical and point- of- care diagnostics, which would be impossible with more complex proteomic technologies that require electrophoresis or chromatography. One disadvantage of the microarray approach is that generally it is a "closed" system - you can only measure proteins for which you have a capturing agent (such as an antibody). 

Google = about 530 July 10, 2002; about 8,080  Sept. 16, 2003; about 34,800 Feb. 28, 2005

Related terms: antibody microarrays, protein arrays, protein chips, protein profiling chips; Narrower terms:  electrospray- fabricated protein microarrays, functional protein microarrays, protein-protein interaction chips, proteome chip

protein-protein interaction chips:   To extend such [gene expression] genetic analyses to the more relevant level of functional protein expression. [National Institute of Allergy & Infectious Disease, NIAID, NIH, US, SBIR Advanced Technology - (SBIR- AT- NIAID) July 26, 2000 PA NUMBER: PAR- 00- 126]  http://grants.nih.gov/grants/guide/pa-files/PAR-00-126.htm

Full-length cDNAs and ORF Full-length cDNAs and ORF clones are prerequisite for the construction of whole proteome arrays, for high throughput protein structural studies and for the rapid creation of protein fusion (GFP, TAP-tagged, etc.) for all proteins Joseph R. Ecker Plant Genome Research Program Grant: DBI9975718/0196098 "Global Expression Studies of the Arabidopsis Genome", The Salk Institute for Biological Studies http://signal.salk.edu/SSP.pdf.

proteome arrays: Full-length cDNAs and ORF clones are prerequisite for the construction of whole proteome arrays, for high throughput protein structural studies and for the rapid creation of protein fusion (GFP, TAP-tagged, etc.) for all proteins  [Joseph R. Ecker Plant Genome Research Program Grant: DBI9975718/0196098 "Global Expression Studies of the Arabidopsis Genome", The Salk Institute for Biological Studies http://signal.salk.edu/SSP.pdf.

Google = about 25 July 10, 2002; about 86  Sept. 16, 2003

Narrower term: protein array

proteome chips:  To facilitate studies of the yeast proteome, we cloned 5800 open reading frames and overexpressed and purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a yeast proteome microarray and screened for their ability to interact with proteins and phospholipids. Global analysis of protein activities using proteome chips. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M., Science 293 (5537): 2101- 2105., Sept. 14, 2001 Epub 2001 Jul 26

Google = about 172 July 10, 2002; about 150 Sept. 16, 2003; about 555 Feb. 28,2005

proteome microarrays: See proteome chip

Google = about 11 July 10, 2002; about 40  Sept. 16, 2003

Broader terms: protein arrays, protein chips, protein microarrays; Narrower term: whole proteome 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." http://www.yale.edu/opa/v29.n26/story15.html [Yale scientists create RNA biochip" Yale Bulletin and Calendar 29 (26) April 13, 2001]

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 glossary 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 glossary

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 glossary 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

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.

Related term:  Cell biology glossary  flow cytometry

tissue array analysis: The simultaneous analysis of multiple samples of TISSUES or CELLS from BIOPSY or in vitro culture that have been arranged in an array format on slides or microchips. MeSH 2005

Tissue Array Research Program, National Cancer Institute http://ccr.cancer.gov/tech_initiatives/tarp/ 

tissue chips: See also tissue microarrays 

Google = "tissue arrays" about 1040 July 10, 2002 "tissue chips" about 77
Sept. 16, 2003 about  3,170                                                     about 213

tissue microarrays: Topics to be addressed will include: Collection, Handling, Laser Capture Microdissection, Sample Extraction, Amplification, FFPE Tissues, Application of Tissue Arrays, Validation of New Genes, Identification of Prognostic Markers, Quality Control Microarrays in Medicine: Optimizing Diagnostics and Therapeutics, May 19-20 2008, Boston MA

Tissue microarrays are produced by a method of re-locating tissue from conventional histologic paraffin blocks such that tissue from multiple patients or blocks can be seen on the same slide. This is done by using a needle to biopsy a standard histologic sections and placing the core into an array on a recipient paraffin block. This technique, originally described by in 1987 by Wan, Fortuna and Furmanski in Journal of Immunological Methods. They published a modification of Battifora's "sausage" block technique whereby tissue cores were placed in specific spatially fixed positions in a block. The technique was popularized by Kononen and colleagues in the laboratory of Ollie Kallioneimi after a publication in Nature Medicine in 1998. This technology should not be confused with DNA microarrays where each tiny spot represents a unique cloned cDNA or oligonucleotide. In tissue microarrays, the spots are larger and contain small histologic sections from unique tissues or tumors. What are tissue microarrays?, Tissue Microarray Facility, Yale University School of Medicine, US http://tissuearray.org/yale/tisarray.html 

Tissue Microarray Project, National Human Genome Research Institute, US http://research.nhgri.nih.gov/tma/about.shtml

Google = about 1071 July 10, 2002; about  5,360 Sept. 16, 2003

Related term  lymphochip

tox-chips: Pharmacogenomics glossary

transcript arrays: Uses patterns to interrogate gene function

Google = about 32 July 10, 2002; about 56  Sept. 16, 2003

transfected cell microarrays See under Microarrays glossary: reverse transfection

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.0000003Viral 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

whole genome oligonucleotide arrays: 

Google = about 60 Jan. 24, 2003; about  144 Sept. 16, 2003

whole proteome microarrays: 

Google = about 2 Aug. 9, 2002; about  5 Sept. 16, 2003

Related term: proteome chip

Bibliography
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

Alpha glossary index

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.

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