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Industry leaders agree that multiplex array technologies are a key to realizing the therapeutic potential of genomic data; however, when microarrays will deliver on this potential and which companies will lead remain to be determined. The microarray industry is advancing rapidly but still faces technical and cost challenges.  Microarrays: Increasing the Capacity of Genomic Analysis, CHI Report, April 2001.  

There is still a great deal of volatility in the area of microarray terminology. See FAQ question # 2 for a methodology for investigating and quantitating use of various terms.  Note that definitions for arrays - chips-  microarrays vary widely in the literature and are far from standard yet.

Related glossaries are Applications Pharmacogenomics, Informatics Algorithms & data management Bioinformatics Technologies Assays Labels, Signaling & Detection Gene Amplification & PCR; Miniaturization  Biology Expression, Genetic variations  Additional Microarray definitions in the In-depth glossary.

AIMS Analysis Information Management System: Given the range and complexity of data derived from microarrays, the demand for tools not just to analyze those data but also to manage these types of projects will increase ... AIMS, similar to the popular LIMS) is the ideal tool to meet the needs of this array-intense phase of genomics research. The fundamental difference between a LIMS and an AIMS is that the former tracks physical processes, while the later tracks computational ones. AIMS are not yet commercially available, but they can be created. [CHI Bioinformatics] Related term analysis - microarray data; cluster analysis, image analysis - microarrays, pattern recognition.

analysis - microarray data: See data analysis - microarrays.

array technology:  See microarray.  “Array technology” in a broader context may refer to computer science, engineering and/ or telecommunications. Array technologies include In-depth 2D gel electrophoresis, CCDs Charged Coupled Devices, CCD cameras, detection technologies, fiber optics. imaging, ink jetting, mass spectrometry, photolithography, phosphorimagers, piezoelectric, semiconductors, spotting robots.

arrays: Narrower terms include bead based arrays, bioarrays, bioelectronic arrays, cDNA arrays, cell arrays, DNA arrays, exon arrays, filter arrays, gene arrays, gene expression arrays, genome arrays,  high density oligonucleotide arrays, hybridization arrays, macroarrays, microelectronic arrays, multiplex DNA hybridization arrays, oligonucleotide arrays, oligosaccharide arrays, protein arrays, small molecule microarrays, spotted arrays, suspension arrays, tiling arrays, tissue arrays, transcript arrays. Related terms include 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. [CHI SNP Update]

Also known as 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. [CHI Microarrays]  Related term fiber optics.

biochip(s): An integrated circuit whose electrical and logical functions are performed by protein molecules appropriately manipulated. [IUPAC Biotech]

bioelectronic arrays: See microelectronic arrays.

blotting: A technique used for transferring DNA, RNA, or protein from gels to a suitable binding matrix, such as nitrocellulose or nylon paper, while maintaining the same physical separation. [IUPAC Biotech] 

Narrower terms Northern blotting, Southern blotting, Western blotting.

 "Southerns, Northerns, Westerns, & Cloning: "Molecular Searching" Techniques" MIT's Biology Hypertextbook http://esg-www.mit.edu:8001/esgbio/rdna/rdna.html

cDNA arrays: cDNA clone inserts are robotically printed onto a glass slide and subsequently hybridized to two differentially fluorescently labeled probes. The probes are pools of  cDNAs, which are generated after isolating mRNA from cells or tissues in two states that one wishes to compare. [NHGRI, Microarray Project]   http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/aboutmicro.html  See also the Schena definition under microarrays. Related terms arrayed library, DNA chips, macroarrays

cell arrays, cell microarrays: Cell assays performed on a microarray.  Related term tissue array.  

chemical microarrays: Molecular diversity immobilized on a chip surface is a highly efficient tool for the study of precious biological samples. Graffinity´s chemical microarrays present molecular diversity of small organic molecules. A chemical shuttle process provides for the creation of "arrayable" compounds: every compound synthesized at Graffinity is born with a reactive spacer moiety ("ChemTag") that releases the compounds after solid- phase assembly and subsequently recaptures the molecules in the microarray format. This process generates soluble intermediates of
chemtagged molecules for full quality control by state- of- the- art LC/MS and mass production of microarray copies. [Graffinity website, ChemTag ^R  Array Process", 2001] http://www.graffinity.com/techno/chemtag.html

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] Narrower terms include GeneChip^R , genome chip, LabChip^R, lab- on- a- chip, oligonucleotide chips,  protein chips In-depth biochips, CellChip^TM System, cell chips,  microchips, microfluidics- based chips, SNP chips, tissue chips, glycochips, lymphochip, pump chips. See also arrays, microarrays.

clones: Cell biology glossary Related term arrayed library.

cluster analysis: Algorithms & data management glossary  Narrower term k- means clustering.

DNA chips, DNA arrays, DNA microarrays: 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] Related term hybridization arrays

data analysis - microarrays: Statistical analysis of gene expression data is at an even earlier stage of development [than cluster analysis]. These tests seek to establish some reliability or confidence measure for the changes seen on arrays. While these tests generally do not determine whether the changes are statistically significant, they are especially needed for ranking or prioritizing genes whose expression levels need to be confirmed by post hoc testing [CHI Microarrays]

A new generation of "high- dimensional" data- analysis (data- mining) tools are now entering the microarray marketplace. These types of tools were developed to address data reduction in situations where the data have multiple dimensions (as in predicting the movement of stock prices) and are now being adapted for microarray work.  [CHI Bioinformatics]

Over 80 percent of laboratories using microarrays expect to increase their utilization over the next year. However, with the "boom" of the technology also comes the need for careful navigation through interpretation of the data minefield. The facilitation of adoption of standards for microarray experimental annotation, data representation, and the introduction of standard experimental controls and data normalization is critical Microarray Data Analysis: Using Statistics and Standards to Navigate the Microarray Data Minefield Nov. 12-14, 2001, Alexandria, VA

Microarray Data Analysis report, Nov. 2001 Focuses on the data researchers get from these powerful instruments and the challenge of designing experiments that yield statistically defensible results. Will describe available commercial and academic software, as well as techniques that are still in research.  Topics include normalization, filtering, clustering, and other pattern discovery methods, biological interpretation of patterns, statistical issues pertaining to data analysis and experimental design, custom chip design (including the use of genomic sequence data to design custom oligo chips), and image analysis and will discuss databases for storing microarray results and efforts to devise standards for microarray data and databases. 

Related terms image analysis - microarrays; standards; cluster analysis, pattern recognition Algorithms & data management glossary

data mining tools: See under data analysis - microarrays.

dendrimer: Miniaturization glossary

density of microarrays: High- density arrays contain many tens of thousands of genes per chip, whereas medium- and low- density contain on the order of between a few thousand and a handful of genes per chip. [Todd R. Nelson "Chip Chip Array: An analysis of  DNA Chip Technology" Dain Rauscher Wessels, Dec. 2000] http://www.tamirfishman.com/download/NELSON_DNA_Technology.pdf

NCGR’s GeneX project was designed to support as many technologies as possible including "high- density silicon chip- based arrays (i.e., from Affymetrix and HySeq), medium- density glass slide- spotted arrays, medium to low-density nylon spotted arrays, Serial Analysis of Gene Expression (SAGE), Amplified Fragment Length Polymorphisms (AFLP), Differential Display, and even Northerns [blots].  http://www.ncgr.org/research/genex/whitepaper.html   

The entire yeast genome (6,000+ genes) has been put on a chip. Narrower terms high density oligonucleotide arrays, macroarrays, ultra high density. See also Expression glossary. 

detection technologies: Assays, labels, signaling & detection glossary

GEML Gene Expression Markup Language: Expression glossary

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] 

gene expression arrays: Expression glossary

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. Related terms In-depth genome chip, genomic arrays, genomic microarrays.

high density oligonucleotide arrays: In this array format, probes are constructed directly on the surface of a slide through photolithography. These chips provide the largest number of probes per array of any array format. Affymetrix’s GeneChips of this type. [CHI Microarrays] Broader terms oligonucleotide arrays, chips, 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. [CHI Microarrays] Also called hybridization array assays

image analysis - microarrays: Involves gridding (in which a rectangular grid is laid on top of the image), segmentation (used to determine where the spots lie within the grid), and intensity extraction (a means of evaluating each spot). The key informatics goal at this step is to record the results of the analysis. Image- analysis software for gene expression studies is often bundled with the imaging instruments and other products.  [CHI Bioinformatics]

Although the visual image of a microarray panel is alluring, its information content, per se, is minimal without significant image processing. To mine its lode effectively, quantitative signal must be determined optimally, which means subtracting background, calculating confidence intervals - outside of which a difference in signal ratio is deemed to be significant - and calibrated. [Editorial “Getting hip to the chip” Nature Genetics 18(3): 195- 197 March 1998]

Analysis, Microarrays, Image Link
Image analysis, Microarray Project (uAP), NHGRI, US  http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/img_analysis.html

in situ array: Oligonucleotides are constructed on the matrix.  From the Latin "in situ" in place. Related term Gene Chip^R

LabChip^R is a Caliper product.

lab-on-a-chip(s): Microfabricated fluidic system for performing biochemical assays. [Gene Cards, Weizmann Institute, Israel] Related term microfluidics based chips. http://bioinformatics.weizmann.ac.il/cards-bin/dicdisp?biochip 

Miniaturized platform technologies are no longer new concepts. Now is the time for proof of the principle for specific applications. Lab- on- a- Chip & Microarrays for Post Genomic Applications Jan. 14-16 2002  Zurich, Switzerland  

Related terms biochip, LabChip^R, protein chip, In-depth microelectronic arrays, microfluidics based chips, pump chip, tissue chip See also chips.

low-density arrays: See under density of microarrays. Related term: 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. [CHI Microarray]

Tool for studying how large numbers of genes interact with each other and how a cell’s regulatory networks control vast batteries of genes simultaneously. Uses a robot to precisely apply tiny droplets containing functional DNA to glass slides. Researchers then attach fluorescent labels to DNA from the cell they are studying. The labeled probes are allowed to bind to cDNA strands on the slides. The slides are put into a scanning microscope to measure … how much of a specific DNA fragment is present. [NHGRI ] http://www.nhgri.nih.gov/DIR/VIP/Glossary/pub_glossary.cgi

I will keep this term for DNA arrays [regardless of the support] in which the spacing between spots is less than 500 um. This translates into densities of at least 400 genes per cm². [S Granjeaud "Expression profiling: DNA arrays in many guises" BioEssays 21: 781-790 Sept. 1999]

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]

This technology finds itself center stage thanks to the successful decoding of the human genome. Regardless of its enormous potential, only recently has the number of application papers surpassed that of review articles. In other words, we have a technology that works well despite, rather than because of, our understanding of the subject. Once again this Boston conference will highlight the best advances in the hardware production and manufacturing of these machines, but we will also examine critical questions to the application of these tools, to their data analysis, and to the tacit assumptions researchers have made in the larger biological picture- sometimes without enough skepticism or innovation. Microarrays Through Macroresults: Advancing Drug Development April 29- May 1, 2002 Boston, MA   

Narrower terms genomic microarrays, oligonucleotide arrays, protein microarrays, In-depth antibody microarrays, BAC microarrays, cell microarrays, DNA microarrays, gene microarrays,  gridded cDNA microarrays,  small molecule microarrays, tissue microarrays. Related terms include data analysis - microarrays, density of microarrays, probes - microarrays. See also arrays, chips.

AMAD Another MicroArray Database, Joe DeRisi's Lab, Biochemistry & Biophysics, Univ. of California- San Francisco, US   http://www.microarrays.org/   Public source for software, technology and protocols.

DNA Microarray (Genome Chip), Leming Shi http://www.gene-chips.com/

GRID IT Resources for Microarray Research, Virginia Tech/NC State Univ., US http://www.bsi.vt.edu/ralscher/gridit/

MGuide, [Pat] Brown Lab’s Guide to Microarraying, Stanford Univ., US http://cmgm.stanford.edu/pbrown/mguide/

Microarray Project (uAP), NHGRI, US  http://www.nhgri.nih.gov/DIR/LCG/15K/HTML/  Collaborative research effort among various NIH institutes and divisions.

Microarray related activities at the EBI, European Bioinformatics Institute, UK http://www.ebi.ac.uk/microarray/

Stanford MicroArray Database (SMD), Stanford Univ., US  http://genome-www4.stanford.edu/MicroArray/SMD/   Stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.

microarray data analysis: See data analysis - microarrays.

microarray- regulation: The FDA is trying to re-define regulatory procedures that are appropriate for technologies that take an entirely different approach to diagnostics and treatment, including microarrays, genotyping and pharmacogenomics. [Joseph Hackett, FDA, Center for Devices and Radiological Health How the Genomics Revolution Affects FDA Regulation [http://www.chiresource.com/newsarticles/issue5-1.ASP ]

microarray technologies: See array technologies.

microchip: Miniaturization glossary

microelectronic arrays (or microelectronic chips): 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. [CHI Microarrays] See also under multiplex DNA hybridization arrays

micron: One one thousandth of a millimeter; 10,000 angstroms. [NIGMS] Represented by u.

microwell chips: Narrower term nanowells

molecular bioprocessing: We are combining the fields of biocatalysis, bioinformatics, metabolic engineering, and high- throughput combinatorial biosynthesis with microsystems engineering to form a new area of fundamental and applied research. This new area, called "molecular bioprocessing" enables us to join the technologies of combinatorial biosynthesis with high- throughput biocatalytic technologies, which allows access to nature's "warehouse" of structures and functions, and to be able to manipulate the synthesis of these molecules to yield novel compounds and materials for use in the pharmaceutical, chemical, and agrochemical industries. One aspect of molecular bioprocessing is the in vitro fabrication and manipulation of single- and multi-enzyme systems on a biochip; the logical extension being metabolic pathway engineering on the microscale. [Jonathan S. Dordick,  Rensselaer Polytechnic Institute, "Metabolic engineering on a chip" CHI's Functional Genomics conference, Oct. 9- 10 2001]  http://www.functionalgenomics2001.com/fgen.htm

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. [CHI Microarrays]

nanoarray: 

nanochip: Miniaturization glossary

nanowell: Aurora has developed a manufacturing system for disposable NanoWell Assay Plates. A key feature is the small assay volume, approximately 100 times smaller than most conventional screening assays. This volume reduction is critical for reducing the cost per test and conserving compound libraries that often consist of only very small amounts of each test compound.... While current screening systems can dispense volumes down to about one microliter (one millionth of a liter), Aurora has developed miniaturized screening dispensers capable of dispensing volumes less than one billionth of a liter. [Vertex Aurora Biosciences Corp, "Aurora Platforms: UTHSS Ultra High Throughput Screening Systems, 2001] http://www.aurorabio.com/discovery/automation/uhtss.html

normalization: Algorithms & data management glossary

oligonucleotide: Biomolecules glossary

oligonucleotide array sequence analysis: 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 in a gene sequence or expression or for gene mapping. [MeSH] Useful to know this MeSH heading for microarrays, but use free- text as well to search PubMed.

oligonucleotide arrays, chips, microarrays, microchips: 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 ‘oligonucleotide array sequence analysis’]

pattern recognition: Algorithms & data management glossary

probes - microarray: In this paper "probe" refers to the (labeled) material that is hybridised with the array of cDNA inserts or oligonucleotides ("targets"). The oligonucleotide chip community tends to use the reverse terminology. [S Granjeaud "Expression profiling: DNA arrays in many guises" BioEssays 21: 781-790, Sept. 1999]  Has this changed?  

Can be made from clones, PCR amplicons or oligonucleotides. See also probes Gene amplification & PCR

protein arrays: Microarrays have revolutionized genomic studies. Protein arrays have the same potential to impact proteomics. Protein arrays can be used to screen for interaction of proteins with other proteins, DNA, antibodies, cells, or small molecules. The two major formats designed to serve rather different applications present different technical challenges and opportunities. Immobilization of numerous proteins requires efficient protein expression and strategies that retain activity. Determination and quantification of protein expression levels require arrays designed to selectively capture proteins in solution. Numerous technical obstacles, such as optimizing protein immobilization or selection of protein- binding ligands, strategies for extending the limits of detection, and novel applications of this exciting technology, are among the issues that will be discussed in detail. Protein Arrays: Technology and Applications January 7-8, 2002 San Diego CA  Protein and peptide arrays: Proteins to profits Mar. 25-27, 2001 Munich, Germany

These arrays can consist of proteins themselves (e.g., for studies of protein/ protein interactions or protein/ small- molecule binding) or of probes for capturing proteins (so that protein levels in a sample can be gauged). [CHI Microarrays] 

The goal of developers of  protein arrays is to allow thousands of proteins to be studied en masse, the way gene expression is currently studied. These arrays could be used to study protein expression, protein- protein interactions, and the interactions between arrayed proteins and potential drugs. Specifically, arrays of a series of protein targets could be used to identify binding of particular proteins or small molecules (e.g., potential therapeutics) to these targets. Or multiple compounds could be screened for activity, in a parallel fashion, against a single protein target deposited at multiple locations on an array. In drug- screening applications, protein arrays could help researchers determine which compounds react with target proteins and which react with non- target proteins, potentially causing side effects. [CHI Target Validation]

Related terms protein chips, protein microarrays. Narrower term proteome chip.

protein chips: With more than a dozen companies poised to enter the market, sales of protein chips are likely to balloon from $45 million in 2000 to almost $500 million in 2006 ... In a new report, BioInsights has identified and analyzed 20 companies that are likely to join current protein chip makers Biacore and Ciphergen in their attempt to meet the strong demand for high- throughput analysis of proteins. [BioInsights, Protein Chips: The Race for High-Throughput Protein Analysis, Dec. 2000] http://www.chireports.com/pressrelease/prochips.asp

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. [CHI Summit Proteomics]

Ciphergen has trademarked ProteinChip™. 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. Related terms protein arrays, protein microarrays; Narrower term proteome chip

protein microarrays. 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). [CHI Summit Proteomics]

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. 

Related terms protein arrays, protein chips; Narrower term proteome chip.

proteome chip: Michael Snyder (Yale Univ.) and colleagues cloned 5800 ORFs from yeast and printed the overexpressed purified proteins onto microarrays to investigate protein- protein interactions. A number of potential applications for proteome chips can be envisioned.  [Zhu H. et. al, "Global analysis of protein activities using proteome chips" Science July 26, 2001 epub ] Broader terms protein arrays, protein chips, protein microarrays.

RNA biochip: 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] Related term Pharmaceutical biology glossary allosteric ribozymes

reverse transfection: A microarray- based system for the functional analysis in mammalian cells of many genes in parallel. Mammalian cells are cultured on a glass slide printed in defined locations with solutions containing different DNAs. Cells growing on the printed areas take up the DNA, creating spots of localized transfection within a lawn of non-transfected cells. We call this approach 'reverse transfection' and we have developed two methods to reverse transfect cells....  By printing sets of complementary DNAs (cDNAs) cloned in expression vectors, we can make microarrays whose features are groups of live cells that express a defined cDNA at each location. These 'transfected cell microarrays' should be of broad utility for the high- throughput expression cloning of genes, particularly in areas such as signal transduction and drug discovery. For many applications these arrays can serve as substitutes for protein microarrays, particularly for proteins that are difficult to purify, such as membrane proteins  [David Sabatini "Reverse transfection" Whitehead Institute, MIT, US]  http://staffa.wi.mit.edu/sabatini_public/reverse_transfection/frame.htm

scanning technologies: See In-depth fluorescent scanners, laser scanning phosphorimagers Related term image analysis - microarrays See also Imaging glossary, Mass Spectrometry

semiconductor: Miniaturization glossary

spotted arrays: See cDNA arrays.

standards: See GEML In-depth glossary ArrayExpress, MAML, MGED, MIAMI; Expression glossary  

Stokes shift: The difference (usually in frequency units) between the spectral positions of the band maxima (or the band origin) of the absorption and luminescence arising from the same electronic transition. Generally, the luminescence occurring at a longer wavelength than the absorption is stronger than the opposite. The latter may be called an anti- Stokes shift.  [IUPAC Photo] Related terms In-depth microspotting, spotted arrays, spotting robots.

target (hybridization): Gene amplification & PCR

ultra dense oligonucleotide arrays: 

ultra high density microarrays Contain hundred to thousands to millions of features. Able to run many types of assays, not just DNA hybridization. [CHI Microarrays] Related term bead based arrays. Broader term density of microarrays, high density oligonucleotide arrays

Bibliography

Nature Genetics, “Chipping Forecast” supplement 21 (1s), Jan 1999 http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v21/n1s/index.html

[CHI Microarrays]: Increasing the Capacity of Genomic Analysis, April 2001. http://www.chireports.com/content/reports/chips.asp

Alpha glossary index

I have tried to determine the status of all words known to be, or are suspected of being, proprietary names or trademarks and to include this information. No judgment concerning the legal status of such words is claimed.

In-depth microarrays glossary

2D electrophoresis: Chromatography & electrophoresis glossary

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

ArrayExpress: The EBI has discussed the possibility of establishing a public repository for DNA microarray based gene expression data with many of the major laboratories developing and using these technologies in Europe and the USA. Following these discussions, the European Bioinformatics Institute is committed to establishing a public repository for microarray based gene expression data, named ArrayExpress. Currently the EBI is establishing a pilot database containing microarray gene expression data that are available publicly. [European Bioinformatics Institute, ArrayExpress, 2001] http://www.ebi.ac.uk/arrayexpress/index.html   Related terms data analysis - microarrays; standards.

arrayed library: Individual primary recombinant clones (hosted in phage, cosmid, YAC, or other vector) that are placed in two- dimensional arrays in microtiter dishes. Each primary clone can be identified by the identity of the plate and the clone location (row and column) on that plate. Arrayed libraries of clones can be used for many applications, including screening for a specific gene or genomic region of interest … Information gathered on individual clones from various genetic linkage and physical map analyses is entered into a relational database and used to construct physical and genetic linkage maps  simultaneously; clone identifiers serve to interrelate the multilevel maps. [DOE] 

Broader terms library, genomic library. (Cell biology glossary)

BAC microarrays: Mapped DNA fragments are arrayed onto a glass surface and covalently coupled using proprietary chemical processes   Have potential for using for high- resolution, high- throughput, genomic profiling.  [Dr. Shirshir Shah CHI's Application of Genomics to Animal Models, Oct. 11-12, 2001 Cambridge MA http://www.functionalgenomics2001.com/amodels.htm

bioarrays: Gene expression arrays, also known as bioarrays. ["Motorola first to license Incyte's gene patent portfolio... for bioarray commercialization" Incyte press release Aug. 17, 2000] http://www.incyte.com/company/news/2000/08_bioarray_commercialization.shtml

CCD Charged Coupled Device: Imaging glossary  

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]  http://www.ncrr.nih.gov/newspub/genomic.pdf 

CellChip™ 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

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.

fiber optics: Imaging glossary

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]

fluorescence scanners: A fluorescence- based detection method used with microarrays, high- density oligonucleotide arrays, and microelectronic chips. Fluorescence is generally detected with a confocal scanning microscope. [CHI Microarray] See also Imaging glossary

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” 1998-2000] http://www.gene-chips.com/  Related terms 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  Related terms genome arrays, genome chip, genomic microarrays.

genomic microarrays: Genomic microarray technology allows assessment of multiple gene targets for  identification of gene amplifications or deletions in a variety of different sample types. [Vysis Products]  http://www.vysis.com/products_sect.asp?ProductLineID=14  Related terms genome arrays, genome chip, genomic arrays. Narrower term Genosensor^TM  system

Genosensor ™ System: Utilizing Vysis’ patented comparative genomic hybridization (CGH) technology to simultaneously survey multiple gene targets, the GenoSensor System is able to screen multiple gene targets in a single test. [Vysis Products “GenoSensor System]  http://www.vysis.com/products_sect.asp?ProductLineID=14

glycochips, oligosaccharide arrays: Still at a fairly preliminary research stage for now.

gridded cDNA microarrays: See cDNA arrays.

ink jetting technologies: The most advanced of these [‘drop- on- demand’ delivery] approaches are adaptations of the ink- jetting technologies, which utilize piezoelectric and other forms of propulsion to transfer biochemical substances from miniature nozzles to solid surfaces. .. [these] allow high- density gridding of virtually any biomolecule of interest, including cDNAs, genomic DNAs, antibodies and small molecules … not currently as robust as photolithography or microspotting, this approach has been used to prepare microarrays of single cDNAs at a density of 10,000 spots cm-2. Because ink jetting does not require direct surface contact, piezoelectric delivery is theoretically amenable to very high throughput.  [Mark Schena et al “Microarrays: biotechnology’s discovery platform for functional genomics” Trends in Biotechnology 16(7):301-306 July 1998]  

laser: Imaging glossary Related terms CCD, image analysis, scanning technology.

laser scanning:  Imaging glossary

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

MAML Microarray Markup Language: A data format for describing information about DNA- array based experiments. MAML is based on the Extensible Markup Language (XML). MAML provides a framework for describing experiments done on all types of DNA-arrays, including spotted and synthesized arrays, and oligo- nucleotide and cDNA arrays. It is independent of the particular image analysis and data normalization methods, and allows representation of both raw and processed microarray data. Over and above the representation of expression measurements, it allows for comprehensive annotation of experimental results. The format is compatible with the definition of the minimum information about a microarray experiment (MIAME), but does not impose its requirements. [MAML specification primer Draft Jan. 19, 2001] Broader term standards Related terms data analysis - microarray, MGED, MIAME http://www.ncbi.nlm.nih.gov/geo/maml/

MGED Microarray Gene Expression Database group: An open discussion group initially established at the Microarray Gene Expression Database meeting MGED 1 (November, 1999, Cambridge, UK). The goal of the group is 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. The underlying goal is to facilitate the establishing of gene expression data repositories, comparability of gene expression data from different sources and interoperability of different gene expression databases and data analysis software.  http://www.mged.org/ Broader term standards Related terms data analysis - microarray, MAML, MIAME.

MIAME Minimum Information About a Microarray Experiment: The goal of the MIAME is to specify the minimum information that must be reported about a microarray (or any DNA array) based gene expression monitoring experiment in order to ensure the interpretability, as well as potential verification of the results by third parties. The background aim is to facilitate the establishing public repositories and data exchange format for microarray based gene expression data. The MGED group will be encouraging the scientific journals and funding agencies to adopt policies requiring data submissions to repositories, once MIAME compliant repositories are established.  The definition of the minimum information is aimed at co- operative data providers, and not for closing possible loopholes in not providing the information. [Annotations Working Group, MGED] http://www.mged.org/Annotations-wg/index.html Broader term standards, Related terms data analysis - microarray, MAML, MGED.

macroarrays: Arrays on which gene-specific probes are robotically spotted onto a nitrocellulose or nylon membrane substrate. The term macroarray refers to the typically lower probe density for these arrays as opposed to microarrays. Generally, macroarrays are the simplest array format and use radioisotopic methods for detection. Note that definitions for arrays vary widely in the literature. [CHI Microarrays] Narrower term nylon macroarrays.

mask: Device which acts as a barrier to the passage of a reagent (often light - see photolithography). A pattern of holes in the mask allows selective passage of reagent and results in a corresponding pattern of reagent deposition or photodeprotection on a surface placed behind the mask. This allows the generation of spatially addressable libraries. [IUPAC Combinatorial Chemistry]

mass spectrometry: This technique can be used to both measure and analyze the molecules contained in microarray spots. It involves introducing enough energy into a target molecule to cause its ionization and disintegration. The resulting fragments are then analyzed, based on the mass/ charge ratio to produce a "molecular fingerprint. [CHI Microarrays] Mass spectrometry glossary

matrix: 1) From the Latin word for womb (in turn from mater or mother), a matrix is either the intercellular substance of a tissue, the material in which a fossil is embedded, or a mold from which a relief surface is made in printing or phonograph manufacturing. 2) In mathematics and computer science, a matrix is a set of numbers laid out in tabular form (in rows and columns). From this meaning, a less formal meaning is derived of a complex of lines intersecting at right angles. [whatis.com] Related term substrates.

microchips: Implantable chips for gene delivery [CHI Microarrays]

microfluidic devices: Miniaturization glossary

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. [CHI Microarray]

microspheres: Microspheres are generally defined as small spheres made of any material and sized from about 0.5 µm to 100 µm. Similar, but smaller spheres sized 10 to 500 nm are called nanospheres. Ideally, microspheres are completely spherical and homogeneous in size, although less perfect particles are often termed microspheres as well. Depending on the preparation method and material used, microspheres show a typical size distribution which often deviates from the mono- sized ideal. [Urs Häfeli "Radioactive Microspheres for Medical Applications" High Care Bochum Germany Feb. 25-27, 2000]  http://www.highcare.de/abstracts/HTML0051.htm

microspotting: An original version of mechanical microspotting was developed by [Dari] Shalon and [Pat] Brown [at Stanford] and later commercialized at Synteni [now Incyte Genomics] …a miniaturized version of earlier DNA spotting techniques, encompasses a family of related deposition technologies that enable automated microarray production by printing small quantities of premade biochemical substances onto solid surfaces. Printing is accomplished by direct surface contact between the printing substrate and a delivery mechanism that contains an array of tweezers, pins or capillaries that serve to transfer the biochemical samples to the surface. [M Schena et al “Microarrays: biotechnology’s discovery platform for functional genomics” Trends in Biotechnology 16(7):301-306 July 1998] Related terms Stokes shift; In-depth spotted arrays, spotting robots.

Northern blotting: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane. [MeSH]

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

peptide arrays:  Steve Fodor and colleagues at Affymax published several articles on these in the early 1990s. Related terms protein arrays, protein chips, protein microarrays

phenotype microarray: Designed to study a range of cell properties (phenotypes) as a means of understanding how a gene or a drug affects living cells - a critical step in identifying potential new drug targets and in developing safe and effective new drugs. Biolog's proprietary PM [phenotype microarray] technology provides researchers with powerful, efficient and cost- effective information for determining gene function by directly measuring the consequence of a genetic change on cellular phenotypes. This technology allows researchers to test hundreds to thousands of cell properties simultaneously, and also has applications in validating and optimizing drug targets, determining a drug's mode of action, assessing toxicology, and basic cellular research. The patented method involves the use of PMs to conduct a very detailed comparison of two cell lines, one of which has been modified by a gene mutation or tested with a drug lead. [Biolog, Inc. "Biolog expands Phenotype Microarray Assay^TM for Cell- Based Analysis, Jan. 9, 2001] http://www.biolog.com/010901-BiologExpandsPhenotypeMicroArrayAssay.htm  Broader term Genomics glossary phenotype

phosphorimagers: Instruments used to quantify the radioactive signal (an indication of the level of hybridization) produced by macroarrays. [CHI Microarrays]

photolithography: Process by which selective masking generates light patterns which direct chemical transformations to certain areas of a photosensitive surface. Coupling of different building blocks to discrete sites may give rise to spatially addressable arrays of compounds. [IUPAC Combinatorial Chemistry] 

Unlike droplet- printing technology, which allows microarrays to be created with relatively inexpensive and user- friendly equipment, photolithography requires expensive equipment and particular expertise and is also protected by patents. [CHI Microarrays]

Related term soft lithography

piezoelectric: Some crystals, especially quartz, will produce an electric charge when squeezed. This charge will typically be high voltage and low amperage. [International Tesla Society Scientific Dictionary, 1996] http://www.studytech.com/cgi-bin/cgiwrap/bware/dotesla.cgi?word=piezoelectric

pump chip: The German company GeSiM uses technology based on ink- jet printing in its piezoelectric pump devices for spotting microarrays. The dispensing head of this device can be considered a "pump chip" (micropipettor), which consists of a glass (or other) support, constructed with an orifice and an inlet hole for the fluid to be dispensed. Just in front of the orifice is a pump chamber with a piezoactuator on one side. The piezoactuator transforms an electric current into a mechanical force that drives a small drip from a fluid chamber out the orifice. The amount of electric current used controls the size of the drop. [CHI Microarrays]

SNP chips: Microarrays used for genome wide genotyping of single nucleotide polymorphisms (SNPs). Related term Genetic variations glossary SNP

semi-conductor: Miniaturization & nanoscience glossary

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

soft lithography: A new technique capable of generating and manufacturing nano- structures rapidly and economically. Inherent in its nature is the ability to produce patterned three dimensional structures on non- planar substrates in a single step. An elastomeric polydimethylsiloxane (PDMS) patterning element (mould) is first prepared by casting the liquid pre- polymer against a previously patterned master and curing. Once cured the patterned PDMS element is removed from the master ...  When a PDMS mould is brought into conformal contact with a solid substrate continuous channels are formed. Micromoulding of patterns on the substrate surface is then made possible by filling these channels with a liquid precursor blend of choice by capillary action. The precursor is then cured and the PDMS element is removed. Since PDMS is transparent to ultra violet radiation and is thermally stable to 150 degrees Celsius, liquid precursors may be easily cured in situ to yield the desired patterned structure.  To date at NMRC, this method has been used to pattern organically modified ceramic gels (ORMOCERS), liquid pre- polymers and aqueous solutions of inorganic salts. [NMRC (Ireland) Nanotechnology Research, Scientific Report 1999] http://www.nmrc.ie/reports/1999/scientific/scinano.html

Southern blotting: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane. [MeSH]

The Southern blot was the first array. [Eric Lander "Array of hope" Nature Genetics 21 (1s): 3-4 Jan 1999]

spotting robots: Most spotting robots use an X-Y-Z robot arm (one that can move in three dimensions) mounted on an antivibration table. Pins held by the arm are dipped into the first microtiter plate to pick up the fluid (probe solution) to be delivered. The tips of the pins are then moved to the array matrix and allowed to touch the surface only minimally; the probe solution is then transferred. The pins are then washed and moved to the next set of wells and probes. This process is repeated until hundreds or thousands of probes are deposited. Currently, solid pins, quills, and pin- and- ring configurations of pins are available. [CHI Microarrays]

Related terms Stokes shift; In-depth microspotting, spotted arrays.

stringency: Gene amplification & PCR glossary

substrates: In hybridization arrays, the particular materials onto which probes are deposited. Substrate materials include glass, nylon, silicon, and ceramic. Traditionally, arrays have been prepared using plastic multiwell plates. As the need for more reaction "vessels" per unit area has increased dramatically, users have turned to flatter supports such as glass slides, which provide greater surface areas. [CHI Microarrays]  Different from substrate Pharmaceutical biology glossary  Related term matrix

suspension arrays: Luminex has demonstrated a DNA- based tissue typing assay that determines the haplotype of the DQA1 locus in less than 30 minutes following sample amplification. This multi- analyte DNA hybridization system analyzed 16 unique sequences with single base discrimination. Oligonucleotide probes complementary to the alleles of interest were coupled to fluorescently coded microspheres. Fluorescein- labeled probes complementary to the microsphere bound oligonucleotide sequences were used to interrogate each microsphere. The microspheres and fluorescent probes were hybridized in the presence of an amplified DNA sample and analyzed. The presence of a specific sequence in the sample was determined by competitive hybridization. This assay demonstrated the utility of the Luminex R/O system and its Suspension Arrays™ for simultaneous interrogation of multiple nucleic acid sequences. [Luminex Technical Bulletins "DNA based tissue typing" 1998] http://www.luminexcorp.com/tech/bulletins/DNA98.htm

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. Related term exon arrays.

tissue arrays,  tissue chips, tissue microarrays: A microarray that permits massive parallel processing of biological samples. But unlike the DNA chip, the tissue chip makes it possible for researchers to simultaneously compare a variety of molecular markers…  in cancer tissues from hundreds [to a thousand  patients. in a single tumor tissue microarray]. [Media release on J Kononen et al “Tissue microarrays for high-throughput molecular profiling of tumor specimens” Nature Medicine 4(7): 844-847 July 1998] http://www.nhgri.nih.gov/NEWS/Gene_Therapy.html  Related term lymphochip

transcript arrays: Uses patterns to interrogate gene function. [CHI Microarrays]

Western blotting: Identification of proteins or peptides that have been electrophoretically separated by blotting and transferred to strips of nitrocellulose paper. The blots are then detected by radiolabeled antibody probes [MeSH].