Microarray technologies have become an invaluable tool for drug discovery as well as for diagnostics. Microarrays are being used to find new drug targets as well as developing personalized medicine in a fast and affordable manner. However, many challenges of the technology remain --  quality control, expression arrays and pharmacokinetics will be addressed as well as new developments in the field, such as microRNA arrays and DNA methylation. Microarrays in Medicine: Optimizing Diagnostics and Therapeutics, May 19-20 2008, Boston MA

There is still a great deal of volatility in the area of microarray terminology. See FAQ question # 3 for a methodology for investigating and quantitating use of various terms.  Note that names and definitions for arrays - chips- and/or  microarrays vary widely in the literature and are far from standard yet.

Technologies map   Finding guide to terms in these glossaries   Site Map
Sub-categories are Microarrays categories Other related glossaries include 
Applications  Molecular Medicine  Drug discovery & development  Pharmacogenomics
Informatics Algorithms, Bioinformatics  
Technologies Labels, Signaling & Detection, Gene Amplification & PCR; Nanoscience & Miniaturization
Biology Expression, SNPs & genetic variations 

analyte specific reagents: Drug approvals glossary

antibody microarrays: Microarrays categories Related terms: protein arrays

applications - microarrays: See Expression glossary gene expression analysis  disease classification; Sequencing glossary genotyping, diagnosis, drug efficacy and toxicity,  sequencing - mutation detection.

array technology:  See microarray.  “Array technology” in a broader context may refer to computer science, engineering and/ or telecommunications. 

Array technologies include 2D gel electrophoresis, CCDs Charged Coupled Devices, CCD cameras, detection technologies, fiber optics. imaging, ink jetting, mass spectrometry, photolithography, phosphorimagers, piezoelectric, semiconductors, spotting robots.

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: Cell biology glossary library, genomic library; Drug discovery & development glossary

arrays: Microarrays categories Narrower terms include bead arrays, bead based arrays, bioarrays, bioelectronic arrays, cDNA arrays, cell arrays, DNA arrays, encoded bead arrays, gel pad arrays, gene arrays, gene expression arrays, genome arrays, genomic arrays,  high density oligonucleotide arrays, high density protein arrays, hybridization arrays, in situ arrays, low density arrays,  microelectronic arrays, multiplex DNA hybridization arrays,  nanoarrays, nylon macroarrays, oligo arrays, oligonucleotide arrays, oligosaccharide arrays, peptide 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; Expression glossary gene expression arrays;   Related terms include arrayed library.  See also chips, microarrays.

BAC microarrays,  bead arrays, bead based arrays, bioarrays: Microarrays categories 

bioassays: Assays & screening glossary See second definition 

biochip(s): Microarrays categories 

bioelectronic arrays: See Microarrays categories under  microelectronic arrays

biofabrication: Biomaterials & bioengineering glossary

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.

cDNA arrays: Microarrays categories 

CCD Charged Coupled Device: Molecular Imaging glossary

cell arrays, cell microarrays; cell chips,  CellChip™ System; chemical microarrays: Microarrays categories 

chips: Microarrays categories 

classification- microarrays: Algorithms glossary

clones: Cell biology glossary Related term: arrayed library.

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

competitive hybridization: Gene Amplification & PCR

concordance: Similarity of results between different microarray platforms.

Related terms: discordance, mismatches

cross hybridization: One of the challenges in measuring mRNA levels on microarrays is that genes can cross- hybridize, depending on whether the probes target unique or common regions. [George Church Lab, "S. cerevisiae cross- hybridization and unique regions", Harvard Medical School, 1999]  http://arep.med.harvard.edu/labgc/adnan/projects/YeastCrossHyb/

Incorrect hybridization that occurs in microarray experiments by virtue of the fact that the number of incorrect molecules in a target is so much greater than the number of correct ones. This phenomenon adds a small amount of noise to every measurement. Cross-hybridization is more of a problem with cDNA arrays than with oligonucleotide arrays.

Related terms: Gene Amplification & PCR

DNA arrays, DNA chips, DNA microarrays, DNA microchips: Microarrays categories 
DNA microarray: Wikipedia http://en.wikipedia.org/wiki/DNA_microarray 

data analysis - microarrays: Microarrays have revolutionized molecular biology. The numbers of applications for microarrays are growing as quickly as their probe density. Paradoxically, microarray data still contains a large number of variables and a small number of replicates creating unique data analysis sets. Still, the first and most important goal is to design microarray experiments that yield statistically defensible results..  Microarray Data Analysis and Interpretation, Aug. 16-17, 2007, Washington DC

It is obvious to reviewers of submitted manuscripts that many researchers have used microarrays to perform experiments that provide no biological insight whatsoever. That's not due to any failure on the part of the technology, but rather on the failure to design experiments or appreciate the limitations of microarray technology. The use of microarrays will not turn a poorly conceived or poorly executed experiment into a groundbreaking scientific achievement, any more than buying a sports car will turn one into a NASCAR driver. Catherine Ball, Director Stanford Microarray Database as part of a panel on Has the Promise of Microarrays been oversold? Science Functional Genomics weblog http://sciencemag.blogs.com/sfgblog/roundtable/ 

Terry Speed's Microarray Data Analysis Group Page, UC- Berkeley, US http://www.stat.Berkeley.EDU/users/terry/zarray/Html/index.html

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

data mining tools: See under data analysis - microarrays.

dendrimer: Nanoscience & Miniaturization glossary

density of microarrays: Low (200-5000 genes): low-density arrays (Clontech, Research Genetics) —Medium: microarrays (14,000 cDNAs/ array; Agilent), spotted oligos (8000; Clontech)  —High (>10,000 genes): high- density oligo arrays (Affymetrix)  CHI, GenomeLink 14.1, 2001 http://www.healthtech.com/newsarticles/issue14_1.asp

The entire yeast genome (6,000+ genes) has been put on a chip. See proteome chip.

Narrower terms: high density oligonucleotide arrays, high density protein arrays, macroarrays, ultra high density. Related terms: Expression glossary

derived bioassay: See under bioassay

deprotection: During the chemical synthesis of DNA and RNA, branching is prevented by ensuring that only one chemically reactive group is present in the growing oligonucleotide and one in the nucleoside 3′-phosphoramidite. This is achieved by blocking other reactive groups within the sugars and bases (e.g. exocyclic amines) with protecting groups. The removal of the protecting groups that block exocyclic amines, commonly known as deprotection, occurs only after synthesis.  Assessing incomplete deprotection of microarray oligonucleotides in situ, Holly K. Dressman, Lise Barley-Maloney,¹ Laura-Leigh Rowlette, Paul F. Agris,^1* and Mariano A. Garcia-Blanco² Nucleic Acids Research v.34(19); Nov 2006   http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1636491 

detection technologies: Labels, signaling & detection glossary

disconcordance: Lack of standard results among microarray experiments.

Related terms: concordance, mismatches

electrospray- fabricated protein microarrays: Microarrays categories 

encoded bead arrays: See under Microarrays categories bead arrays

exon arrays: Microarrays categories 

External RNA Control Consortium ERCC: http://www.cstl.nist.gov/biotech/workshops/ERCC2003/ 

FDA draft guidelines - multiplex tests: Drug and device approvals glossary Primarily considers nucleic acid arrays, but principles apply to protein arrays and tissue arrays.

Related term: analyte specific reagent

FDA -- microarrays - regulating: The Food and Drug Administration (FDA) must balance the interests of the public for thorough review of new products for safety and efficacy, against the interests of the industry for a low cost, expedited process of regulatory approval. But all too often the process can place a significant drain on the resources of a company, particularly smaller companies that are introducing new products or innovative technology. It is actually in the interest of all parties to meet each of these requirements. Patients also have an interest in expedited review of new drugs, devices and diagnostics. Companies welcome a regulatory regime that ensures safety and thus public confidence in their products. And it is in nobody’s interest to have a company bankrupt itself just as it is trying to bring an innovative drug or technology to market. The FDA, however, is faced with extraordinary challenges, not only in terms of increased workload of conventional products, but also in 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. How the genomic revolution affects FDA Regulation,  CHI GenomeLink 5.1 http://www.healthtech.com/newsarticles/issue5-1.ASP

false negative: The chance of declaring an expression change (e.g., in gene expression) to be insignificant when in fact a change has occurred. The opposite situation is the false positive. 

false positive: The chance of declaring an expression change to be significant when in fact no change has occurred. This tends to be a more pressing concern than false negatives in microarray experiments. 

fiber optics: Imaging glossary

filter arrays:  Microarrays categories 

filtering: A process whose aim is to reduce a dataset to a more manageable size, by getting rid of genes that show no significant expression changes across the experiment or that are uninteresting for biological reasons. 

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 Microarrays report]

Related terms:  Imaging glossary

fold change: A way of describing now much larger or smaller one number is compared with another. When the first number is larger than the second, it is simply the ratio of the first to the second. When the first number is smaller than the second, it is the ratio of the second to the first with a minus sign in the front. When the numbers are equal, it is 1. For example, the fold change of 50 versus 10 is 50/10 = 5, while the fold change of 10 versus 50 is -5. 

functional protein microarrays: Microarrays categories 

gel-pad arrays: Microarrays categories 

gene arrays, gene microarrays:  Microarrays categories: See also DNA chip, DNA arrays, DNA microarrays

GeneChip ®; genome arrays: Microarrays categories 

gene expression arrays: Expression glossary

Related terms: genome chip, genomic arrays, genomic microarrays.

genome chip: Microarrays categories  Related terms genome arrays, genome chip, genomic microarrays.

genomic microarrays: Microarrays categories  Related terms genome arrays, genome chip, genomic arrays. Narrower term: Genosensor^TM  system

global normalization or mean scaling:. The standard solution for errors that effect entire arrays is to scale the data so that the average measurement is the same for each array (and each color). The scaling is accomplished by computing the average expression level for each array, calculating a scale factor equal to the desired average divided by the actual average, and multiplying every measurement from the array by that scale factor. The desired average can be arbitrary, or computed from the average of a group of arrays. 

glycochips: Microarrays categories  Related terms: Glycosciences glycoinformatics, glycobiology

gridded cDNA microarrays: See Microarrays categories: cDNA arrays.

high density oligonucleotide arrays: Microarrays categories  Broader terms: oligonucleotide arrays, oligonucleotide chips, oligonucleotide microarrays, microchips. Related term: density of microarrays

high-density protein arrays: Microarrays categories 

hybridization: Gene amplification & PCR glossary 

hybridization arrays: Microarrays categories  Also called hybridization array assays

image analysis - microarrays: 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

This process starts with the image of a microarray that is produced in the laboratory and produces intensity information indicating the amount of light emitted by each probe. In particular, after the array has been hybridized, it is scanned to obtain an image that shows the amount of light emitted across the surface of the microarray. The image is then analyzed to identify the "spots" (i.e., the parts of the image corresponding to the DNA probes on the microarray) and the amount of light that can be attributed to target molecules bound to each probe. 

Related term: normalization

in situ array:  Microarrays categories

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   

See also note under probes- microarrays

LabChip^R Microarrays categories 

lab-on-a-chip: Microarrays categories  Related terms: biochip, LabChip^R, protein chip, microelectronic arrays, microfluidics based chips, pump chip, tissue chip See also chips. 

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

learning algorithms: Algorithms glossary

lithography: Lithography Overview, Intel Research, US http://www.intel.com/research/silicon/lithography.htm

Narrower terms: photolithography, soft lithography

log ratios: DNA microarray assays typically compare two biological samples and present the results of those comparisons gene-by-gene as the logarithm base two of the ratio of the measured expression levels for the two samples. The limits of log ratios, Vasily Sharov,¹ Ka Yin Kwong,¹ Bryan Frank,¹ Emily Chen,¹ Jeremy Hasseman,¹ Renee Gaspard,¹ Yan Yu,¹ Ivana Yang,¹ and John Quackenbush BMC Biotechnology 4, 2004 doi: 10.1186/1472-6750-4-3. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=400743 

low-density arrays: Microarrays categories  See also under density of microarrays. Related term: macroarrays

lymphochip: Microarrays categories 

MAGE  Microarray and Gene Expression: The group aims to provide a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems.  http://www.mged.org/Workgroups/MAGE/mage.html

MAGE-ML MicroArray and Gene Expression Markup Language: A language designed to describe and communicate information about microarray based experiments. MAGE-ML is based on XML and can describe microarray designs, microarray manufacturing information, microarray experiment setup and execution information, gene expression data and data analysis results. MAGE-ML has been automatically derived from Microarray Gene Expression Object Model (MAGE-OM), which is developed and described using the Unified Modelling Language (UML) -- a standard language for describing object models. [Robin Cover, XML Cover Pages: Microarray and Gene Expression Markup Language, 2002] http://xml.coverpages.org/mageML.html

Related terms: GEML, MAML, MIAME

MAML Microarray Markup Language: MAML (Microarray Markup Language) is no longer supported by MGED and has been replaced by MAGE-ML. http://www.mged.org/Workgroups/MAGE/mage.html

Broader term: standards; Related terms: data analysis - microarray, MGED, MIAME  

MGED Microarray Gene Expression Database group: The MGED group is a grass- roots movement whose goal 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 normalization methods. The group was founded at the Microarray Gene Expression Database meeting MGED1 (November, 1999, Cambridge, UK).  There are four major standardization projects being pursuing by the group:, MIAME, MAGE, Ontologies, Normalisation. http://www.mged.org/

Broader term: standards; Related terms: data analysis - microarray, MAGE, MAML, MIAME.

MIAME Minimum Information About a Microarray Experiment: MIAME aims to outline the minimum information required to unambiguously interpret microarray data and to subsequently allow independent verification of this data at a later stage if required. MIAME is not a dogma for microarray experiments to follow, but just a set of guidelines. This set of guidelines will then assist with the development of microarray repositories and data analysis tools. [MIAME homepage 2003] http://www.mged.org/Workgroups/MIAME/miame.html

MIAME Checklist, MGED, 2003 http://www.mged.org/Workgroups/MIAME/miame_checklist.html

MIAME glossary, MGED, MIAME, 2003 http://www.mged.org/Workgroups/MIAME/miame_glossary.html

MIAME software, MGED, 2003 http://www.mged.org/Workgroups/MIAME/miame_software.html A list of possibly MIAME compliant software

Broader term: standards; Related terms: data analysis - microarray, MAGE, MAML, MGED

MIAME/MAGE-OM:  The boundaries between MIAME concepts, the MIAME- compliant MAGE-OM and the MGED ontology (that try to define and structure the MIAME concepts) is neither well defined nor easy to understand. In order to provide some help, this webpage contains explanatory documentation to understand the MIAME concepts, how its requirements map to the MAGE-OM and where the MGED ontology inclusion is required. [MGED, MIAME MAGE-OM, 2002] http://www.mged.org/Workgroups/MIAME/miame_mage-om.html

macroarrays: Microarrays categories 

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 report] 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.

measured bioassay: See under Assays & screening glossary bioassay

measurement error: Has two components: variance and bias. Variance results from uncontrolled (or uncontrollable) variation that occurs in biological samples, experimental procedures, and arrays themselves. These factors cause measurements of expression level to vary in an apparently random fashion between replicas. Bias is a systematic error that causes the measurement to differ from the correct value. Since bias is systematic, it affects all replicas the same way. 

medium density microarrays:  See under density of microarrays

MGED Network, Ontology Working Group: The primary purpose of the MGED Ontology is to provide standard terms for the annotation of microarray experiments. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed. The terms will be provided in the form of an ontology which means that the terms will be organized into classes with properties and will be defined. A standard ontology format will be used. http://mged.sourceforge.net/ontologies/index.php

microarray informatics: See data analysis - microarrays

microarray technology: Hybridization based tool used to analyze how large numbers of genes interact with each other and how a cell's regulatory network controls a vast battery of genes simultaneously; used for genotyping, mapping, sequencing, sequence detection; usually constructed by applying biomolecules onto a slide or chip, labeled with fluorescent probe and scanned with microscope or imaging equipment. CRISP Thesaurus, NIH, US  http://crisp.cit.nih.gov/Thesaurus/00018498.htm

microarrays:  Microarray based technologies have evolved into a very viable diagnostic tool, due to the reliability of their data, as recently confirmed by a study published in Nature Biotechnology. Gene expression results of known quality are key to the successful employment of microarrays for diagnosis and prognosis of diseases, for predicting the patient’s response to new or existing therapeutics, or to identify new diagnostic markers. These are just some of the potentials they offer and such make them also an exciting tool for therapeutic development. Getting Optimized Targets: Microarrays in Medicine April 11-13, 2007 • Boston, MA

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 glossary 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

The term microarray originally referred to spotted cDNA arrays, but now we and others use it for any hybridization- based array. [When the term microarray was first introduced, the prefix micro served to distinguish this new generation of arrays from their predecessors, which came to be called macroarrays. Traditionally, microarrays differ from macroarrays based on the physical size of the surface and the spots. 

Microarrays  were developed in large part by Patrick O. Brown and colleagues at Stanford University. The major characteristics of microarrays - under the strictest definition of this term - are that they have a glass or plastic slide as a matrix, use fluorescent dye labeling for the detection of hybridization, and are created with robots that deposit probes on the slides. Microarrays also tend to have a large number and high density of probes; however, their probe density is less than that of high- density oligonucleotide arrays. The probes used on these arrays can be made from clones, PCR amplicons, or oligonucleotides.   

The market for DNA microarrays has grown significantly since its inception in the mid- 1990s. New players have entered the market in recent years, driving improvements in product quality and a search for new market opportunities. The prospect of participation in the $20 billion in vitro diagnostics industry serves as a further incentive to current and emerging industry players, creating a fiercely competitive environment.  

Narrower terms: Microarrays- categories Related terms: density of microarrays  

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 databases: Databases & software directory

Narrower terms: Microarrays categories antigen microarrays,  chemical microarrays, electrospray fabricated protein microarrays, functional protein microarrays, genomic microarrays, glycoprotein microarrays,  oligonucleotide arrays, protein microarrays, antibody microarrays, BAC microarrays, cell microarrays, DNA microarrays, gene microarrays,  gridded cDNA microarrays,  small molecule microarrays, tissue microarrays. Related terms: arrays, chips, data analysis - microarrays, density of microarrays, probes - microarrays. 

microarray data analysis: See data analysis - microarrays.

microarray informatics: The microarray field is experiencing an overwhelming push toward robust statistics and mathematical analytic methods that go far beyond the simple fold analysis and basic clustering that were once the mainstays of researchers in this area. This push toward better statistics is also driving the recognition of the need for more replication of experiments. These stronger analytical techniques also help researchers identify problem areas in the technology and laboratory processes, and these improvements, in turn, greatly improve the quality of results that can be provided. 

microarrays- categories:  Numerous types of microarrays are in common use today, but for our purposes, it suffices to categorize them into three main groups: spotted cDNA microarrays, spotted oligonucleotide microarrays, and Affymetrix GeneChips, which are sufficiently unique to warrant their own grouping. In the spotted- array categories, we include both traditional arrays produced using contact printing in the style of Pat Brown (Stanford University), and ones produced using the newer ink- jet technology pioneered in the laboratory of  Lee Hood of the University of Washington and developed to commercial fruition by Rosetta Inpharmatics and Agilent Technologies.

Current DNA array formats can be categorized into various groups based on the type of matrix, the probe number and/or density, the physical size of the array, and the type of target labeling. The general categories we describe are macroarrays, microarrays, high- density oligonucleotide arrays (e.g., Affymetrix’s GeneChips), and microelectronic arrays.  

microarrays - regulation:   Drug approvals glossary

microarray technologies: See array technologies.

microchips: Nanoscience & Miniaturization glossary

microelectronic arrays: Microarrays categories Also called microelectronic chips See also under multiplex DNA hybridization arrays

microelectrophoresis chips, microfluidics-based chips: Microarrays categories 

microfluidic devices: Nanoscience & Miniaturization glossary

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

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,  spotted arrays, spotting robots.

microwell chips: Narrower term: nanowells

mismatches: Gene expression microarray data is notoriously subject to high signal variability. Moreover, unavoidable variation in the concentration of transcripts applied to microarrays may result in poor scaling of the summarized data which can hamper analytical interpretations. This is especially relevant in a systems biology context, where systematic biases in the signals of particular genes can have severe effects on subsequent analyses. Conventionally it would be necessary to replace the mismatched arrays, but individual time points cannot be rerun and inserted because of experimental variability. It would therefore be necessary to repeat the whole time series experiment, which is both impractical and expensive. Correction of scaling mismatches in oligonucleotide microarray data, Mrtino Barenco, Jaroslav Stark^{3 ,1}, Daniel Brewer^{2 ,1}, Daniela Tomescu¹, Robin Callard^{1 ,2} and Michael Hubank¹ BMC bioinformatics 2006, 7:251 doi:10.1186/1471-2105-7-251 http://www.biomedcentral.com/1471-2105/7/251 

multiplex assays: Insight Pharma Report forthcoming 2009

multiplex DNA hybridization arrays: Microarrays categories 

nanoarray: Microarrays categories 

nanochip: Nanoscience & miniaturization glossary

noise characterization:  Noise is a big problem in analyzing gene expression microarray data. 

normality: The collection of log ratios from a single microarray experiment is typically quite unlike a random sample from a single normal population. This is particularly so when a lot (say > 10%) of genes are differentially expressed. ..Conclusion. It is dangerous to use normal statistical theory to guide your selection of differentially expressed genes. The normal thinking which says that about 68% should be within 1 standard deviation (SD), 95% within 2 SDs and 99% within 3 SDs of the mean does not apply, even when no differential expression is present.  Avoid assuming normality, Terry Speed Group Microarray Page, 2000  http://stat-www.berkeley.edu/users/terry/zarray/Html/normality.html

Related term: Clinical genomics glossary normal

normalization: One approach is to place a modest number of control probes on the array and add known quantities of matching target molecules to the sample. This is often called a spike-in method, because the sample is "spiked" with known quantities of control target. The idea is that by correlating the readout of each control with the known amount of target, it should be possible to better account for variations in the process. A nice study of this approach for Affymetrix GeneChips was done by Gene Brown’s laboratory at Genetics Institute/ Wyeth- Ayerst Research. Footnote: Hill AA, Brown EL, et al. "Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls." Genome Biology. 2001 2(12): research0055.1-0055.13 ] http://www.genomebiology.com/2001/2/12/research/0055.  

There are many sources of systematic variation in microarray experiments which affect the measured gene expression levels. Normalization is the term used to describe the process of removing such variation. ... Such sources of systematic variation include: Differences in labelling efficiency between the two dyes. Differences in the power of the two lasers. Differing amounts of RNA labelled between the 2 channels. Spatial biases in ratios across the surface of the microarray. MGED Normalization Working Group, 2002 http://www.dnachip.org/mged/normalization.html

The conversion of intensity information (from image analysis) into estimates of gene expression levels. For researchers who are using statistical methods, this process also characterizes the uncertainty in the measurements. The goal of normalization is to convert the intensity measurements generated by image analysis into estimates of gene expression levels in the original biological source. Concretely, the challenge is to compensate for as many sources of error as possible.  

Normalization for cDNA microarrays, Yee Hwa Yang, Sandrine Dudoit, Percy Luu and Terry Speed, 2001  http://www.stat.berkeley.edu/users/terry/zarray/Html/normspie.html

Related terms: fold changes, image analysis, log ratios; See also normalization: Algorithms glossary

Northern blotting: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES. MeSH, 1991

nylon macroarrays: Microarrays categories 

oligo arrays, oligo chips: See Microarrays categories: oligonucleotide arrays, oligonucleotide chips, oligonucleotide microarrays

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, 1999

Useful to know this MeSH heading for microarrays, but use free- text as well to search PubMed.

oligonucleotide arrays, oligonucleotide chips, oligonucleotide microarrays: Microarrays categories 

oligosaccharide arrays: See Microarrays categories: glycochips.

Ontology Working Group: Charged with developing an ontology for describing samples used in microarray experiments. MGED Network, Ontology Working Group   http://mged.sourceforge.net/ontologies/index.php

pattern recognition: Algorithms & data management glossary

peptide arrays: Microarrays categories  Related terms: protein arrays, protein chips, protein microarrays  

phenotypic microarray: Microarrays categories Related term: Genomics glossary phenotype

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

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. 

Related term: soft lithography

physical bioassay: See under Assays & screening glossary bioassay

piezoelectric: A material that generates an electric charge when mechanically deformed. ..[About.com http://chemistry.about.com/library/glossary/bldef700.htm

planar arrays: Microarrays categories

primer extension: Gene amplification & PCR glossary

printing:  The placing of probes on an array - a process often called printing - is accomplished by automated machinery that can produce very small spots and place them quite close to one another with high precision. With modern equipment, spot diameters are in the range of 100 mm, and it is possible to place 10,000- 30,000 probes on a standard 1" x 3" glass slide. The large number of probes is a bit misleading in that it is often necessary to represent each gene by two different probes to achieve adequate reproducibility. Thus, an array with 30,000 probes might represent only 15,000 genes.

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

We use the term probe for the DNA affixed to the array, and target for the DNA or RNA being hybridized to the array. This usage is fairly common, although some authors reverse the meanings of probe and target. CHI Microarray Informatics report

Two technologies are available for placing the DNA probes on the array. The traditional and most popular approach involves contact spotting, in which the DNA is loaded into a print tip and deposited by physically tapping the tip on the surface. There is also a newer noncontact method in which DNA is sprayed onto the surface using technology adapted from computer ink- jet printers. [The ink- jet method is sometimes called indirect because the DNA is sprayed onto the surface rather than being directly placed.] The ink- jet method is capable of producing smaller spots, and because it avoids physical contact with the surface may prove to be more reliable. (The physical contact can introduce more variability into spots.)   

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

profiling: SEE gene expression

protein array analysis: Ligand-binding assays that measure protein- protein, protein- small molecule or protein- nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on the solid support, to measure the presence or interaction of target molecules in the sample. MeSH 2003

protein arrays: Protein arrays are poised to become a central proteomics technology allowing for the global observation of biochemical activities on an unprecedented scale. Hundreds or thousands of proteins can be simultaneously screened for protein-protein, protein-nucleic acid, and small molecule interactions. The value of multiplexed protein measurement is being established in applications including: comprehensive proteomic surveys, studies of protein networks and pathways, validation of genomic discoveries, and clinical biomarker development. This technology holds great potential for basic molecular biology research, serum profiling, protein abundance determination, disease biomarker identification, immune and toxicological response profiling, and pharmaceutical target screening. Protein Arrays January 11-12, 2007, San Diego CA

Google = about 1,720 July 10, 2002; about 6,350  Sept. 16, 2003; about 10,800 Aug. 6, 2004, about 137,000 Oct. 5, 2005; about 176,000 Nov 10, 2006

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

protein biochips: Microarrays categories 

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.

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.  

Google = about 56,400 Oct. 5, 2005; about 92,400 Aug 29, 2007

See also Microarrays categories  Related terms: protein arrays, protein microarrays; Narrower terms: high- density protein microarrays, protein-protein interaction chips,  proteome chip

protein expression arrays: Expression glossary

protein microarrays: 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 report]  More...Microarrays categories   

Related terms: protein arrays, protein chips; Narrower terms:  electrospray- fabricated protein microarrays, functional protein microarrays, protein- protein interaction chips, proteome chip  Wikipedia http://en.wikipedia.org/wiki/Protein_microarray    

proteome microarray: See Microarrays categories: proteome chip  

Broader terms: protein arrays, protein chips, protein microarrays.

pump chip, RNA biochip, RNA chips: Microarrays categories 

RNA expression arrays: Expression glossary

regulating microarrays: See FDA -- microarrays - regulating

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 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

Rolling Circle Amplification RCA: Gene amplification & PCR glossary

Systems Literature Analysis SLA: Information Management & Interpretation glossary

SNP chips: Microarrays categories 

sample: In microarray work, this term often refers to the biological material from which mRNA is extracted (e.g., tissue or serum from patients or laboratory animals). However, sample is also an important term in statistics, where it means the subset of a population that is surveyed for the purpose of estimating properties of the entire population. 

See also Drug discovery & development glossary sample 

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

semiconductor : Miniaturization & nanoscience glossary

small molecule microarrays: Microarrays categories

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

solution arrays: Labels, signaling & detection glossary

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, 1989

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

spike-in: See under normalization

spots:   Parts of the image corresponding to the DNA probes on the microarray.  

spotted arrays: See Microarrays categories: cDNA arrays, microarrays - categories of

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. 

Related terms: Stokes shift,  microspotting, spotted arrays.

standards:  See GEML, MGED, MIAMI  

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: microspotting, spotted arrays, spotting robots.

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.    

Different from substrate Pharmaceutical biology glossary  Related term: matrix

suspension arrays:  Microarrays categories 

target (hybridization): Gene amplification & PCR
G.O.T. Summit Getting Optimized Targets April 10-13, 2007 • Boston, Massachusetts

theme arrays: Microarrays containing genes thought to be involved in specific diseases or processes. 

tissue arrays, tissue chips: Microarrays categories tissue microarrays 

tox-chips: Pharmacogenomics glossary

transcript arrays: Microarrays categories 

ultra high density microarrays Microarrays categories Related term: bead based arrays Broader term:  density of microarrays, high density oligonucleotide arrays

universal microarrays: Microarrays categories 

universal probe technologies: Gene amplification & PCR glossary

variance: See under measurement error  

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, 1989

Bibliography
BioChipNet Glossary, 2002, 150 + definitions  http://www.biochipnet.com/glossary 
Chipping Forecast III, Nature Genetics, 37 (65): June 2005 http://www.nature.com/ng/journal/v37/n6s/index.html 
Chipping Forecast II, Nature Genetics 32 (supp): 509- 514, 2002  http://www.nature.com/cgi-taf/dynapage.taf?file=/ng/journal/v32/n4s/index.html
“Chipping Forecast”, Nature Genetics supplement 21 (1s), Jan 1999 http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v21/n1s/index.html
MicroArray Explorer Glossary, NCI, Lab of Experimental & Computational Biology http://www.lecb.ncifcrf.gov/searchframes.html about 50 definitions.
Profiling Microarrays, Nature Genome Gateway - Post- Genomics http://www.nature.com/genomics/post-genomics/microarrays.html
DNA Microarray (Genome Chip), Leming Shi http://www.gene-chips.com/
Microarray related activities at the EBI, European Bioinformatics Institute, UK http://www.ebi.ac.uk/microarray/
GRID IT Resources for Microarray Research, Virginia Tech/NC State Univ., US http://www.gridit.vt.edu/profile_VT.htm 
MGuide, [Pat] Brown Lab’s Guide to Microarraying, Stanford Univ., US http://cmgm.stanford.edu/pbrown/mguide/
MIAME Glossary, MGED, 2005 about 80 terms  http://www.mged.org/Workgroups/MIAME/miame_glossary.html 
Science Functional Genomics Blog, Microarray Discussion, 2004 http://sciencemag.blogs.com/sfgblog/2004/10/a_microarray_di.html 

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