DNA microarray - Knowledge

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which cluster together can enable the discovery of new groups that otherwise were not previously known to exist. During knowledge discovery analysis, various unsupervised classification techniques can be employed with DNA microarray data to identify novel clusters (classes) of arrays. This type of approach is not hypothesis-driven, but rather is based on iterative pattern recognition or statistical learning methods to find an "optimal" number of clusters in the data. Examples of unsupervised analyses methods include self-organizing maps, neural gas, k-means cluster analyses, hierarchical cluster analysis, Genomic Signal Processing based clustering and model-based cluster analysis. For some of these methods the user also has to define a distance measure between pairs of objects. Although the Pearson correlation coefficient is usually employed, several other measures have been proposed and evaluated in the literature. The input data used in class discovery analyses are commonly based on lists of genes having high informativeness (low noise) based on low values of the coefficient of variation or high values of Shannon entropy, etc. The determination of the most likely or optimal number of clusters obtained from an unsupervised analysis is called cluster validity. Some commonly used metrics for cluster validity are the silhouette index, Davies-Bouldin index, Dunn's index, or Hubert's

767:, the arrays provide intensity data for each probe or probe set indicating a relative level of hybridization with the labeled target. However, they do not truly indicate abundance levels of a gene but rather relative abundance when compared to other samples or conditions when processed in the same experiment. Each RNA molecule encounters protocol and batch-specific bias during amplification, labeling, and hybridization phases of the experiment making comparisons between genes for the same microarray uninformative. The comparison of two conditions for the same gene requires two separate single-dye hybridizations. Several popular single-channel systems are the Affymetrix "Gene Chip", Illumina "Bead Chip", Agilent single-channel arrays, the Applied Microarrays "CodeLink" arrays, and the Eppendorf "DualChip & Silverquant". One strength of the single-dye system lies in the fact that an aberrant sample cannot affect the raw data derived from other samples, because each array chip is exposed to only one sample (as opposed to a two-color system in which a single low-quality sample may drastically impinge on overall data precision even if the other sample was of high quality). Another benefit is that data are more easily compared to arrays from different experiments as long as batch effects have been accounted for. 641:

resulting "grid" of probes represents the nucleic acid profiles of the prepared probes and is ready to receive complementary cDNA or cRNA "targets" derived from experimental or clinical samples. This technique is used by research scientists around the world to produce "in-house" printed microarrays in their own labs. These arrays may be easily customized for each experiment, because researchers can choose the probes and printing locations on the arrays, synthesize the probes in their own lab (or collaborating facility), and spot the arrays. They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally scan the arrays with their own equipment. This provides a relatively low-cost microarray that may be customized for each study, and avoids the costs of purchasing often more expensive commercial arrays that may represent vast numbers of genes that are not of interest to the investigator. Publications exist which indicate in-house spotted microarrays may not provide the same level of sensitivity compared to commercial oligonucleotide arrays, possibly owing to the small batch sizes and reduced printing efficiencies when compared to industrial manufactures of oligo arrays.

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washing after hybridization. Total strength of the signal, from a spot (feature), depends upon the amount of target sample binding to the probes present on that spot. Microarrays use relative quantitation in which the intensity of a feature is compared to the intensity of the same feature under a different condition, and the identity of the feature is known by its position.

405:, genomic regions bound by a protein of interest can be isolated and used to probe a microarray to determine binding site occupancy. Unlike ChIP, DamID does not require antibodies but makes use of adenine methylation near the protein's binding sites to selectively amplify those regions, introduced by expressing minute amounts of protein of interest fused to bacterial 586: 652:. Although oligonucleotide probes are often used in "spotted" microarrays, the term "oligonucleotide array" most often refers to a specific technique of manufacturing. Oligonucleotide arrays are produced by printing short oligonucleotide sequences designed to represent a single gene or family of gene splice-variants by 669:

reaction takes place and the next set of probes are unmasked in preparation for a different nucleotide exposure. After many repetitions, the sequences of every probe become fully constructed. More recently, Maskless Array Synthesis from NimbleGen Systems has combined flexibility with large numbers of probes.

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technology, that enables a whole transcriptome shotgun approach to characterize and quantify gene expression. Unlike microarrays, which need a reference genome and transcriptome to be available before the microarray itself can be designed, RNA-Seq can also be used for new model organisms whose genome

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Dimensional reduction: Analysts often reduce the number of dimensions (genes) prior to data analysis. This may involve linear approaches such as principal components analysis (PCA), or non-linear manifold learning (distance metric learning) using kernel PCA, diffusion maps, Laplacian eigenmaps, local

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synthesis (Affymetrix) on a silica substrate where light and light-sensitive masking agents are used to "build" a sequence one nucleotide at a time across the entire array. Each applicable probe is selectively "unmasked" prior to bathing the array in a solution of a single nucleotide, then a masking

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that it is expected to detect is not trivial. Some mRNAs may cross-hybridize probes in the array that are supposed to detect another mRNA. In addition, mRNAs may experience amplification bias that is sequence or molecule-specific. Thirdly, probes that are designed to detect the mRNA of a particular

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Within the organisms, genes are transcribed and spliced to produce mature mRNA transcripts (red). The mRNA is extracted from the organism and reverse transcriptase is used to copy the mRNA into stable ds-cDNA (blue). In microarrays, the ds-cDNA is fragmented and fluorescently labelled (orange). The

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Multi-stranded DNA and RNA microarrays can be used to identify novel drugs that bind to these multi-stranded nucleic acid sequences. This approach can be used to discover new drugs and biologicals that have the ability to inhibit gene expression. These microarrays also allow for characterization of

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Class prediction analysis: This approach, called supervised classification, establishes the basis for developing a predictive model into which future unknown test objects can be input in order to predict the most likely class membership of the test objects. Supervised analysis for class prediction

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Class discovery analysis: This analytic approach, sometimes called unsupervised classification or knowledge discovery, tries to identify whether microarrays (objects, patients, mice, etc.) or genes cluster together in groups. Identifying naturally existing groups of objects (microarrays or genes)

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as a requirement for the submission of papers incorporating microarray results. But MIAME does not describe the format for the information, so while many formats can support the MIAME requirements, as of 2007 no format permits verification of complete semantic compliance. The "MicroArray Quality

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There are three main elements to consider when designing a microarray experiment. First, replication of the biological samples is essential for drawing conclusions from the experiment. Second, technical replicates (e.g. two RNA samples obtained from each experimental unit) may help to quantitate

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Microarrays can be manufactured in different ways, depending on the number of probes under examination, costs, customization requirements, and the type of scientific question being asked. Arrays from commercial vendors may have as few as 10 probes or as many as 5 million or more micrometre-scale

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Left-handed double-stranded Z-DNA microarrays can be used to identify short sequences of the alternative Z-DNA structure located within longer stretches of right-handed B-DNA genes (e.g., transcriptional enhancement, recombination, RNA editing). The microarrays also allow for characterization of

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bonding between the two strands. After washing off non-specific bonding sequences, only strongly paired strands will remain hybridized. Fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the hybridization conditions (such as temperature), and

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Right-handed double-stranded B-DNA microarrays can be used to characterize novel drugs and biologicals that can be employed to bind specific regions of immobilized, intact, double-stranded DNA. This approach can be used to inhibit gene expression. They also allow for characterization of their

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5 with a fluorescence emission wavelength of 670 nm (corresponding to the red part of the light spectrum). The two Cy-labeled cDNA samples are mixed and hybridized to a single microarray that is then scanned in a microarray scanner to visualize fluorescence of the two fluorophores after

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prior to deposition on the array surface and are then "spotted" onto glass. A common approach utilizes an array of fine pins or needles controlled by a robotic arm that is dipped into wells containing DNA probes and then depositing each probe at designated locations on the array surface. The

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of the same extraction. Third, spots of each cDNA clone or oligonucleotide are present as replicates (at least duplicates) on the microarray slide, to provide a measure of technical precision in each hybridization. It is critical that information about the sample preparation and handling is

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Hacia JG; Fan JB; Ryder O; Jin L; Edgemon K; Ghandour G; Mayer RA; Sun B; Hsie L; Robbins CM; Brody LC; Wang D; Lander ES; Lipshutz R; Fodor SP; Collins FS (1999). "Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays".

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the hybridization measurements for the target probes. Although absolute levels of gene expression may be determined in the two-color array in rare instances, the relative differences in expression among different spots within a sample and between samples is the preferred method of

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for a gene. It is of intermediate density, or coverage, to a typical gene expression array (with 1–3 probes per gene) and a genomic tiling array (with hundreds or thousands of probes per gene). It is used to assay the expression of alternative splice forms of a gene.

115:-labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by 1877:

Adomas A; Heller G; Olson A; Osborne J; Karlsson M; Nahalkova J; Van Zyl L; Sederoff R; Stenlid J; Finlay R; Asiegbu FO (2008). "Comparative analysis of transcript abundance in Pinus sylvestris after challenge with a saprotrophic, pathogenic or mutualistic fungus".

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The video shows the process of extracting genotypes from a human spit sample using microarrays. Genotyping is a major use of DNA microarrays, but with some modifications they can also be used for other purposes such as measurement of gene expression and epigenetic

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The mixture is denatured and added to the pinholes of the microarray. The holes are sealed and the microarray hybridized, either in a hyb oven, where the microarray is mixed by rotation, or in a mixer, where the microarray is mixed by alternating pressure at the

587: 30: 31: 588: 664:) depending on the desired purpose; longer probes are more specific to individual target genes, shorter probes may be spotted in higher density across the array and are cheaper to manufacture. One technique used to produce oligonucleotide arrays include 2514:

Nuwaysir EF; Huang W; Albert TJ; Singh J; Nuwaysir K; Pitas A; Richmond T; Gorski T; Berg JP; Ballin J; McCormick M; Norton J; Pollock T; Sumwalt T; Butcher L; Porter D; Molla M; Hall C; Blattner F; Sussman MR; Wallace RL; Cerrina F; Green RD (2002).

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involves use of techniques such as linear regression, k-nearest neighbor, learning vector quantization, decision tree analysis, random forests, naive Bayes, logistic regression, kernel regression, artificial neural networks, support vector machines,

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Bammler T, Beyer RP; Consortium, Members of the Toxicogenomics Research; Kerr, X; Jing, LX; Lapidus, S; Lasarev, DA; Paules, RS; Li, JL; Phillips, SO (2005). "Standardizing global gene expression analysis between laboratories and across platforms".

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The raw data is normalized; the simplest normalization method is to subtract background intensity and scale so that the total intensities of the features of the two channels are equal, or to use the intensity of a reference gene to calculate the

26: 119:. An example of its application is in SNPs arrays for polymorphisms in cardiovascular diseases, cancer, pathogens and GWAS analysis. It is also used for the identification of structural variations and the measurement of gene expression. 1526:

Microarray data may require further processing aimed at reducing the dimensionality of the data to aid comprehension and more focused analysis. Other methods permit analysis of data consisting of a low number of biological or technical

590: 1624:: an experimental design paradigm especially suited to the two-colour array system, in which a condition chosen as control (such as healthy tissue or state) is compared to an altered condition (such as a diseased tissue or state). 1480:. Input data for class prediction are usually based on filtered lists of genes which are predictive of class, determined using classical hypothesis tests (next section), Gini diversity index, or information gain (entropy). 510:

Genome tiling arrays consist of overlapping probes designed to densely represent a genomic region of interest, sometimes as large as an entire human chromosome. The purpose is to empirically detect expression of

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is widely used for identifying co-expression modules and intramodular hub genes. Modules may corresponds to cell types or pathways. Highly connected intramodular hubs best represent their respective modules.

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The alternative bead array is a collection of microscopic polystyrene beads, each with a specific probe and a ratio of two or more dyes, which do not interfere with the fluorescent dyes used on the target

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Network-based methods: Statistical methods that take the underlying structure of gene networks into account, representing either associative or causative interactions or dependencies among gene products.

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in two-channel experiments; for a dye flip, a second slide is used, with the labels swapped (the sample that was labeled with Cy3 in the first slide is labeled with Cy5, and vice versa). In this example,

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of the data. Normalization methods may be suited to specific platforms and, in the case of commercial platforms, the analysis may be proprietary. Algorithms that affect statistical analysis include:

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Ben Gal, I.; Shani, A.; Gohr, A.; Grau, J.; Arviv, S.; Shmilovici, A.; Posch, S.; Grosse, I. (2005). "Identification of transcription factor binding sites with variable-order Bayesian networks".

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The traditional solid-phase array is a collection of orderly microscopic "spots", called features, each with thousands of identical and specific probes attached to a solid surface, such as

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across the array indicates the abundance of a predetermined set of sequences. These sequences are typically specifically chosen to report on genes of interest within the organism's genome.

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J Biochem Biophys Methods. 2000 Mar 16;42(3):105–10. DNA-printing: utilization of a standard inkjet printer for the transfer of nucleic acids to solid supports. Goldmann T, Gonzalez JS.

2295: 25: 3982: 1370:(FDA) to develop standards and quality control metrics which will eventually allow the use of MicroArray data in drug discovery, clinical practice and regulatory decision-making. The 289:, and developmental stages on gene expression. For example, microarray-based gene expression profiling can be used to identify genes whose expression is changed in response to 3163:

Wouters L; Gõhlmann HW; Bijnens L; Kass SU; Molenberghs G; Lewi PJ (2003). "Graphical exploration of gene expression data: a comparative study of three multivariate methods".

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Gagna, Claude E.; Lambert, W. Clark (1 May 2009). "Novel multistranded, alternative, plasmid and helical transitional DNA and RNA microarrays: implications for therapeutics".

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have a different design, employing probes designed to detect each individual exon for known or predicted genes, and can be used for detecting different splicing isoforms.

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samples need to be compared: then the number of experiments required using the two channel arrays quickly becomes unfeasible, unless a sample is used as a reference.

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Data processing: background subtraction (based on global or local background), determination of spot intensities and intensity ratios, visualisation of data (e.g. see

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Taub, Floyd (1983). "Laboratory methods: Sequential comparative hybridizations analyzed by computerized image processing can identify and quantitate regulated RNAs".

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beam of a defined wavelength. Relative intensities of each fluorophore may then be used in ratio-based analysis to identify up-regulated and down-regulated genes.

1564:), and curation efforts associated with the datasets require specialized databases to store the data. A number of open-source data warehousing solutions, such as 977: 1009:

which includes details for a particular case to better explain DNA microarray experiments, while listing modifications for RNA or other alternative experiments.

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microarrays. The oligo design strategy enables combined measurements of chimeric transcript junctions with exon-wise measurements of individual fusion partners.

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Image analysis: gridding, spot recognition of the scanned image (segmentation algorithm), removal or marking of poor-quality and low-intensity features (called

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The advent of inexpensive microarray experiments created several specific bioinformatics challenges: the multiple levels of replication in experimental design (

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Microarray data is difficult to exchange due to the lack of standardization in platform fabrication, assay protocols, and analysis methods. This presents an

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The labeling can be direct (not used) or indirect (requires a coupling stage). For two-channel arrays, the coupling stage occurs before hybridization, using

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Mortazavi, Ali; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold (July 2008). "Mapping and quantifying mammalian transcriptomes by RNA-Seq".

1065: 1663:: an instrument used to detect and quantify the intensity of fluorescence of spots on a microarray slide, by selectively exciting fluorophores with a 1506:. These methods assess statistical power based on the variation present in the data and the number of experimental replicates, and can help minimize 1962:"Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis" 4580: 1792: 1483:

Hypothesis-driven statistical analysis: Identification of statistically significant changes in gene expression are commonly identified using the

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microarrays ligate an oligonucleotide to the purified small RNA (isolated with a fractionator), which is then reverse transcribed and amplified.

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contains amine groups). The aminoallyl group is an amine group on a long linker attached to the nucleobase, which reacts with a reactive dye.

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Microarray data was found to be more useful when compared to other similar datasets. The sheer volume of data, specialized formats (such as

1169:)) are added enzymatically in a low ratio to normal nucleotides, typically resulting in 1 every 60 bases. The aaDNA is then purified with a 2729: 478: 396: 3458: 3544: 2299: 656:

this sequence directly onto the array surface instead of depositing intact sequences. Sequences may be longer (60-mer probes such as the

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Barbosa-Morais, N. L.; Dunning, M. J.; Samarajiwa, S. A.; Darot, J. F. J.; Ritchie, M. E.; Lynch, A. G.; Tavare, S. (18 November 2009).

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with cDNA prepared from two samples to be compared (e.g. diseased tissue versus healthy tissue) and that are labeled with two different

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Gagna, Claude E.; Clark Lambert, W. (1 March 2007). "Cell biology, chemogenomics and chemoproteomics – application to drug discovery".

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The microarray is dried and scanned by a machine that uses a laser to excite the dye and measures the emission levels with a detector.

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Yuk Fai Leung and Duccio Cavalieri, Fundamentals of cDNA microarray data analysis. Trends in Genetics Vol.19 No.11 November 2003.

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Bolshakova N, Azuaje F (2003) Cluster validation techniques for genome expression data, Signal Processing, Vol. 83, pp. 825–833.

1072:) which isolates most RNA (whereas column methods have a cut off of 200 nucleotides) and if done correctly has a better purity. 192:

Many types of arrays exist and the broadest distinction is whether they are spatially arranged on a surface or on coded beads:

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3, which has a fluorescence emission wavelength of 570 nm (corresponding to the green part of the light spectrum), and

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Microarrays can be fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides,

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Due to the biological complexity of gene expression, the considerations of experimental design that are discussed in the

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Pollack JR; Perou CM; Alizadeh AA; Eisen MB; Pergamenschikov A; Williams CF; Jeffrey SS; Botstein D; Brown PO (1999).

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article are of critical importance if statistically and biologically valid conclusions are to be drawn from the data.

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The image is gridded with a template and the intensities of each feature (composed of several pixels) is quantified.

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The label is added either during the reverse transcription step, or following amplification if it is performed. The

107:) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of 4489: 4285: 3942: 3825: 3537: 3420: 2914:

De Souto M et al. (2008) Clustering cancer gene expression data: a comparative study, BMC Bioinformatics, 9(497).

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discussed, in order to help identify the independent units in the experiment and to avoid inflated estimates of

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Rasheed, Awais; Hao, Yuanfeng; Xia, Xianchun; Khan, Awais; Xu, Yunbi; Varshney, Rajeev K.; He, Zhonghu (2017).

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Microarray data sets are commonly very large, and analytical precision is influenced by a number of variables.

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has developed standards for the representation of gene expression experiment results and relevant annotations.

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precision. The biological replicates include independent RNA extractions. Technical replicates may be two

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The two samples to be compared (pairwise comparison) are grown/acquired. In this example treated sample (

363:) allowing the determination of protein binding site occupancy throughout the genome. Example protein to 3259:"A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data" 1323: 427:

within or between populations. Several applications of microarrays make use of SNP detection, including

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levels of thousands of genes are simultaneously monitored to study the effects of certain treatments,

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Assessing genome content in different cells or closely related organisms, as originally described by

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PNAS Commentary: Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data

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or other organisms by comparing gene expression in infected to that in uninfected cells or tissues.

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projects are trying to ease the exchange and analysis of data produced with non-proprietary chips:

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of genes with similar expression levels in an effort to compensate for insufficient replication.

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The core principle behind microarrays is hybridization between two DNA strands, the property of

4002: 3172: 2274: 1657:: reciprocal labelling of DNA targets with the two dyes to account for dye bias in experiments. 1618:: a group of spots, typically made in one print round; several subarrays/ blocks form an array. 1549: 1201: 1166: 648:, the probes are short sequences designed to match parts of the sequence of known or predicted 609:

using pre-made masks, photolithography using dynamic micromirror devices, ink-jet printing, or

599: 448: 436: 372: 1468:, and supervised neural gas. In addition, various metaheuristic methods are employed, such as 912: 4338: 4146: 3768: 3763: 3705: 3619: 2517:"Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography" 1495: 1443: 1432:

normalization of intensity ratios, and segmentation into different copy number regions using

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amplification. The RNA is reverse transcribed with either polyT primers (which amplify only

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at early stages to lower the number of unneeded seedlings tried out in breeding operations.

4600: 4494: 4368: 4280: 4116: 4106: 3868: 3725: 3574: 3517: 2468: 2362:"POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer" 1811: 1767: 1499: 1315: 1150: 1087:). If the material is of acceptable quality and sufficient quantity is present (e.g., >1 1033: 516: 497: 460: 248: 223:). Thousands of these features can be placed in known locations on a single DNA microarray. 55:) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA 4406: 1091:, although the required amount varies by microarray platform), the experiment can proceed. 8: 4514: 4441: 4436: 4358: 4333: 4300: 4161: 3737: 3732: 3710: 3656: 2605:

Tang T; François N; Glatigny A; Agier N; Mucchielli MH; Aggerbeck L; Delacroix H (2007).

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labeling is dependent on the microarray; e.g. if the label is added with the RT mix, the

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and RMA (robust multichip analysis) for Affymetrix chips (single-channel, silicon chip,

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is antisense and the microarray probe is sense, except in the case of negative controls.

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Multi-stranded DNA microarrays (triplex-DNA microarrays and quadruplex-DNA microarrays)

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After an overnight hybridization, all nonspecific binding is washed off (SDS and SSC).

731:. The degree of hybridization between the spike-ins and the control probes is used to 4499: 4469: 4426: 4363: 4348: 4260: 4151: 3909: 3553: 3399: 3381: 3343: 3331: 3323: 3288: 3239: 3190: 3186: 3143: 3120: 3069: 3009: 3001: 2957: 2895: 2865: 2752: 2710: 2669: 2628: 2587: 2546: 2496: 2491: 2456: 2441: 2429: 2393: 2325: 2317: 2255: 2237: 2198: 2180: 2133: 2125: 2085: 2077: 2029: 1993: 1934: 1895: 1859: 1731: 1469: 1351: 696: 665: 444: 384: 112: 3434: 3234: 3217: 3202: 3089:"Sample size for detecting differentially expressed genes in microarray experiments" 2997: 2764: 2623: 2606: 2337: 2145: 2041: 1158: 4290: 4275: 4045: 3389: 3373: 3315: 3278: 3270: 3229: 3182: 3110: 3100: 3059: 3049: 2993: 2947: 2937: 2855: 2847: 2744: 2700: 2659: 2618: 2577: 2536: 2528: 2486: 2476: 2421: 2383: 2373: 2307: 2245: 2229: 2188: 2172: 2117: 2069: 2021: 1983: 1973: 1926: 1887: 1851: 1503: 1429: 1409:

challenges include taking into account effects of background noise and appropriate

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labelled fragments bind to an ordered array of complementary oligonucleotides, and

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design uses probes specific to the expected or potential splice sites of predicted

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Oligonucleotide microarrays often carry control probes designed to hybridize with

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or regulation studies. In this example total RNA is isolated (both nuclear and

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for the two-color system. Examples of providers for such microarrays includes

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A form of replicate known as a dye flip can be performed to control for dye

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spatially arranged in a two dimensional grid, arranged in columns and rows.

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One channel microarray may be the only choice in some situations. Suppose

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Gene expression values from microarray experiments can be represented as

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Micro Scale Products and Services for Biochemistry and Molecular Biology

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Advances in massively parallel sequencing has led to the development of

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Pease AC; Solas D; Sullivan EJ; Cronin MT; Holmes CP; Fodor SP (1994).

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linear embedding, locally preserving projections, and Sammon's mapping.

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nucleic acid sequences to specifically pair with each other by forming

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For example, the "Minimum Information About a Microarray Experiment" (

3715: 2425: 1988: 1912: 1565: 1061: 414: 359:), these fragments can be then hybridized to a microarray (such as a 334: 290: 3522: 3377: 3256: 3162: 1960:

Moran G; Stokes C; Thewes S; Hube B; Coleman DC; Sullivan D (2004).

677: 496:

from cancer specimens. The principle behind this is building on the

4524: 4295: 4071: 4066: 3778: 3773: 3666: 2748: 2454: 2303: 1757: 1711: 1668: 1286:); the number of platforms and independent groups and data format ( 1275: 1111: 561: 440: 432: 368: 323:

Small microarrays to check IDs of organisms in food and feed (like

3504: – a free web-server for online microarray analysis 2513: 1930: 1725: 1498:

methods tailored to microarray data sets, which take into account

1165:. The modified nucleotides (usually in a ratio of 1 aaUTP: 4 TTP ( 4244: 3884: 3859: 3834: 3830: 3810: 3623: 3216:

Jain N; Thatte J; Braciale T; Ley K; O'Connell M; Lee JK (2003).

2924:

Jaskowiak, Pablo A; Campello, Ricardo JGB; Costa, Ivan G (2014).

2604: 2025: 1772: 1750: 1581: 1569: 1425: 1250: 1246: 1209: 1205: 1154: 1143: 1045: 741: 712: 708: 657: 424: 286: 208: 205: 201: 52: 2687:

Tinker, Anna V.; Boussioutas, Alex; Bowtell, David D.L. (2006).

1876: 4320: 4126: 3695: 3673: 3480: 3471: 3462: 3453: 3359: 1484: 1249:

for all of the intensities. More sophisticated methods include

1069: 351:

DNA sequences bound to a particular protein can be isolated by

16:

Collection of microscopic DNA spots attached to a solid surface

4239: 4206: 4040: 4025: 3897: 3501: 3215: 3035: 1959: 1664: 1561: 1488: 1358: 1217: 1106:) or random primers (which amplify all RNA, most of which is 721: 595: 197: 185: 68: 1088: 127: 3700: 3360:

Wang, Zhong; Mark Gerstein; Michael Snyder (January 2009).

3137: 1552:

information that is incorrectly associated with that gene.

1544: 1295: 1174: 1122: 1107: 1103: 633: 625: 553: 512: 473: 402: 274: 236: 100: 92: 2730:"Fundamentals of experimental design for cDNA microarrays" 2507: 2010: 1270: 546:

their structure under different environmental conditions.

537:

their structure under different environmental conditions.

3613: 3603: 1302:); the sheer volume of data and the ability to share it ( 1037: 1029: 576: 560:

applications. In the future they could be used to screen

324: 48: 2686: 2563: 672: 492:

A fusion gene microarray can detect fusion transcripts,

2159:

Mukherjee, Anirban; Vasquez, Karen M. (1 August 2011).

1531:; for example, the Local Pooled Error (LPE) test pools 519:

which may not have been previously known or predicted.

2923: 2218:"G-quadruplexes and their regulatory roles in biology" 1196:

The labeled samples are then mixed with a proprietary

63:

levels of large numbers of genes simultaneously or to

3086: 1446: 1366:

Control (MAQC) Project" is being conducted by the US

959: 915: 894: 873: 776: 103:

or cRNA (also called anti-sense RNA) sample (called

67:

multiple regions of a genome. Each DNA spot contains

3140:

Analysis of Microarray Data A Network-Based Approach

2983: 1707: 1066:

guanidinium thiocyanate-phenol-chloroform extraction

528:

structure under different environmental conditions.

439:

to disease, identifying drug-candidates, evaluating

3362:"RNA-Seq: a revolutionary tool for transcriptomics" 2404: 2216:Rhodes, Daniela; Lipps, Hans J. (15 October 2015). 1189:-UTP is present in the reverse-transcribed mixture. 2266: 2107: 1452: 971: 944: 900: 879: 782: 2887: 2828: 2272: 1636:output recorded in the scanner for an individual 1265: 994:Examples of levels of application of microarrays. 231:DNA microarrays can be used to detect DNA (as in 4557: 2977: 2793:NCTR Center for Toxicoinformatics – MAQC Project 2158: 2448: 2103: 2101: 2099: 2055: 2053: 2051: 1793:Methylation specific oligonucleotide microarray 1428:), and log-transformation of ratios, global or 748:with their DualChip platform for colorimetric 660:design) or shorter (25-mer probes produced by 4465:Conservation and restoration of glass objects 4010: 3538: 3299: 2557: 1906: 1775:dyes, such as Cy3 and Cy5, are commonly used 1075:The purified RNA is analysed for quality (by 707:dyes commonly used for cDNA labeling include 171:The steps required in a microarray experiment 3477:Online Services for Gene Expression Analysis 2096: 2059: 2048: 1870: 1520:Weighted gene co-expression network analysis 188:is shown at bottom left for size comparison. 3355: 3353: 3138:Emmert-Streib, F. & Dehmer, M. (2008). 3029: 2883: 2881: 2879: 2648:"Eukaryotic and prokaryotic gene structure" 2598: 2215: 2004: 1953: 1575: 4017: 4003: 3545: 3531: 3036:Priness I.; Maimon O.; Ben-Gal I. (2007). 2891:Classification Analysis of DNA Microarrays 2645: 1387:National Center for Toxicological Research 1290:); the statistical treatment of the data ( 752:labeling, and TeleChem International with 552:Specialised arrays tailored to particular 3468:Products and Services for Gene Expression 3393: 3282: 3233: 3176: 3114: 3104: 3063: 3053: 2951: 2941: 2859: 2727: 2704: 2663: 2622: 2581: 2540: 2490: 2480: 2387: 2377: 2359: 2311: 2249: 2192: 1987: 1977: 1278:to visualize the result of data analysis. 4024: 3492:PLoS Biology Primer: Microarray Analysis 3350: 2876: 1381: 1283: 1269: 1079:) and quantity (for example, by using a 988: 806:two channel microarray (with reference) 676: 584: 337:for disease detection, mostly combining 179: 166: 131:Hybridization of the target to the probe 126: 20: 1173:(using a phosphate buffer solution, as 142: 75:) of a specific DNA sequence, known as 36:How to use a microarray for genotyping. 4581:Glass coating and surface modification 4558: 3131: 1667:and measuring the fluorescence with a 1309: 95:or other DNA element that are used to 3998: 3552: 3526: 2564:Shalon D; Smith SJ; Brown PO (1996). 1543:The relation between a probe and the 1472:, covariance matrix self-adaptation, 1303: 1216:, salmon sperm DNA, calf thymus DNA, 1094:The labeled product is generated via 1028:of interest is purified: this can be 984: 673:Two-channel vs. one-channel detection 556:are becoming increasingly popular in 347:Chromatin immunoprecipitation on Chip 91:). These can be a short section of a 2646:Shafee, Thomas; Lowe, Rohan (2017). 1841: 1788:Significance analysis of microarrays 1287: 1261:synthesized short oligonucleotides). 999:measurement of fluorescent intensity 594:A DNA microarray being printed by a 3977: 3080: 1835: 1555: 1044:, or DNA/RNA bound to a particular 235:), or detect RNA (most commonly as 13: 3087:Wei C; Li J; Bumgarner RE (2004). 2839:Proceedings of the Royal Society A 2829:Little, M.A.; Jones, N.S. (2011). 1746:Serial analysis of gene expression 1447: 1389:scientist reviews microarray data. 1334: 1291: 533:Double-stranded Z-DNA microarrays 524:Double-stranded B-DNA microarrays 14: 4612: 3821:Post-transcriptional modification 3518:DNA microarray virtual experiment 3414: 1691:Glossary of gene expression terms 299:Comparative genomic hybridization 233:comparative genomic hybridization 175: 3976: 3965: 3964: 3497:Rundown of microarray technology 3187:10.1111/j.0006-341X.2003.00130.x 2110:Expert Opinion on Drug Discovery 1724: 1710: 1377: 447:mutations in cancers, assessing 4535:Radioactive waste vitrification 4490:Glass fiber reinforced concrete 3826:Post-translational modification 3250: 3209: 3156: 3020: 2968: 2917: 2908: 2822: 2805:"Prosigna | Prosigna algorithm" 2797: 2786: 2721: 2680: 2639: 2360:Lausted C; et al. (2004). 2353: 2344: 1548:gene may be relying on genomic 1299: 1149:(aminoallyl-UTP, or aaUTP) and 744:with their Dual-Mode platform, 681:Diagram of typical dual-colour 3508:Microarray – How does it work? 2209: 2152: 1763:Microarray analysis techniques 1687:For other relevant terms see: 1395:Microarray analysis techniques 1266:Microarrays and bioinformatics 1200:solution which can consist of 931: 919: 567: 421:single nucleotide polymorphism 1: 4402:Chemically strengthened glass 3948:Post-translational regulation 3235:10.1093/bioinformatics/btg264 2998:10.1093/bioinformatics/bti410 2624:10.1093/bioinformatics/btm399 1828: 1538: 1298:transcript that it measures ( 1294:); mapping each probe to the 1153:amino-reactive dyes (such as 407:DNA adenine methyltransferase 4596:Molecular biology techniques 4235:Glass-ceramic-to-metal seals 3896:High-throughput technique (" 3440:Resources in other libraries 2177:10.1016/j.biochi.2011.04.001 1741:Transcriptomics technologies 1640:and can even be ultraviolet. 1585:has not been sequenced yet. 1368:Food and Drug Administration 1212:, a blocking agent (such as 1098:and followed by an optional 632:products that correspond to 443:mutations in individuals or 122: 7: 3774:Functional biology/medicine 1703: 1696:Protocol (natural sciences) 1588: 1474:particle swarm optimization 1255:loess and lowess regression 646:oligonucleotide microarrays 517:alternatively spliced forms 375:(PRC2:Suz12, PRC1:YY1) and 371:, H3K4me2, H3K9me3, etc.), 367:are histone modifications ( 341:and microarray technology. 10: 4617: 2943:10.1186/1471-2105-15-S2-S2 2888:Peterson, Leif E. (2013). 2313:10.1016/j.molp.2017.06.008 1398: 1392: 761:single-channel microarrays 613:on microelectrode arrays. 260:Application or technology 140: 137:Nucleic acid hybridization 134: 4455: 4387: 4319: 4266:Chemical vapor deposition 4253: 4215: 4187:Ultra low expansion glass 4077:Borophosphosilicate glass 4059: 4033: 3960: 3923: 3843: 3798: 3791: 3746: 3633: 3590: 3583: 3560: 3435:Resources in your library 2706:10.1016/j.ccr.2006.05.001 1892:10.1093/treephys/28.6.885 1508:type I and type II errors 1077:capillary electrophoresis 1042:comparative hybridization 1007:DNA microarray experiment 279:gene expression profiling 269:Gene expression profiling 143:§ A typical protocol 4505:Glass-reinforced plastic 4167:Sodium hexametaphosphate 2122:10.1517/17460441.2.3.381 1576:Alternative technologies 1329:statistical significance 1132:; only one machine uses 1017:) and untreated sample ( 1005:This is an example of a 945:{\displaystyle i(i-1)/2} 184:Two Affymetrix chips. A 47:(also commonly known as 4397:Anti-reflective coating 4271:Glass batch calculation 4152:Photochromic lens glass 3055:10.1186/1471-2105-8-111 2894:. John Wiley and Sons. 2652:WikiJournal of Medicine 2482:10.1073/pnas.91.11.5022 2379:10.1186/gb-2004-5-8-r58 1822:Whole genome sequencing 1478:ant colony optimization 1453:{\displaystyle \Gamma } 1128:The label is typically 802:two channel microarray 799:one-channel microarray 693:two-channel microarrays 389:transcription landscape 377:trithorax-group protein 3263:Nucleic Acids Research 3106:10.1186/1471-2164-5-87 2852:10.1098/rspa.2010.0671 2728:Churchill, GA (2002). 2222:Nucleic Acids Research 1856:10.1089/dna.1983.2.309 1454: 1390: 1279: 1167:thymidine triphosphate 1002: 973: 946: 902: 881: 784: 685: 628:or small fragments of 602: 600:University of Delaware 449:loss of heterozygosity 373:Polycomb-group protein 254:Applications include: 189: 172: 155:between complementary 132: 40: 4530:Prince Rupert's drops 4379:Transparent materials 4339:Gradient-index optics 4147:Phosphosilicate glass 3769:Developmental biology 3764:Computational biology 2665:10.15347/wjm/2017.002 2300:Shanghai Inst Bio Sci 1979:10.1099/mic.0.27221-0 1455: 1385: 1273: 1096:reverse transcription 992: 974: 947: 903: 882: 785: 765:one-color microarrays 689:Two-color microarrays 683:microarray experiment 680: 593: 241:reverse transcription 211:(commonly known as a 183: 170: 157:nucleotide base pairs 141:Further information: 130: 34: 4495:Glass ionomer cement 4369:Photosensitive glass 4296:Liquidus temperature 4117:Fluorosilicate glass 3943:Post-transcriptional 3486:Microarray Animation 1972:(Pt 10): 3363–3382. 1812:Phenotype microarray 1768:Microarray databases 1500:multiple comparisons 1444: 1316:expression profiling 1034:expression profiling 957: 913: 892: 871: 774: 498:alternative splicing 461:Alternative splicing 435:analysis, measuring 381:epigenetic landscape 379:(Ash1) to study the 333:in cell culture, or 307:, Jonathan Pollack, 249:expression profiling 4576:Genetics techniques 4515:Glass-to-metal seal 4437:Self-cleaning glass 4359:Optical lens design 3738:Histone methylation 2846:(2135): 3088–3114. 2473:1994PNAS...91.5022P 1602:is a collection of 1533:standard deviations 1310:Experimental design 1284:Experimental design 1222:Denhardt's solution 972:{\displaystyle i-1} 650:open reading frames 618:spotted microarrays 469:exon junction array 353:immunoprecipitating 245:expression analysis 4500:Glass microspheres 4422:Hydrogen darkening 4344:Hydrogen darkening 4092:Chalcogenide glass 4082:Borosilicate glass 3320:10.1038/nmeth.1226 3275:10.1093/nar/gkp942 3042:BMC Bioinformatics 2930:BMC Bioinformatics 2583:10.1101/gr.6.7.639 2296:Chin Soc Plant Bio 2234:10.1093/nar/gkv862 1783:Gene chip analysis 1470:genetic algorithms 1466:mixture of experts 1450: 1401:Gene chip analysis 1391: 1280: 1083:or NanoPhotometer 1050:immunoprecipitated 1003: 985:A typical protocol 969: 942: 898: 877: 796:number of samples 780: 686: 603: 581:synthesised arrays 558:molecular breeding 311:and colleagues at 190: 173: 133: 41: 4553: 4552: 4470:Glass-coated wire 4442:sol–gel technique 4427:Insulated glazing 4364:Photochromic lens 4349:Optical amplifier 4301:sol–gel technique 3992: 3991: 3971:Molecular biology 3956: 3955: 3910:Mass spectrometry 3787: 3786: 3554:Molecular biology 3421:Library resources 3228:(15): 1945–1951. 3149:978-3-527-31822-3 2992:(11): 2657–2666. 2901:978-0-470-17081-6 2617:(20): 2686–2691. 2533:10.1101/gr.362402 2527:(11): 1749–1755. 2467:(11): 5022–5026. 2228:(18): 8627–8637. 2074:10.2217/pgs.09.27 1732:Technology portal 1496:Mann–Whitney test 982: 981: 901:{\displaystyle i} 880:{\displaystyle i} 783:{\displaystyle i} 666:photolithographic 636:. The probes are 620:, the probes are 591: 550: 549: 385:RNA polymerase II 365:immunoprecipitate 113:chemiluminescence 32: 4608: 4291:Ion implantation 4046:Glass transition 4019: 4012: 4005: 3996: 3995: 3980: 3979: 3968: 3967: 3901: 3796: 3795: 3649: 3644: 3588: 3587: 3547: 3540: 3533: 3524: 3523: 3408: 3407: 3397: 3357: 3348: 3347: 3303: 3297: 3296: 3286: 3254: 3248: 3247: 3237: 3213: 3207: 3206: 3180: 3171:(4): 1131–1139. 3160: 3154: 3153: 3135: 3129: 3128: 3118: 3108: 3084: 3078: 3077: 3067: 3057: 3033: 3027: 3024: 3018: 3017: 2981: 2975: 2972: 2966: 2965: 2955: 2945: 2921: 2915: 2912: 2906: 2905: 2885: 2874: 2873: 2863: 2835: 2826: 2820: 2819: 2817: 2815: 2801: 2795: 2790: 2784: 2783: 2781: 2779: 2773: 2767:. Archived from 2734: 2725: 2719: 2718: 2708: 2684: 2678: 2677: 2667: 2643: 2637: 2636: 2626: 2602: 2596: 2595: 2585: 2561: 2555: 2554: 2544: 2511: 2505: 2504: 2494: 2484: 2452: 2446: 2445: 2426:10.1038/nmeth754 2408: 2402: 2401: 2391: 2381: 2357: 2351: 2348: 2342: 2341: 2315: 2279: 2270: 2264: 2263: 2253: 2213: 2207: 2206: 2196: 2171:(8): 1197–1208. 2156: 2150: 2149: 2105: 2094: 2093: 2062:Pharmacogenomics 2057: 2046: 2045: 2008: 2002: 2001: 1991: 1981: 1957: 1951: 1950: 1910: 1904: 1903: 1874: 1868: 1867: 1839: 1779:with microarrays 1734: 1729: 1728: 1720: 1715: 1714: 1556:Data warehousing 1510:in the analyses. 1504:cluster analysis 1459: 1457: 1456: 1451: 1341:interoperability 1304:Data warehousing 978: 976: 975: 970: 951: 949: 948: 943: 938: 907: 905: 904: 899: 886: 884: 883: 878: 793: 792: 789: 787: 786: 781: 622:oligonucleotides 611:electrochemistry 607:photolithography 592: 257: 256: 117:Patrick O. Brown 33: 4616: 4615: 4611: 4610: 4609: 4607: 4606: 4605: 4591:Microtechnology 4566:Gene expression 4556: 4555: 4554: 4549: 4485:Glass electrode 4480:Glass databases 4457: 4451: 4389: 4383: 4315: 4249: 4225:Bioactive glass 4211: 4197:Vitreous enamel 4182:Thoriated glass 4177:Tellurite glass 4162:Soda–lime glass 4132:Gold ruby glass 4102:Cranberry glass 4055: 4029: 4023: 3993: 3988: 3952: 3925:Gene regulation 3919: 3895: 3856:Model organisms 3839: 3816:Cell signalling 3783: 3742: 3647: 3642: 3629: 3600:DNA replication 3579: 3556: 3551: 3502:ArrayMining.net 3450:Gene Expression 3446: 3445: 3444: 3429: 3428: 3426:DNA microarrays 3424: 3417: 3412: 3411: 3378:10.1038/nrg2484 3358: 3351: 3304: 3300: 3255: 3251: 3214: 3210: 3178:10.1.1.730.3670 3161: 3157: 3150: 3136: 3132: 3085: 3081: 3034: 3030: 3025: 3021: 2982: 2978: 2973: 2969: 2936:(Suppl 2): S2. 2922: 2918: 2913: 2909: 2902: 2886: 2877: 2833: 2827: 2823: 2813: 2811: 2803: 2802: 2798: 2791: 2787: 2777: 2775: 2771: 2737:Nature Genetics 2732: 2726: 2722: 2685: 2681: 2644: 2640: 2603: 2599: 2562: 2558: 2512: 2508: 2453: 2449: 2409: 2405: 2358: 2354: 2349: 2345: 2283:Molecular Plant 2277: 2271: 2267: 2214: 2210: 2157: 2153: 2106: 2097: 2058: 2049: 2009: 2005: 1958: 1954: 1911: 1907: 1875: 1871: 1840: 1836: 1831: 1826: 1817:Systems biology 1730: 1723: 1716: 1709: 1706: 1672:photomultiplier 1669:filter (optics) 1591: 1578: 1558: 1541: 1493:Bayesian method 1445: 1442: 1441: 1403: 1397: 1380: 1337: 1335:Standardization 1312: 1288:Standardization 1268: 1210:dextran sulfate 987: 958: 955: 954: 934: 914: 911: 910: 893: 890: 889: 872: 869: 868: 775: 772: 771: 675: 585: 583: 570: 453:genetic linkage 401:Analogously to 281:experiment the 178: 145: 139: 125: 111:-, silver-, or 59:to measure the 21: 17: 12: 11: 5: 4614: 4604: 4603: 4598: 4593: 4588: 4583: 4578: 4573: 4571:Bioinformatics 4568: 4551: 4550: 4548: 4547: 4542: 4537: 4532: 4527: 4522: 4517: 4512: 4507: 4502: 4497: 4492: 4487: 4482: 4477: 4472: 4467: 4461: 4459: 4453: 4452: 4450: 4449: 4447:Tempered glass 4444: 4439: 4434: 4429: 4424: 4419: 4417:DNA microarray 4414: 4412:Dealkalization 4409: 4404: 4399: 4393: 4391: 4385: 4384: 4382: 4381: 4376: 4371: 4366: 4361: 4356: 4351: 4346: 4341: 4336: 4331: 4325: 4323: 4317: 4316: 4314: 4313: 4308: 4303: 4298: 4293: 4288: 4286:Glass modeling 4283: 4278: 4273: 4268: 4263: 4257: 4255: 4251: 4250: 4248: 4247: 4242: 4237: 4232: 4227: 4221: 4219: 4217:Glass-ceramics 4213: 4212: 4210: 4209: 4204: 4199: 4194: 4189: 4184: 4179: 4174: 4169: 4164: 4159: 4157:Silicate glass 4154: 4149: 4144: 4139: 4134: 4129: 4124: 4119: 4114: 4109: 4104: 4099: 4094: 4089: 4084: 4079: 4074: 4069: 4063: 4061: 4057: 4056: 4054: 4053: 4048: 4043: 4037: 4035: 4031: 4030: 4028:science topics 4022: 4021: 4014: 4007: 3999: 3990: 3989: 3987: 3986: 3974: 3961: 3958: 3957: 3954: 3953: 3951: 3950: 3945: 3940: 3935: 3929: 3927: 3921: 3920: 3918: 3917: 3912: 3907: 3905:DNA microarray 3902: 3892: 3891: 3878: 3877: 3876: 3871: 3863: 3853: 3847: 3845: 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1047–1064. 2265: 2208: 2151: 2116:(3): 381–401. 2095: 2068:(5): 895–914. 2047: 2020:(2): 164–167. 2003: 1952: 1905: 1886:(6): 885–897. 1869: 1850:(4): 309–327. 1833: 1832: 1830: 1827: 1825: 1824: 1819: 1814: 1809: 1804: 1795: 1790: 1785: 1780: 1770: 1765: 1760: 1755: 1754: 1753: 1748: 1737: 1736: 1735: 1721: 1718:Biology portal 1705: 1702: 1701: 1700: 1699: 1698: 1693: 1685: 1675: 1658: 1641: 1625: 1619: 1609: 1590: 1587: 1577: 1574: 1557: 1554: 1540: 1537: 1524: 1523: 1515: 1511: 1481: 1461: 1449: 1437: 1434:step detection 1422: 1393:Main article: 1379: 1376: 1345:bioinformatics 1336: 1333: 1311: 1308: 1267: 1264: 1263: 1262: 1242: 1239: 1236: 1233: 1229: 1194: 1193: 1192: 1191: 1190: 1137: 1126: 1092: 1073: 1022: 986: 983: 980: 979: 968: 965: 962: 952: 941: 937: 933: 930: 927: 924: 921: 918: 908: 897: 887: 876: 865: 864: 861: 858: 855: 851: 850: 847: 844: 841: 837: 836: 833: 830: 827: 823: 822: 819: 816: 813: 809: 808: 803: 800: 797: 779: 695:are typically 674: 671: 582: 575: 569: 566: 548: 547: 543: 539: 538: 534: 530: 529: 525: 521: 520: 508: 502: 501: 490: 483: 482: 464: 457: 456: 437:predisposition 417: 411: 410: 399: 393: 392: 355:that protein ( 349: 343: 342: 321: 317: 316: 301: 295: 294: 271: 265: 264: 261: 229: 228: 224: 177: 176:Uses and types 174: 153:hydrogen bonds 135:Main article: 124: 121: 45:DNA microarray 15: 9: 6: 4: 3: 2: 4613: 4602: 4599: 4597: 4594: 4592: 4589: 4587: 4584: 4582: 4579: 4577: 4574: 4572: 4569: 4567: 4564: 4563: 4561: 4546: 4543: 4541: 4538: 4536: 4533: 4531: 4528: 4526: 4523: 4521: 4518: 4516: 4513: 4511: 4508: 4506: 4503: 4501: 4498: 4496: 4493: 4491: 4488: 4486: 4483: 4481: 4478: 4476: 4473: 4471: 4468: 4466: 4463: 4462: 4460: 4454: 4448: 4445: 4443: 4440: 4438: 4435: 4433: 4430: 4428: 4425: 4423: 4420: 4418: 4415: 4413: 4410: 4408: 4405: 4403: 4400: 4398: 4395: 4394: 4392: 4386: 4380: 4377: 4375: 4372: 4370: 4367: 4365: 4362: 4360: 4357: 4355: 4354:Optical fiber 4352: 4350: 4347: 4345: 4342: 4340: 4337: 4335: 4332: 4330: 4327: 4326: 4324: 4322: 4318: 4312: 4311:Vitrification 4309: 4307: 4304: 4302: 4299: 4297: 4294: 4292: 4289: 4287: 4284: 4282: 4281:Glass melting 4279: 4277: 4276:Glass forming 4274: 4272: 4269: 4267: 4264: 4262: 4259: 4258: 4256: 4252: 4246: 4243: 4241: 4238: 4236: 4233: 4231: 4228: 4226: 4223: 4222: 4220: 4218: 4214: 4208: 4205: 4203: 4200: 4198: 4195: 4193: 4192:Uranium glass 4190: 4188: 4185: 4183: 4180: 4178: 4175: 4173: 4172:Soluble glass 4170: 4168: 4165: 4163: 4160: 4158: 4155: 4153: 4150: 4148: 4145: 4143: 4140: 4138: 4135: 4133: 4130: 4128: 4125: 4123: 4120: 4118: 4115: 4113: 4110: 4108: 4105: 4103: 4100: 4098: 4095: 4093: 4090: 4088: 4087:Ceramic glaze 4085: 4083: 4080: 4078: 4075: 4073: 4070: 4068: 4065: 4064: 4062: 4058: 4052: 4049: 4047: 4044: 4042: 4039: 4038: 4036: 4032: 4027: 4020: 4015: 4013: 4008: 4006: 4001: 4000: 3997: 3985: 3984: 3975: 3973: 3972: 3963: 3962: 3959: 3949: 3946: 3944: 3941: 3939: 3936: 3934: 3931: 3930: 3928: 3926: 3922: 3916: 3915:Lab-on-a-chip 3913: 3911: 3908: 3906: 3903: 3899: 3894: 3893: 3890: 3889:Radioactivity 3886: 3882: 3879: 3875: 3872: 3870: 3867: 3866: 3864: 3861: 3857: 3854: 3852: 3849: 3848: 3846: 3842: 3836: 3832: 3829: 3827: 3824: 3822: 3819: 3817: 3814: 3812: 3809: 3807: 3806:Cultured meat 3804: 3803: 3801: 3797: 3794: 3790: 3780: 3777: 3775: 3772: 3770: 3767: 3765: 3762: 3760: 3757: 3755: 3752: 3751: 3749: 3745: 3739: 3736: 3734: 3731: 3727: 3726:trp repressor 3724: 3722: 3721:lac repressor 3719: 3718: 3717: 3714: 3712: 3709: 3707: 3704: 3702: 3699: 3697: 3694: 3690: 3687: 3685: 3682: 3680: 3677: 3676: 3675: 3672: 3668: 3665: 3663: 3660: 3659: 3658: 3655: 3654: 3646: 3641: 3640: 3639: 3638: 3636: 3632: 3625: 3621: 3618: 3615: 3611: 3610:Transcription 3608: 3605: 3601: 3598: 3597: 3595: 3593: 3592:Central dogma 3589: 3586: 3582: 3576: 3573: 3571: 3568: 3566: 3563: 3562: 3559: 3555: 3548: 3543: 3541: 3536: 3534: 3529: 3528: 3525: 3519: 3516: 3514: 3511: 3509: 3506: 3503: 3500: 3498: 3495: 3493: 3490: 3487: 3484: 3482: 3478: 3475: 3473: 3469: 3466: 3464: 3460: 3457: 3455: 3451: 3448: 3447: 3441: 3438: 3436: 3433: 3432: 3427: 3422: 3405: 3401: 3396: 3391: 3387: 3383: 3379: 3375: 3371: 3367: 3366:Nat Rev Genet 3363: 3356: 3354: 3345: 3341: 3337: 3333: 3329: 3325: 3321: 3317: 3313: 3309: 3302: 3294: 3290: 3285: 3280: 3276: 3272: 3268: 3264: 3260: 3253: 3245: 3241: 3236: 3231: 3227: 3223: 3219: 3212: 3204: 3200: 3196: 3192: 3188: 3184: 3179: 3174: 3170: 3166: 3159: 3151: 3145: 3142:. Wiley-VCH. 3141: 3134: 3126: 3122: 3117: 3112: 3107: 3102: 3098: 3094: 3090: 3083: 3075: 3071: 3066: 3061: 3056: 3051: 3047: 3043: 3039: 3032: 3023: 3015: 3011: 3007: 3003: 2999: 2995: 2991: 2987: 2980: 2971: 2963: 2959: 2954: 2949: 2944: 2939: 2935: 2931: 2927: 2920: 2911: 2903: 2897: 2893: 2892: 2884: 2882: 2880: 2871: 2867: 2862: 2857: 2853: 2849: 2845: 2841: 2840: 2832: 2825: 2810: 2806: 2800: 2794: 2789: 2774:on 8 May 2005 2770: 2766: 2762: 2758: 2754: 2750: 2746: 2742: 2738: 2731: 2724: 2716: 2712: 2707: 2702: 2698: 2694: 2690: 2683: 2675: 2671: 2666: 2661: 2657: 2653: 2649: 2642: 2634: 2630: 2625: 2620: 2616: 2612: 2608: 2601: 2593: 2589: 2584: 2579: 2575: 2571: 2567: 2560: 2552: 2548: 2543: 2538: 2534: 2530: 2526: 2522: 2518: 2510: 2502: 2498: 2493: 2488: 2483: 2478: 2474: 2470: 2466: 2462: 2458: 2451: 2443: 2439: 2435: 2431: 2427: 2423: 2419: 2415: 2407: 2399: 2395: 2390: 2385: 2380: 2375: 2371: 2367: 2363: 2356: 2347: 2339: 2335: 2331: 2327: 2323: 2319: 2314: 2309: 2305: 2301: 2297: 2293: 2292:Chin Acad Sci 2289: 2285: 2284: 2276: 2269: 2261: 2257: 2252: 2247: 2243: 2239: 2235: 2231: 2227: 2223: 2219: 2212: 2204: 2200: 2195: 2190: 2186: 2182: 2178: 2174: 2170: 2166: 2162: 2155: 2147: 2143: 2139: 2135: 2131: 2127: 2123: 2119: 2115: 2111: 2104: 2102: 2100: 2091: 2087: 2083: 2079: 2075: 2071: 2067: 2063: 2056: 2054: 2052: 2043: 2039: 2035: 2031: 2027: 2023: 2019: 2015: 2007: 1999: 1995: 1990: 1985: 1980: 1975: 1971: 1967: 1963: 1956: 1948: 1944: 1940: 1936: 1932: 1931:10.1038/12640 1928: 1924: 1920: 1916: 1909: 1901: 1897: 1893: 1889: 1885: 1881: 1873: 1865: 1861: 1857: 1853: 1849: 1845: 1838: 1834: 1823: 1820: 1818: 1815: 1813: 1810: 1808: 1807:Pathogenomics 1805: 1803: 1799: 1798:Microfluidics 1796: 1794: 1791: 1789: 1786: 1784: 1781: 1778: 1774: 1771: 1769: 1766: 1764: 1761: 1759: 1756: 1752: 1749: 1747: 1744: 1743: 1742: 1739: 1738: 1733: 1727: 1722: 1719: 1713: 1708: 1697: 1694: 1692: 1689: 1688: 1686: 1683: 1679: 1676: 1673: 1670: 1666: 1662: 1659: 1656: 1654: 1649: 1645: 1642: 1639: 1635: 1631: 1630: 1626: 1623: 1620: 1617: 1613: 1610: 1607: 1606: 1601: 1597: 1593: 1592: 1586: 1583: 1573: 1571: 1567: 1563: 1553: 1551: 1546: 1536: 1534: 1530: 1521: 1516: 1512: 1509: 1505: 1501: 1497: 1494: 1490: 1486: 1482: 1479: 1475: 1471: 1467: 1462: 1438: 1435: 1431: 1427: 1423: 1420: 1416: 1415: 1414: 1412: 1411:normalization 1408: 1402: 1396: 1388: 1384: 1378:Data analysis 1375: 1373: 1369: 1364: 1360: 1355: 1353: 1350: 1346: 1342: 1332: 1330: 1325: 1319: 1317: 1307: 1305: 1301: 1297: 1293: 1292:Data analysis 1289: 1285: 1277: 1272: 1260: 1256: 1252: 1248: 1243: 1240: 1237: 1234: 1230: 1227: 1223: 1220:, or PolyT), 1219: 1215: 1211: 1207: 1203: 1199: 1198:hybridization 1195: 1188: 1183: 1179: 1178: 1176: 1172: 1168: 1164: 1160: 1156: 1152: 1148: 1145: 1142: 1138: 1135: 1131: 1127: 1124: 1120: 1116: 1115: 1113: 1109: 1105: 1101: 1097: 1093: 1090: 1086: 1082: 1078: 1074: 1071: 1067: 1063: 1059: 1055: 1051: 1047: 1043: 1039: 1035: 1031: 1027: 1023: 1020: 1016: 1012: 1011: 1010: 1008: 1000: 995: 991: 966: 963: 960: 953: 939: 935: 928: 925: 922: 916: 909: 895: 888: 874: 867: 866: 862: 859: 856: 853: 852: 848: 845: 842: 839: 838: 834: 831: 828: 825: 824: 820: 817: 814: 811: 810: 807: 804: 801: 798: 795: 794: 791: 777: 768: 766: 762: 757: 755: 751: 747: 743: 739: 738:data analysis 734: 730: 729:RNA spike-ins 725: 723: 719: 714: 710: 706: 702: 698: 694: 690: 684: 679: 670: 667: 663: 659: 655: 651: 647: 642: 639: 635: 631: 627: 623: 619: 614: 612: 608: 601: 597: 580: 574: 565: 563: 559: 555: 544: 541: 540: 535: 532: 531: 526: 523: 522: 518: 514: 509: 507: 504: 503: 499: 495: 491: 488: 485: 484: 480: 475: 471: 470: 465: 462: 459: 458: 454: 450: 446: 442: 438: 434: 430: 426: 422: 418: 416: 415:SNP detection 413: 412: 408: 404: 400: 398: 395: 394: 390: 387:to study the 386: 382: 378: 374: 370: 366: 362: 358: 354: 350: 348: 345: 344: 340: 336: 332: 328: 326: 322: 319: 318: 314: 310: 306: 305:Patrick Brown 302: 300: 297: 296: 292: 288: 284: 280: 276: 272: 270: 267: 266: 262: 259: 258: 255: 252: 250: 246: 242: 238: 234: 225: 222: 218: 214: 210: 207: 203: 199: 195: 194: 193: 187: 182: 169: 165: 162: 158: 154: 150: 149:complementary 144: 138: 129: 120: 118: 114: 110: 106: 102: 98: 94: 90: 89: 84: 80: 79: 74: 70: 66: 62: 58: 54: 50: 46: 37: 19: 4520:Porous glass 4475:Safety glass 4432:Porous glass 4416: 4390:modification 4202:Wood's glass 4122:Fused quartz 4097:Cobalt glass 4051:Supercooling 3981: 3969: 3904: 3881:Fluorescence 3869:Nucleic acid 3860:C57BL/6 mice 3851:Cell culture 3759:Biochemistry 3754:Cell biology 3425: 3372:(1): 57–63. 3369: 3365: 3311: 3307: 3301: 3266: 3262: 3252: 3225: 3221: 3211: 3168: 3164: 3158: 3139: 3133: 3096: 3093:BMC Genomics 3092: 3082: 3045: 3041: 3031: 3022: 2989: 2985: 2979: 2970: 2933: 2929: 2919: 2910: 2890: 2843: 2837: 2824: 2812:. Retrieved 2809:prosigna.com 2808: 2799: 2788: 2776:. Retrieved 2769:the original 2740: 2736: 2723: 2696: 2692: 2682: 2655: 2651: 2641: 2614: 2610: 2600: 2573: 2569: 2559: 2524: 2520: 2509: 2464: 2460: 2450: 2417: 2413: 2406: 2369: 2365: 2355: 2346: 2287: 2281: 2268: 2225: 2221: 2211: 2168: 2164: 2154: 2113: 2109: 2065: 2061: 2026:10.1038/9674 2017: 2013: 2006: 1969: 1966:Microbiology 1965: 1955: 1925:(1): 41–46. 1922: 1918: 1908: 1883: 1880:Tree Physiol 1879: 1872: 1847: 1843: 1837: 1777:fluorophores 1681: 1677: 1660: 1651: 1647: 1643: 1634:fluorescence 1627: 1622:Case/control 1621: 1615: 1611: 1603: 1599: 1595: 1579: 1559: 1542: 1525: 1418: 1404: 1372:MGED Society 1356: 1338: 1320: 1313: 1281: 1258: 1163:streptavidin 1161:and labeled 1155:cyanine dyes 1147:triphosphate 1085:spectrometer 1054:ChIP-on-chip 1026:nucleic acid 1006: 1004: 993: 805: 769: 764: 760: 758: 726: 701:fluorophores 692: 688: 687: 654:synthesizing 645: 643: 617: 615: 604: 578: 577:Spotted vs. 571: 551: 506:Tiling array 493: 487:Fusion genes 467: 419:Identifying 361:tiling array 309:Ash Alizadeh 253: 230: 220: 216: 212: 191: 161:non-covalent 146: 104: 86: 82: 76: 44: 42: 35: 18: 4601:Microarrays 4545:Glass fiber 4510:Glass cloth 4254:Preparation 4230:CorningWare 4112:Flint glass 4107:Crown glass 4060:Formulation 3983:WikiProject 3792:Engineering 3747:Linked life 3662:Pribnow box 3620:Translation 3308:Nat Methods 2778:12 December 2693:Cancer Cell 2414:Nat Methods 1802:lab-on-chip 1638:fluorophore 1436:algorithms. 1407:Statistical 1352:open-source 1349:grass-roots 1343:problem in 1134:radiolabels 1130:fluorescent 1062:cytoplasmic 750:Silverquant 705:Fluorescent 638:synthesized 568:Fabrication 513:transcripts 489:microarray 479:Exon arrays 213:genome chip 109:fluorophore 57:microarrays 4560:Categories 4540:Windshield 4374:Refraction 4334:Dispersion 4142:Milk glass 4137:Lead glass 3933:Epigenetic 3844:Techniques 3706:Terminator 3689:trp operon 3684:lac operon 3679:gal operon 3269:(3): e17. 3165:Biometrics 3048:(1): 111. 2570:Genome Res 2521:Genome Res 2372:(8): R58. 1829:References 1539:Annotation 1529:replicates 1460:statistic. 1399:See also: 1347:. Various 1300:Annotation 1187:aminoallyl 1141:aminoallyl 1058:epigenetic 718:excitation 697:hybridized 662:Affymetrix 463:detection 455:analysis. 429:genotyping 331:mycoplasms 283:expression 221:gene array 61:expression 4407:Corrosion 4306:Viscosity 4261:Annealing 3858:(such as 3716:Repressor 3386:1471-0056 3344:205418589 3328:1548-7091 3173:CiteSeerX 3006:1367-4803 2743:: 490–5. 2715:1535-6108 2674:2002-4436 2442:195368323 2322:1674-2052 2242:1362-4962 2185:1638-6183 2165:Biochimie 2130:1746-0441 2082:1744-8042 2014:Nat Genet 1989:2262/6097 1919:Nat Genet 1566:InterMine 1448:Γ 1276:heat maps 1232:pinholes. 1226:formamine 1214:Cot-1 DNA 1182:artifacts 1048:which is 964:− 926:− 746:Eppendorf 733:normalize 562:seedlings 335:pathogens 291:pathogens 263:Synopsis 227:sequence. 123:Principle 97:hybridize 83:reporters 69:picomoles 4525:Pre-preg 4329:Achromat 4072:Bioglass 4067:AgInSbTe 3865:Methods 3799:Concepts 3779:Genetics 3733:Silencer 3711:Enhancer 3667:TATA box 3657:Promoter 3648:Heredity 3584:Overview 3575:Glossary 3488:1Lec.com 3404:19015660 3336:18516045 3293:19923232 3244:14555628 3203:16248921 3195:14969494 3125:15533245 3074:17397530 3014:15797905 2962:24564555 2870:22003312 2765:15412245 2757:12454643 2633:17698492 2551:12421762 2434:15846362 2398:15287980 2338:33780984 2330:28669791 2304:Elsevier 2260:26350216 2203:21501652 2146:41959328 2138:23484648 2090:19450135 2042:41718227 2034:10369258 1998:15470115 1939:10471496 1900:18381269 1758:MAGIChip 1704:See also 1655:reversal 1648:dye swap 1644:Dye flip 1616:subarray 1605:features 1589:Glossary 1419:flagging 1363:journals 1324:aliquots 1081:NanoDrop 573:probes. 441:germline 433:forensic 369:H3K27me3 313:Stanford 287:diseases 217:DNA chip 65:genotype 51:chip or 39:markers. 4456:Diverse 4388:Surface 4245:Zerodur 3938:Genetic 3885:Pigment 3874:Protein 3835:Wet lab 3831:Dry lab 3811:Mitosis 3643:Genetic 3634:Element 3624:protein 3565:History 3395:2949280 3284:2817484 3065:1858704 2953:4072854 2861:3191861 2814:22 June 2592:8796352 2501:8197176 2469:Bibcode 2251:4605312 2194:3545518 1864:6198132 1773:Cyanine 1751:RNA-Seq 1682:feature 1674:system. 1661:Scanner 1629:Channel 1582:RNA-Seq 1570:BioMart 1426:MA plot 1259:in situ 1251:z-ratio 1247:t-value 1144:uridine 1046:protein 1019:control 754:Arrayit 742:Agilent 720:with a 658:Agilent 598:at the 579:in situ 445:somatic 425:alleles 320:GeneID 209:biochip 206:silicon 202:plastic 53:biochip 4458:topics 4321:Optics 4127:GeSbTe 4034:Basics 3898:-omics 3887:& 3696:Intron 3674:Operon 3481:Curlie 3472:Curlie 3463:Curlie 3454:Curlie 3423:about 3402: 3392: 3384: 3342: 3334: 3326: 3291: 3281: 3242: 3201: 3193: 3175: 3146: 3123: 3116:533874 3113: 3099:: 87. 3072: 3062: 3012: 3004: 2960: 2950: 2898: 2868: 2858: 2763: 2755: 2713: 2672: 2631: 2590: 2549: 2542:187555 2539: 2499: 2489: 2440: 2432: 2396: 2389:507883 2386: 2336: 2328: 2320: 2258: 2248: 2240: 2201: 2191: 2183: 2144: 2136: 2128: 2088: 2080: 2040: 2032: 1996: 1947:997032 1945: 1937: 1898: 1862: 1632:: the 1485:t-test 1476:, and 1171:column 1159:biotin 1070:Trizol 1068:(e.g. 1056:) for 423:among 273:In an 239:after 105:target 88:oligos 78:probes 4240:Macor 4207:ZBLAN 4041:Glass 4026:Glass 3570:Index 3340:S2CID 3199:S2CID 2834:(PDF) 2772:(PDF) 2761:S2CID 2733:(PDF) 2658:(1). 2492:43922 2438:S2CID 2334:S2CID 2290:(8). 2278:(PDF) 2142:S2CID 2038:S2CID 1943:S2CID 1665:laser 1653:fluor 1612:Block 1600:slide 1596:array 1562:MIAME 1489:ANOVA 1430:local 1359:MIAME 1224:, or 1218:PolyA 1119:sense 1112:miRNA 1064:) by 722:laser 634:mRNAs 596:robot 554:crops 474:exons 451:, or 397:DamID 198:glass 186:match 73:moles 3701:Exon 3400:PMID 3382:ISSN 3332:PMID 3324:ISSN 3289:PMID 3240:PMID 3191:PMID 3144:ISBN 3121:PMID 3070:PMID 3010:PMID 3002:ISSN 2958:PMID 2896:ISBN 2866:PMID 2816:2017 2780:2013 2753:PMID 2711:ISSN 2670:ISSN 2629:PMID 2588:PMID 2547:PMID 2497:PMID 2461:PNAS 2430:PMID 2394:PMID 2326:PMID 2318:ISSN 2256:PMID 2238:ISSN 2199:PMID 2181:ISSN 2134:PMID 2126:ISSN 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