DNA microarray

A DNA microarray (also commonly known as DNA chip or

biochip) is a collection of microscopic DNA spots attached to a
solid surface. Scientists use DNA microarrays to measure the
expression levels of large numbers of genes simultaneously or to
genotype multiple regions of a genome. Each DNA spot contains
picomoles (10−12 moles) of a specific DNA sequence, known as
probes (or reporters or oligos). These can be a short section of a
gene or other DNA element that are used to hybridize a cDNA or
cRNA (also called anti-sense RNA) sample (called target) under How to use a microarray for
high-stringency conditions. Probe-target hybridization is usually genotyping. The video shows the
process of extracting genotypes from
detected and quantified by detection of fluorophore-, silver-, or
a human spit sample using
chemiluminescence-labeled targets to determine relative abundance
microarrays. Genotyping is a major
of nucleic acid sequences in the target. The original nucleic acid use of DNA microarrays, but with
arrays were macro arrays approximately 9 cm × 12 cm and the first some modifications they can also be
computerized image based analysis was published in 1981.[1] It was used for other purposes such as
invented by Patrick O. Brown. An example of its application is in measurement of gene expression
SNPs arrays for polymorphisms in cardiovascular diseases, cancer, and epigenetic markers.

pathogens and GWAS analysis. It is also used for the identification

of structural variations and the measurement of gene expression.

Principle
The core principle behind microarrays is hybridization between two
DNA strands, the property of complementary nucleic acid
sequences to specifically pair with each other by forming hydrogen
bonds between complementary nucleotide base pairs. A high
number of complementary base pairs in a nucleotide sequence
means tighter non-covalent bonding between the two strands. After
washing off non-specific bonding sequences, only strongly paired
strands will remain hybridized. Fluorescently labeled target Hybridization of the target to the
probe
sequences that bind to a probe sequence generate a signal that
depends on the hybridization conditions (such as temperature), and
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.

Uses and types

Many types of arrays exist and the broadest distinction is whether they are spatially arranged on a surface or
on coded beads:
 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 glass, plastic or silicon biochip The steps required in a microarray
(commonly known as a genome chip, DNA chip or gene experiment
array). Thousands of these features can be placed in
known locations on a single DNA microarray.
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 sequence.
DNA microarrays can be used to detect DNA (as in comparative genomic
hybridization), or detect RNA (most commonly as cDNA after reverse
transcription) that may or may not be translated into proteins. The process of
measuring gene expression via cDNA is called expression analysis or Two Affymetrix chips. A
expression profiling. match is shown at
bottom left for size
Applications include: comparison.
Application or technology Synopsis

In an mRNA or gene expression profiling experiment the expression levels of

thousands of genes are simultaneously monitored to study the effects of certain
treatments, diseases, and developmental stages on gene expression. For
Gene expression profiling example, microarray-based gene expression profiling can be used to identify
genes whose expression is changed in response to pathogens or other organisms
by comparing gene expression in infected to that in uninfected cells or tissues.[2]
Assessing genome content in different cells or closely related organisms, as
Comparative genomic originally described by Patrick Brown, Jonathan Pollack, Ash Alizadeh and
hybridization
colleagues at Stanford.[3][4]
Small microarrays to check IDs of organisms in food and feed (like GMO [1] (http
s://web.archive.org/web/20090228210111/http://bgmo.jrc.ec.europa.eu/home/docs.
GeneID
htm)), mycoplasms in cell culture, or pathogens for disease detection, mostly
combining PCR and microarray technology.

DNA sequences bound to a particular protein can be isolated by

immunoprecipitating that protein (ChIP), these fragments can be then hybridized to
a microarray (such as a tiling array) allowing the determination of protein binding
Chromatin
site occupancy throughout the genome. Example protein to immunoprecipitate are
immunoprecipitation on Chip
histone modifications (H3K27me3, H3K4me2, H3K9me3, etc.), Polycomb-group
protein (PRC2:Suz12, PRC1:YY1) and trithorax-group protein (Ash1) to study the
epigenetic landscape or RNA Polymerase II to study the transcription landscape.
Analogously to ChIP, 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
DamID
methylation near the protein's binding sites to selectively amplify those regions,
introduced by expressing minute amounts of protein of interest fused to bacterial
DNA adenine methyltransferase.

Identifying single nucleotide polymorphism among alleles within or between

populations.[5] Several applications of microarrays make use of SNP detection,
SNP detection including genotyping, forensic analysis, measuring predisposition to disease,
identifying drug-candidates, evaluating germline mutations in individuals or
somatic mutations in cancers, assessing loss of heterozygosity, or genetic linkage
analysis.
An exon junction array design uses probes specific to the expected or potential
splice sites of predicted exons for a gene. It is of intermediate density, or
coverage, to a typical gene expression array (with 1–3 probes per gene) and a
Alternative splicing genomic tiling array (with hundreds or thousands of probes per gene). It is used to
detection assay the expression of alternative splice forms of a gene. Exon arrays 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.

A Fusion gene microarray can detect fusion transcripts, e.g. from cancer
specimens. The principle behind this is building on the alternative splicing
Fusion genes microarray microarrays. The oligo design strategy enables combined measurements of
chimeric transcript junctions with exon-wise measurements of individual fusion
partners.

Genome tiling arrays consist of overlapping probes designed to densely represent

a genomic region of interest, sometimes as large as an entire human
Tiling array chromosome. The purpose is to empirically detect expression of transcripts or
alternatively spliced forms which may not have been previously known or
predicted.
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
Double-stranded B-DNA immobilized, intact, double-stranded DNA. This approach can be used to inhibit
microarrays
gene expression.[6][7] They also allow for characterization of their structure under
different environmental conditions.
 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
Double-stranded Z-DNA right-handed B-DNA genes (e.g., transcriptional enhancement, recombination, RNA
microarrays
editing).[6][7] The microarrays also allow for characterization of their structure under
different environmental conditions.

Multi-stranded DNA and RNA microarrays can be used to identify novel drugs that
Multi-stranded DNA bind to these multi-stranded nucleic acid sequences. This approach can be used
microarrays (triplex-DNA to discover new drugs and biologicals that have the ability to inhibit gene
microarrays and quadruplex-
DNA microarrays) expression.[6][7][8][9] These microarrays also allow for characterization of their
structure under different environmental conditions.

Specialised arrays tailored to particular crops are becoming increasingly popular in molecular breeding
applications. In the future they could be used to screen seedlings at early stages to lower the number of
unneeded seedlings tried out in breeding operations.[10]

Fabrication
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 probes.

Spotted vs. in situ synthesised arrays

Microarrays can be fabricated using a variety of technologies,
including printing with fine-pointed pins onto glass slides,
photolithography using pre-made masks, photolithography using
dynamic micromirror devices, ink-jet printing,[11][12] or
electrochemistry on microelectrode arrays.

In spotted microarrays, the probes are oligonucleotides, cDNA or

small fragments of PCR products that correspond to mRNAs. The
probes are synthesized prior to deposition on the array surface and A DNA microarray being printed by a
are then "spotted" onto glass. A common approach utilizes an array robot at the University of Delaware
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 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,[13] possibly owing to the small batch sizes and reduced printing efficiencies when compared to
industrial manufactures of oligo arrays.
In oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of
known or predicted open reading frames. 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 synthesizing this sequence directly onto the array surface
instead of depositing intact sequences. Sequences may be longer (60-mer probes such as the Agilent design)
or shorter (25-mer probes produced by Affymetrix) 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
photolithographic 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.[14] Each applicable probe is
selectively "unmasked" prior to bathing the array in a solution of a single nucleotide, then a masking
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.[15]

Two-channel vs. one-channel detection

Two-color microarrays or two-channel microarrays are typically
hybridized with cDNA prepared from two samples to be compared
(e.g. diseased tissue versus healthy tissue) and that are labeled with
two different fluorophores.[16] Fluorescent dyes commonly used for
cDNA labeling include Cy3, which has a fluorescence emission
wavelength of 570 nm (corresponding to the green part of the light
spectrum), and Cy5 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 excitation with
a laser 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.[17]

Oligonucleotide microarrays often carry control probes designed to

Diagram of typical dual-colour
hybridize with RNA spike-ins. The degree of hybridization
microarray experiment
between the spike-ins and the control probes is used to normalize
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 data analysis for the two-color system. Examples of providers for such microarrays includes
Agilent with their Dual-Mode platform, Eppendorf with their DualChip platform for colorimetric
Silverquant labeling, and TeleChem International with Arrayit.

In single-channel microarrays or one-color microarrays, 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.

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

number of one-channel two channel

two channel microarray (with
samples microarray microarray reference)

1 1 1 1

2 2 1 1

3 3 3 2
4 4 6 3

A typical protocol
This is an example of a DNA microarray experiment which includes details for a particular case to better
explain DNA microarray experiments, while listing modifications for RNA or other alternative experiments.

1. The two samples to be compared (pairwise comparison) are grown/acquired. In this example
treated sample (case) and untreated sample (control).
2. The nucleic acid of interest is purified: this can be RNA for expression profiling, DNA for
comparative hybridization, or DNA/RNA bound to a particular protein which is
immunoprecipitated (ChIP-on-chip) for epigenetic or regulation studies. In this example total
RNA is isolated (both nuclear and cytoplasmic) by Guanidinium thiocyanate-phenol-
chloroform extraction (e.g. Trizol) which isolates most RNA (whereas column methods have
a cut off of 200 nucleotides) and if done correctly has a better purity.
3. The purified RNA is analysed for quality (by capillary electrophoresis) and quantity (for
example, by using a NanoDrop or NanoPhotometer spectrometer). If the material is of
acceptable quality and sufficient quantity is present (e.g., >1μg, although the required
amount varies by microarray platform), the experiment can proceed.
4. The labeled product is generated via reverse transcription and followed by an optional PCR
amplification. The RNA is reverse transcribed with either polyT primers (which amplify only
mRNA) or random primers (which amplify all RNA, most of which is rRNA). miRNA
microarrays ligate an oligonucleotide to the purified small RNA (isolated with a fractionator),
which is then reverse transcribed and amplified.
 The label is added either during the reverse
transcription step, or following amplification if it is
performed. The sense labeling is dependent on the
microarray; e.g. if the label is added with the RT mix,
the cDNA is antisense and the microarray probe is
sense, except in the case of negative controls.
The label is typically fluorescent; only one machine
uses radiolabels.
The labeling can be direct (not used) or indirect
(requires a coupling stage). For two-channel arrays,
the coupling stage occurs before hybridization, using
Examples of levels of application of
aminoallyl uridine triphosphate (aminoallyl-UTP, or
microarrays. Within the organisms,
aaUTP) and NHS amino-reactive dyes (such as
genes are transcribed and spliced to
cyanine dyes); for single-channel arrays, the coupling
stage occurs after hybridization, using biotin and produce mature mRNA transcripts
labeled streptavidin. The modified nucleotides (red). The mRNA is extracted from
(usually in a ratio of 1 aaUTP: 4 TTP (thymidine the organism and reverse
triphosphate)) are added enzymatically in a low ratio transcriptase is used to copy the
to normal nucleotides, typically resulting in 1 every mRNA into stable ds-cDNA (blue). In
60 bases. The aaDNA is then purified with a column microarrays, the ds-cDNA is
(using a phosphate buffer solution, as Tris contains fragmented and fluorescently labelled
amine groups). The aminoallyl group is an amine (orange). The labelled fragments bind
group on a long linker attached to the nucleobase, to an ordered array of
which reacts with a reactive dye. complementary oligonucleotides, and
measurement of fluorescent intensity
A form of replicate known as a dye flip can be across the array indicates the
performed to control for dye artifacts in two- abundance of a predetermined set of
channel experiments; for a dye flip, a second
sequences. These sequences are
slide is used, with the labels swapped (the
typically specifically chosen to report
sample that was labeled with Cy3 in the first slide
on genes of interest within the
is labeled with Cy5, and vice versa). In this
example, aminoallyl-UTP is present in the organism's genome.[18]
reverse-transcribed mixture.
5. The labeled samples are then mixed with a proprietary hybridization solution which can
consist of SDS, SSC, dextran sulfate, a blocking agent (such as Cot-1 DNA, salmon sperm
DNA, calf thymus DNA, PolyA, or PolyT), Denhardt's solution, or formamine.
6. 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 pinholes.
7. After an overnight hybridization, all nonspecific binding is washed off (SDS and SSC).
8. 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.
9. The image is gridded with a template and the intensities of each feature (composed of
several pixels) is quantified.
10. 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 t-value for all of the intensities.
More sophisticated methods include z-ratio, loess and lowess regression and RMA (robust
multichip analysis) for Affymetrix chips (single-channel, silicon chip, in situ synthesized short
oligonucleotides).

Microarrays and bioinformatics

The advent of inexpensive microarray experiments created several
specific bioinformatics challenges: the multiple levels of replication
in experimental design (Experimental design); the number of
platforms and independent groups and data format
(Standardization); the statistical treatment of the data (Data
analysis); mapping each probe to the mRNA transcript that it
measures (Annotation); the sheer volume of data and the ability to
share it (Data warehousing).

Experimental design
Due to the biological complexity of gene expression, the Gene expression values from
considerations of experimental design that are discussed in the microarray experiments can be
expression profiling article are of critical importance if statistically represented as heat maps to
visualize the result of data analysis.
and biologically valid conclusions are to be drawn from the data.

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 precision. The biological replicates include independent RNA extractions. Technical
replicates may be two aliquots 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
discussed, in order to help identify the independent units in the experiment and to avoid inflated estimates of
statistical significance.[19]

Standardization
Microarray data is difficult to exchange due to the lack of standardization in platform fabrication, assay
protocols, and analysis methods. This presents an interoperability problem in bioinformatics. Various grass-
roots open-source projects are trying to ease the exchange and analysis of data produced with non-
proprietary chips:

For example, the "Minimum Information About a Microarray Experiment" (MIAME) checklist helps define
the level of detail that should exist and is being adopted by many journals 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 Control (MAQC) Project" is being
conducted by the US Food and Drug Administration (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.[20] The MGED Society has developed standards for the representation of gene
expression experiment results and relevant annotations.

Data analysis
Microarray data sets are commonly very large, and analytical
precision is influenced by a number of variables. Statistical
challenges include taking into account effects of background noise
and appropriate normalization of the data. Normalization methods
may be suited to specific platforms and, in the case of commercial
platforms, the analysis may be proprietary.[21] Algorithms that affect
statistical analysis include:
National Center for Toxicological
Image analysis: gridding, spot recognition of the scanned
image (segmentation algorithm), removal or marking of Research scientist reviews
poor-quality and low-intensity features (called flagging). microarray data

Data processing: background subtraction (based on

global or local background), determination of spot
intensities and intensity ratios, visualisation of data (e.g. see MA plot), and log-transformation
of ratios, global or local normalization of intensity ratios, and segmentation into different copy
number regions using step detection algorithms.[22]
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) 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.[23] 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,[24] 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.[25] 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,[26] Dunn's index, or Hubert's
statistic.
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[23] for class prediction 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, mixture of experts, and supervised neural gas. In addition, various metaheuristic
methods are employed, such as genetic algorithms, covariance matrix self-adaptation,
particle swarm optimization, and ant colony optimization. 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).
Hypothesis-driven statistical analysis: Identification of statistically significant changes in
gene expression are commonly identified using the t-test, ANOVA, Bayesian
method[27]Mann–Whitney test methods tailored to microarray data sets, which take into
account multiple comparisons[28] or cluster analysis.[29] These methods assess statistical
 power based on the variation present in the data and the number of experimental replicates,
and can help minimize Type I and type II errors in the analyses.[30]
Dimensional reduction: Analysts often reduce the number of dimensions (genes) prior to data
analysis.[23] 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 linear embedding, locally preserving projections, and
Sammon's mapping.
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.[31] Weighted gene co-expression network analysis 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.
Microarray data may require further processing aimed at reducing the dimensionality of the data to aid
comprehension and more focused analysis.[32] Other methods permit analysis of data consisting of a low
number of biological or technical replicates; for example, the Local Pooled Error (LPE) test pools standard
deviations of genes with similar expression levels in an effort to compensate for insufficient replication.[33]

Annotation
The relation between a probe and the mRNA that it is expected to detect is not trivial.[34] 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 gene may be relying on genomic EST information that is incorrectly
associated with that gene.

Data warehousing
Microarray data was found to be more useful when compared to other similar datasets. The sheer volume of
data, specialized formats (such as MIAME), and curation efforts associated with the datasets require
specialized databases to store the data. A number of open-source data warehousing solutions, such as
InterMine and BioMart (http://www.biomart.org/), have been created for the specific purpose of integrating
diverse biological datasets, and also support analysis.

Alternative technologies
Advances in massively parallel sequencing has led to the development of RNA-Seq technology, that
enables a whole transcriptome shotgun approach to characterize and quantify gene expression.[35][36]
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 has not been
sequenced yet.[36]

Glossary
An array or slide is a collection of features spatially arranged in a two dimensional grid,
arranged in columns and rows.
Block or subarray: a group of spots, typically made in one print round; several subarrays/
blocks form an array.
 Case/control: 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).
Channel: the fluorescence output recorded in the scanner for an individual fluorophore and
can even be ultraviolet.
Dye flip or dye swap or fluor reversal: reciprocal labelling of DNA targets with the two dyes to
account for dye bias in experiments.
Scanner: an instrument used to detect and quantify the intensity of fluorescence of spots on a
microarray slide, by selectively exciting fluorophores with a laser and measuring the
fluorescence with a filter (optics) photomultiplier system.
Spot or feature: a small area on an array slide that contains picomoles of specific DNA
samples.
For other relevant terms see:
Glossary of gene expression terms
Protocol (natural sciences)

See also
Biology portal

Technology portal

Transcriptomics technologies
Serial analysis of gene expression
RNA-Seq
MAGIChip
Microarray analysis techniques
Microarray databases
Cyanine dyes, such as Cy3 and Cy5, are commonly used fluorophores with microarrays
Gene chip analysis
Significance analysis of microarrays
Methylation specific oligonucleotide microarray
Microfluidics or lab-on-chip
Pathogenomics
Phenotype microarray
Systems biology
Whole genome sequencing

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External links
Gene Expression (https://curlie.org/Science/Biology/Biochemistry_and_Molecular_Biology/
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Online Services for Gene Expression Analysis (https://curlie.org/Science/Biology/Bioinformat
ics/Online_Services/Gene_Expression_and_Regulation) at Curlie
Microarray Animation (http://www.1lec.com/microarray/) 1Lec.com
PLoS Biology Primer: Microarray Analysis (http://www.plosbiology.org/article/info%3Adoi%2
F10.1371%2Fjournal.pbio.0000015)
Rundown of microarray technology (https://web.archive.org/web/20150924040600/http://ww
w.genome.gov/page.cfm?pageID=10000533)
ArrayMining.net (http://www.arraymining.net) – a free web-server for online microarray
analysis
Microarray – How does it work? (http://www.unsolvedmysteries.oregonstate.edu/microarray_
07)
 PNAS Commentary: Discovery of Principles of Nature from Mathematical Modeling of DNA
Microarray Data (http://www.pnas.org/content/103/44/16063.extract)
DNA microarray virtual experiment (http://learn.genetics.utah.edu/content/labs/microarray/)

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