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Research essay by Kedar Ghimire/ Jacobs University Bremen

"Microarrays”
Application and potential

Submitted by
Kedar Ghimire,
Earth

Jacobs University Bremen 9/5/2007

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

Introduction
The central dogma of biology suggests us that the genetic information flows from
DNA to RNA and finally to the translation of proteins. This theory was first proposed by
Francis Crick in 1957. The DNA gets coded to mRNA (messenger RNA) by the process
called transcription. This process is facilitated by RNA polymerase and transcription
factors. RNA structure resembles with that of DNA in many aspects except that RNA is
single stranded and the DNA is double stranded and also has uracil instead of thymine in
DNA. This mature mRNA will be transported into ribosome where it will be translated
into amino acids. A series of 3 nucleotides determines the coding one amino acid.

Eukaryotes genes contain coding regions (exons) and non-coding regions
(introns). RNA goes through a series of modifications where exons are joined. The
introns are removed by post-transcriptional modifications. This RNA formed after
removing the non coding region is now termed as the mRNA. The process from
transcription to translation can be referred to as gene expression. Epigenetics,
environmental factors, cellular developmental stages are critical parameters guiding the
gene expression pattern. One of the consequences of central dogma is that the genes
codes for proteins. In order to study the expression pattern of thousands of genes we need
a technology which is relatively convenient and can give a faster and reliable high-
throughput. Older technologies to study gene expression pattern were often tedious and
time consuming. Hence Microarrays has proven to be a revolution to molecular biologist
in studying the gene expression.

Research in molecular biology increased its scope in recent decades from the need
of monitoring expression level of few genes to thousands of genes. By the help of this
technique a gene can be monitored at its transcription level. Expression data of a mRNA
from a large pool of genes can be easily collected by the help of DNA microarrays. DNA
Microarray technology can be simply defined as a recent development that helps to know
how much mRNA corresponding to a particular cell is present. This technique is a result
of the technological advancement in the field of micro-fluidics, robotics and computer
technology. Human Genome Project (HGP), Polymerase Chain reaction (PCR) and the
base pairing rule found by Watson and Crick are some of the important groundwork
which led to the development of this gene technology. Today, we can get
thousand-fold high sensitivity in just a few minutes using modern
microarray slides, fluorescent dye probes and laser detectors. What
once used to take two days to visualize on X-ray film using radioactive
test DNA now takes only few minutes, and also is automatically saved
as a computer file. Microarray has revolutionized the field of life
science today.

Various types of microarrays are in development like protein microarray, antibody
microarray, tissue microarray but this article would focus on DNA microarray.
Complementary DNA Microarray (cDNA Microarrays) and oligonucleotide microarrays
are two common types of microarrays used for gene expression. The main difference
between these two is in their experimental design. C-DNA which can be obtained from

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

mRNA can be used as targets and upon fluorescent labeling they will be hybridized onto
the Microarray.

In order to understand the basic principle, a very simple application is provided.
Suppose we are interested in studying whether a particular cell expresses the protein
myoglobin. In order to achieve this we should isolate mRNA from the cell under
observation. This single stranded RNA can be made to bind with the DNA probes that are
in the chip surface. Finally a fluorescent dye can be used to study whether a particular
DNA in the DNA chip has hybridized with the RNA or not.

Suppose if we have following mRNA sequence available:
5' GAGCAAGCAU CCCGGGACU UUGGUGCUGA UGCCAGGGG 3'

Then the correct DNA target would be:
3’CTCGTTCGTA GGGCCCCTGA AACCACGAC ACGGGTCCCC5’

From the above mentioned sequences RNA-DNA hybrid, the following of the double
stranded hybrid is made:
5' GAGCAAGCAU CCCGGGACU UUGGUGCUGA UGCCAGGGG 3'
3’ CTCGTTCGTA GGGCCCCTGA AACCACGAC ACGGGTCCCC 5’

In this particular example, we do not see a great advantage of this DNA chip
because we are looking at only a single gene. But if we were to use older techniques for
100000 genes then we had to carry the experiment 100000 times. But if we use a DNA
chip then we can have 100000 different probes where the single stranded RNA can
hybridize with DNA probes. One good advantage of DNA chip is that we can reuse it.

Design of DNA chips
The design of DNA chips is usually divided into three different phases:

Step 1: Designing Gene Probes
A known sequence of DNA strands can be made by using Polymerase chain
reaction (PCR). This known sequence acts as a probe to be hybridized with the single
stranded RNA from the sample under investigation.

Probes can be generated by two different methods. One of the methods uses PCR
to generate cDNA probes. The other method utilizes synthetic oligonucleotide generated
by chemical methods and spotted onto the chip by using photolithography. This latter
approach is widely used by companies such as Affymetrix and Agilent Chips.

While other companies like Nanogen Inc. use their own particular techniques to
prepare probes and arrays and a lot of varieties are thus available according to the need to
research and experiment.

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

Fig 1: Photolithography used in designing Microarray
Figure adapted from: http://www.devicelink.com/ivdt/archive/98/09/009.html
Step 2: Design of Water Surface
Techniques such as photolithography can turn the rough glass surface desirable
for being able to act as a receptacle for DNA probes.

Step 3.Genetic sequence deposition
By the use of Robotic techniques we can deposit the genetic materials to the
substrate.

Various Applications of Micro arrays
DNA microarray is a useful tool in identifying the changes at the cellular level.
Now, various applications of microarrays from molecular biological perspectives are
described. DNA microarray finds its wide use in medicine, biotechnology,
pharmaceuticals, bioinformatics etc. The application of DNA microarray has already been
witnessed in identification of a diseased gene or novel drugs.

Gene Expression and profiling
Wen et. al. (1998) in PNAS has explained the use of microarray with Reverse
transcriptase PCR (RT-PCR) to observe a high-resolution temporal map of fluctuations in
mRNA expression of 112 genes during the development of the central nervous system of
a rat. A functional relationship was found among the genes fluctuating in parallel. Genes
categorized to distinct functional classes showed a particular expression profiles.

Khan et. al (1999) in PNAS has shown the use of cDNA microarray for studying
gene expression profile of 1238 cDNAs to investigate the gene expression profile of a
group of a seven alveolar rhabdomyosarcoma (ARMS) cell lines which were
characterized by the presence of PAX3-FKHR fusion gene. They reported that the
clustering of the cells were due to the consistent pattern of gene expression by ARMS
cells. Their research was of importance in using cDNA microarray technology in
showing tumor-specific gene expression profile in human cancers.

Each microarray experiment requires relatively large amount of material that has
posed restrictions on the use of this high throughput technique. Development of sample
amplification procedures has tried to solve this obstacle. Linear and exponential sample
amplifications are two used methods to obtain gene expression data from small samples
using microarray. The conservation of transcript abundance throughout the procedures,

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

has generally found to be at an acceptable limit in both strategies. Exponential
amplification was found to be accurate than the linear strategy. Amplification efficiencies
technically allow profiling of extremely small samples, from tens of nanograms to single
cells. Various options were found by Nygaard and Eivind in 2005 for profiling small
samples with the combination of amplification technology and microarray technology.
cDNA microarrays are capable of profiling gene expression patterns of tens of thousands
of genes in a single experiment (Duggan et. al., 1999).

DNA microarray in detecting cancerous cells
Microarray potential is virtually unlimited. Recently, Cowell and Hawthorn
(2007) in the journal of Current Molecular Medicine reported about the application of
microarray technology to the analysis of the cancer genome. The genetic events occurring
in the development of a cancerous tissue can be traced by the use of DNA microarrays.
The gene expression arrays give an estimation of the gain and loss of function of a
tumorous cell.

Traditionally, rodent bioassays were used to identify carcinogenic and
toxicological substances. However these assays often take a long time and the dose
required for these essays are relatively larger. Eric Lander from Massachusetts institute of
Technology (MIT) first reported that it is possible to distinguish different types of cancers
depending on their gene expression profile. One of the important finding made by Lander
was that he was able to distinguish between acute myeloid leukemia (AML) and acute
lymphoblastic leukemia (ALL). This distinction between AML and ALL was not possible
by pathological examination. In order to achieve this distinction mRNAs were obtained
from bone marrow of 38 patients with either AML or ALL. These samples were labeled
with Biotin and applied in a microarray containing probes for nearly 6800 genes.

Chang et. al. (2005) in Stanford reported that a unique pattern of gene expression
can be found in the cells recruited by breast cancers. Similarly it is also possible for
researchers now to see how cancer promoting oncogenes disturb the expression of other
genes. Microarrays are also used to see how these cancerous cells show response to some
chemotherapeutic agents.

Genes involved in transcription factor binding sites is made possible by using
chromatin immunoprecipitation coupled with promoter microarrays (ChIP-chip). This
helps to identify the genes involved in various cell cycles and in identifying cancer
signatures. Rhodes et.al. compared 265 gene expression signatures with 361 sequence
derived transcription factor binding site profile. Roughly 300 cases in which transcription
factor was associated with cancer signature were identified. One possible conclusion that
might be found from this experiment is that the transcription factors might be responsible
for the expression of the gene.

Usually when we see cells affected by different types of tumors by microscope, it
is not distinct what type of tumor it is. But when we use Microarray technology this
confusion can be avoided as the expression pattern for different type of tumor cells will
be different.

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

DNA micro arrays in anesthesia
Not much has been understood regarding the effects of long term side effects of
anesthetic agents. DNA microarray can screen mammalian genome to see which genes
are expressed or suppressed due to its exposure to anesthetic agents. There might be side
effects associated with anesthetic agents. These side effects can be as such as
preconditioning, post-operative depression, hepatotoxicity etc. If these side effects result
in change in the gene expression then this change can be figured out by using DNA
microarrays.

Primate behavioral neuroscience research
A unique problem for primate research is the limited availability of species-
specific arrays. Arrays designed for humans are often used, but expression level
differences are inevitably limited by gene sequence differences in all cross-species array
applications. Karssen et. al., 2005 showed that the application of human microarrays in
nonhuman primate neuroscience research recovers useful information from thousands of
genes, and provides an important strategy for explaining the molecular complexity of
behavior and mental health. Non human primate research is important because they play
a vital role in research on the neural basis of emotional, cognitive, and social aspects of
behavior. The application of microarrays still presents various limitations and challenges
for primate neuroscience research which is hoped to be overcome in coming days. For
now, it is critical that the outcomes of microarray studies of nonhuman primates are
validated and extended by the classic techniques (e.g., quantitative PCR, in situ
hybridization, and immunohistochemistry) applied to new, independent sets of brain
tissue samples.

DNA micro arrays in C. elegans
Microarray studies are used in C. elegans to study the gene expression patterns
that are linked with a specific cell. The C. elegans gene chip designed by Affymetrix
contains nearly 22,500 transcripts probes. DNA Microarray studies of C. elegans are
useful in studying aging and age related diseases.

Enzyme specificities and protein interactions
Recently a lot of Biotech industries are using Microarray technology to identify
enzyme specificities. By using techniques such as chemoselective coupling it is possible
to generate microarray data from covalently attached peptides. This technology can help
to understand about signal transduction pathways. Similarly, any contamination in the
enzyme activities can also be detected. Optimal substrate for a particular enzyme can be
identified. Just by performing one peptide synthesis it is possible to get hundreds of
identical microarray copies.

It is estimated that there are nearly 500 genes which encodes for protein kinase.
But so far only few kinase encoding genes have been characterized. Because Kinase can
serve as a potential drug targets, these days many research groups have attempted to
identify the peptidic kinase substrates by using microarray-based approaches.
Schutkowski et. al. (2004) were the first to perform the high density peptide microarray.

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

They were able to array 6912 peptides in one microscopic slide. Edwin southern (1999)
discussed in nature genetics how arrays of oligonucleotides provide powerful tools to
study the molecular basis of these interactions on a scale which is impossible using
conventional analysis, which also should highlight the importance of understanding
molecular interactions using microarrays.

Two general approaches are followed for peptide Microarray technology. Peptide
scans covering common kinase substrate proteins such as myelin basic proteins were
printed onto chips (Reimer et.al, 2002). In the second approach, peptide libraries derived
from phosphorylation sites in human proteins were used. Autoradiography and
fluorescent labeling was carried out for detection approaches.

Forensics
Genetic fingerprints often serve as an important issue in identifying a criminals or
personnel involved in the crime site. Since the expression pattern of genes from different
people will be different, this indirect microarray technology can be used in identifying
criminals in rape cases, paternity claims etc. A recent famous example of this can be seen
on the issue of resolving who was the father of former playmate girl Anna Nicole smith
and it was found that Larry Birkhead was the father at relative percent of 99.99% through
genetic fingerprinting, which dissolved the court case.

Using DNA microarrays to study Natural Variations (Gilad et al., 2006)
The genetic and phenotypic variations occurring within and between different
species are useful to understand the natural variations. Along with different technologies
such as Solexa, DNA microarray has become a useful tool in detection and genotyping of
single nucleotide polymorphism (SNPs). But the hybridization in the microarray is
detected by various factors and hence it is exactly difficult to know the particular source
of variation.

Biomedical Applications and drug screening
One of the future potential of Microarrays can be in the field of Biomarker
discovery. Single gene biomarkers such as CD20 have been detected for the treatment of
Acute Rejection (Sarwal et. al., 2003). The so called autoantibody microarrays have also
been used for biomarker discovery (Caiazzo Jr et. al., 2007). Such high-density arrays
have the ability to detect multiple autoantigens and improve sensitivity and specificity of
detection for autoantibody profiling as the main challenge till now had been to working
with autoantibodies which are usually very sensitive. Identification of potential
prognostic markers for vulvar cancer has been done using simple immunohistochemical
staining of tissue microarrays (Fons et. al., 2007).

The procedure for this was rather simple and this might even change the
medical expense for designing such markers and the cost of diagnostics might go down.
Fossey et. al, (2007) claimed the identification of biomarkers for multiple sclerosis.
Multiple sclerosis affects neurons, the cells of the brain and spinal cord that carry
information, create thought and perception, and allow the brain to control the body. Their
approach may have diagnostic utility not only for multiple sclerosis but also for other

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

clinically complex autoimmune diseases. They used quantitative real-time polymerase
chain reaction analysis to identify a minimum number of genes of which transcript levels
discriminated multiple sclerosis patients from patients with other chronic diseases and
from controls.
Gene expression can be used to see which particular genes will be stimulated by
the effect of a particular drug. Similarly DNA chips can be used to decide which drug
would be the most effective by their expression ways.

Microarray Application in Microbial Ecology Research
The activity of different microbial population can be measured in relation to the
environment in which the microorganisms grow (Gentry et. al., 2006).
Rhee et.al. (2004) reported the use of 50-Mer Oligonucleotide Microarrays in detecting
the genes that are responsible for the biodegradation in the microbial communities. It was
also possible to infer about the pathways involved in the biodegradation and metal
resistance by using the microarrays.

Usually the microarrays used in the environmental studies are classified into 3
major groups based on the types of probes arrayed. These three major classes are:
Functional gene arrays (FGAs), community genome arrays (CGAs) and phylogenetic
oligonucleotide array. The major enzymes responsible for environmental processes are
probed by FGAs. CGAs are designed by using the DNA obtained from pre-culture
microorganisms. Short synthetic oligonucleotide obtained from Ribosomal RNA (rRNA)
was used in constructing phylogenetic oligonucleotide arrays.

Tissue Microarrays: applications in urological cancer research
Tissue Microarray (TMAs) is a useful tool in screening a large number of tissue
banks for biomarker expression. Li et al. in 2003 showed that neutral amino acid
transporter ASCT2 plays is role in intratumoral metabolism. 640 different tissues
obtained by the surgical removal of prostate gland were microarrayed. "ASCT2
expression was inversely correlated (P = 0.046) to the duration of recurrence-free survival
following surgical treatment (Li et al. 2003)"

Microarray applications in infectious disease
A gene expression data from can be obtained from an infectious host. This
would help in predicting the virulence mechanism. Monitoring whole-genome host and
pathogen gene expression can aid in providing a complete understanding of the progress
of the infectious disease. This array can also show the response of host to its pathogens
and vice versa.

Before the microarray technology came into existence scientists used to
sequence and monitor the events of a small-subset of genes which they suspect to be
involved in virulence. But now a genome wide expression pattern gives a clear picture in
understanding a wide range of genes.

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

One of the experiments in understanding pathogens response to its host
environment was recently done. by Wolfgang et. al., 2004. They used GeneChip
Pseudomonas aeruginosa genome arrays in order to understand the interaction occurring
between the airway liquids infected from cystic fibrosis (CF) patients and P. aeruginosa.
By understanding the genomic expression and the toxins expressed by P. aeruginosa,
scientists have been able to recognize the mechanism for disease pathway. This has
potential therapeutic applications.

Similarly in understanding pathogens impact for host expression; Izmailova
reported that Tat protein (a major HIV virulence factor) is the first to be infected by
retroviruses. This gave an understanding of complete interferon pathway. According to
Izamailova et.al. (2003), the expression of viral infection is carried on by the chemokines
molecules as the ultimate virus target. A potential therapeutic outcome of this study may
be in designing therapies against Tat proteins and therapeutic pathways.

Yu et, al,. (2007) have implicated the use of genotyping microarray as the Rapid
and sensitive detection of fluoroquinolone-resistant Escherichia coli from urine samples.
This method can be used to diagnose various types of urinary tract infections (UTI) as
UTI is among the most common bacterial in human beings with E coli being the major
cause of infection. The DNA microarray test displayed an assay time of 3.5h, a sensitivity
of 100CFU/ml, and the ability to detect fluoroquinolone-resistant E. coli in the presence
of a 10-fold excess of fluoroquinolone-susceptible E. coli cells which is very rapid
compared to other assays.

Some of the other breakthroughs are that the microarray has been used to
resequence the complete genome of SARS virus. These microarray technologies are also
used in identifying an infecting pathogen. Each pathogen will have a unique combination
of genetic make-up and hence the array sequencing can easily identify the distinct genetic
composition of the pathogens.

Multi-Pathogen Identification (MPID) microarray performed by Wilson et. al,
(2002). This technology was successful in identifying eighteen different prokaryotes,
eukaryotes and viruses. A major advantage of this technique was that it could detect
pathogenic DNA as little as 10 femtograms. This amount of DNA was not detected by
other detection methods.

Microarray applications in other diseases
Till now, scientists have not been able to use microarray for diseases like
atherosclerosis but they might be able to add microparticles to the array of understanding
of this disease process to have the chance to decrease its harmful effect on the individual
and society in near future. Microarray allows the detection of labeled RNA hybridizing to
DNA molecules attached to a solid surface, using this simple idea, it has already
identified a thousand of genes potentially involved in cardiovascular medicine.(Joerg
Herrmann, 2003).

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

Fig 1: Microarray used in Multi-Pathogen Identification (MPID)

Figure adapted from Affymetrix application notes

Microarray application in ion channels
Ion channels are a group of membrane proteins and these proteins are very
important target for drug discovery. Whole-genome microarrays have proved to be very
important in case of cardiac ion channels. A large number of data sets obtained from
whole-genome microarrays will be useful in various pathophysiological applications.
Demolombe et.al.(2005) reported that they have developed a specialized DNA microarray
compromising PCR amplified probes for most of the voltage gated Na+, Ca2+ , Cl-, and K+
channels alpha and beta subunits. A 3' untranslated region sequence specific for each
channel genes was used as probes in their case.

Anderle et.al (2003) studied the mRNA expression profiles of various genes
that encodes for transporters and ion channels, in differentiating Caco-2 cells and human
small intestine. In order to find the expression of the mRNA; microarray chip with 750
deoxyoligonucleotide probes was used. The expression profile of Caco-2 cells were
compared with that of total RNA of human intestines by taking the ratio between
fluorescence dye labeled cDNA derived from poly(A)+ RNA samples Caco-2 cells with
the total RNA of human intestines. The finding of their report was that the Caco-2 cells
are a suitable model in career-mediated transport in human intestines. But the expression
of number of transporters and ion channel genes varied significantly and did not reflect
mRNA levels in human intestine.

Microarray screening in food safety
Microarrays are excellent potential tools for monitoring and tracking food-
borne pathogens. For this, cDNA microarray and tools of bioinformatics have been fused.
The DNA microarray technology has been used to compare the gene expression profiles
in liver among three groups of mice fed a diet containing 5% royal jelly, a diet containing
5% royal jelly stored at 40 °C for 7 d (40 – 7 d royal jelly) or a control diet which

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

provides the same total energy as royal jelly. The results suggest that the efficacy of royal
jelly decreased and the toxicity of royal jelly increased during storage at high
temperature. Rapid and sensitive detection of microbial pathogens is needed to ensure
food safety. Recently, a fiber-optic DNA microarray using microsphere-immobilized
oligonucleotide probes specific for the Salmonella invA and spvB genes was developed
for the detection of Salmonella spp. A disposable microarray (ArrayTubes) has been
developed for the detection of up to 90 antibiotic resistance genes in gram-positive
bacteria by hybridization. A novel DNA-microarray based detection method has been
recently reported (Roy and Sen, 2005). The technique has been used to analyse
Campylobacter and non-Campylobacter reference strains and to detect Campylobacter
directly from the faecal swabs. In order to utilize microarray technology to mainstream
food safety it is important to develop various user-friendly tools that may be applied in a
field setting. In addition, a standardized process for regulatory agencies is immediately
needed to be developed which should act upon microarray-based data.

Future potential
The future potential of Microarray is unbound and limitless. Affymetrix
manufactured arrays can detect the expression patterns in the genes in yeast, mice, rats,
humans etc. But the technology in itself is still in its infancy. Of course the major reason
why it has superseded other technologies might be due to its small size which makes it
portable.

Recently, imaging-guided microarray had been established (Pereira et. Al, 2007).
Its use has been implicated in Neuronal and aging diseases. Both of these diseases
contribute to hippocampal dysfunction but molecular mechanisms underlying these
diseases could be very different. Gene expression profiling can provide hints to these
mechanisms. The analytical challenges in this process can be overcome with image-
guided microarray and the separate mechanisms could be elucidated.

While Baldwin and Salama (2007) have used genomic microarrays to study
insertional/transposon mutant libraries, which is a novel method in enzymology. Such a
combination of these methods facilitates pointing out large numbers of mutants for
phenotypic studies, consequently improving both in the efficiency of genome-saturating
library screens and in the functional annotation of unknown genes.

Cobo and Concha (2007) hinted to the application of microarray technology for
microbial diagnosis in stem cell cultures. Stem cell cultures are contaminated by different
pathogens which renders them useless to use in regenerative medicine and transplantation
in humans. Thus, microbial diagnosis for stem cell cultures can be done in a cheap and
effective manner.

These were just few future potentials which have turned into reality now. One
thing to notice is that biological variability can arise from independently-prepared RNA
samples. Hence multiple arrays might be needed to overcome this variability. Similarly

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

some other questions for the experimental design can be as the amount of RNA needed
for hybridization. Usually 2–5μg of total RNA is sufficient for single array hybridization.

One of the biggest problems in Microarray analysis is that the gene expression
level might not exactly correlate with protein levels. Techniques such as
immunolocalization can be used to determine the protein level.

It is also a debated topic that biologists need to know more mathematics than they
currently   know.   In   order   to   analyze   various   potential   biological   data   that   might   be 
obtained from Microarray, biologists should be more motivated and keen to understand 
that mathematical languages. However transdisciplinary courses such as bioinformatics, 
biostatistics, and biomechanics are some of the backgrounds that are trying to cover both 
the   aspects  of  mathematics  and  biology.  There  are  various  web  based  tools  for  gene 
analysis such as gene expression pattern analysis suite (GEPAS), Expression Profiler: next 
generation (EP: NG), and Microarray data analysis web tool (MIDAW). These web based 
tools   have   greatly   aided   in   understanding   the   enormous   data   potential.   Similarly   the 
analysis technique called clustering includes a number of statistical and computational 
tools.  Agglomerative hierarchical clustering, k­means, k­medians, self­organizing maps, 
and   self­organizing   tree   algorithm   are   some   of   the   statistical   tools   in   analyzing   the 
Microarray data. 

Gene expression microarrays are being used widely to address a myriad of
complex biological questions. Microarrays offer the promise of discoveries far
greater than those happened when recombinant DNA methods were
developed. Molecular biology and genetics have advanced much in the recent years.
But still much not have been understood in terms of analyzing the data obtained from
Microarray. Lot can be done to make all these analyzing methods more robust and
efficient. Some of the areas that must be looked into in the future are the efficient data
analysis techniques, image recognition techniques. Though DNA chip has been one of the
breakthroughs, there lies a lot of challenges like increasing the number of arrays in a
single chip. Similarly the current price of a single Microarray is rather expensive for most
of the labs that are not well equipped financially. Thus scientists working in this field
should also look at minimizing the cost factor involved in the production of DNA chip.

Today, lasers can detect very low levels of fluorescent dyes, and
this is a plus point for microarray technology. A hybridized microarray
slide is inserted into the microarray reader or scanner. Filters
distinguish the red and green wavelengths of the fluorescent dyes. A
detector measures the intensity of each spot. New approaches in
statistics are being developed to help us interpret the gene expression
patterns and verify results. DNA chips promise to carry the way of understanding
genomes to a whole new level, and to bring tools for getting DNA-sequence information
out of research labs into hospitals in near future.

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

Thus for future, microarray should be combined with other powerful technology
to make it more efficient, useful and multipurpose then only can its true potential can be
exploited.

References
Ana Carolina Pereira, William Wu and Scott a small (2007) Imaging-Guided
Microarray: Isolating Molecular Profiles That Dissociate Alzheimer's Disease from
Normal Aging; Ann. N.Y. Acad. Sci. 1097: 225-238

Alter O, Brown P, Botstein D (2000) Singular value decomposition for genome-wide
expression data processing and modeling. Proc Nat Acad Sci USA.

Adriaan M. Karssen, Jun Z. Li, Song Her, Paresh D. Patel, Fan Meng, Simon J.
Evans, Marquis P. Vawter, Hiroaki Tomita, Prabhakara V. Choudary, William E.
Bunney, Jr., Edward G. Jones, Stanley J. Watson, Huda Akil, Richard M. Myers,
Alan F. Schatzberg and David M. Lyons (2005) Application of microarray technology
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David J Duggan, Michael Bittner, Yidong Chen, Paul Meltzer & Jeffrey M. Trent
(1999), Expression profiling using cDNA microarrays, Nature Genetics 21, 10 - 14

David N. Baldwin and Nina R. Salama (2007), Using Genomic Microarrays to Study
Insertional/Transposon Mutant Libraries, methods in enzymology, volume 421, 2007, 90-
110

Edwin Southern, Kalim Mir & Mikhail Shchepinov (1999), Molecular interactions on
microarrays, Nature Genetics 21, 5 - 9

F. Cobo and Á Concha (2007) Application of microarray technology for microbial
diagnosis in stem cell cultures: a review, Cytotherapy, volume 9, I1, 53-59

Fons G, Burger MP, Ten Kate FJ, van der Velden J (2007) Identification of potential
prognostic markers for vulvar cancer using immunohistochemical staining of tissue
microarrays. International Journal of Gynecological Pathology. 26(2):188-193.

Cowell and Hawthorn (2007) The application of microarray technology to the analysis
of the cancer genome. Curr Molec Med 7:1:103-120

Wen et al. (1998) Large-scale temporal gene expression mapping of central nervous
system development. PNAS, 334-339

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

Khan et al, (1998) Gene Expression Profiling of Alveolar Rhabdomyosarcoma with
cDNA Microarrays, Cancer Research 58, 5009-5013

Demolombe et.al.(2005) Functional genomics of cardiac ion channel genes, Cardiovasc
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Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart
Research essay by Kedar Ghimire/ Jacobs University Bremen

Yu X, Susa M, Weile J, Knabbe C, Schmid RD and Bachmann TT (2007) Rapid and
sensitive detection of fluoroquinolone-resistant Escherichia coli from urine samples using
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Websites consulted
http://genome-www5.stanford.edu/microarray/SMD/index.shtml
http://en.wikipedia.org/wiki/DNA_microarray
http://science-education.nih.gov/newsnapshots/TOC_Chips/Chips_RITN/chips_ritn.html
http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html
http://www.bio.davidson.edu/Courses/genomics/chip/chip.html
http://learn.genetics.utah.edu/units/biotech/microarray/
http://www.microarray.org/sfgf/

© Kedar Ghimire

Course High-throughput Screening Technology II / Instructor of record: Dr. Helge Weingart