Microarrays allow researchers to analyze gene expression levels across thousands of genes simultaneously. DNA microarrays work by hybridizing fluorescently-labeled cDNA or cRNA to complementary DNA probes attached to a solid surface. This technology has applications in gene expression profiling, disease diagnosis, drug discovery, and toxicology research. While microarrays provide high-throughput analysis, their limitations include not reflecting true protein levels, complex data analysis, expense, and short shelf life of DNA chips.

1. Microarry ( DNA microarray)
S.Rasoulinejad
Ms.c Microbial Biotechnology
Prof. Mousavi

2. Microarray
Introduction
principle
Applications
 Advantages
 Limitations
 References

3. introductions

4. history
 Microarray technology evolved from Southern
blotting.
 The concept of microarrays was first proposed in the
late 1980s by Augenlicht and his colleagues.
They spotted 4000 cDNA sequences on nitrocellulose
membrane and used radioactive labeling to analyze
differences in gene expression patterns among different
types of colon tumors in various stages of malignancy.

5. PRINCIPLE
• The principle of DNA microarrays lies on the
hybridization between the nucleotide. Using this
technology the presence of one genomic or cDNA
sequence in 1,00,000 or more sequences can be
screened in a single hybridization.
 Fluorescent labeled target sequences that bind to a
probe sequence generate a signal that depends on
the strength of the hybridization determined by the
number of paired bases.

6. why use this technic?
• By using an array containing many DNA
samples, scientists can determine, in a
single experiment, the expression levels
of hundreds or thousands of genes within
a cell by measuring the amount of mRNA
bound to each site on the array.

7. DNA MICROARRAY TECHNOLOGY
DNA microarray technology defined as a high-throughput
and versatile technology used for parallel gene expression
analysis for thousands of genes of known and unknown
functions.
A DNA microarray is a collection of microscopic DNA
spots on solid surface. Each spot contains picomoles of a
specific DNA sequence, known as probes or reporters.
A microarray is a pattern of ssDNA probes which are
immobilized on a surface called a chip or a slide.
 Microarrays use hybridization to detect a specific DNA or
RNA in a sample.

10. Contact Printing
InkJet (HP/Canon) technology
• 1 drop = 100 picolitres
Non Contact Printing

12. Technique used for the Preparation of DNA
chip
Fig: Photolithography

16. The colors of microarray.…
GREEN represents Control DNA, where either DNA or cDNA derived from
normal tissue is hybridized to the target DNA.
RED represents Sample DNA, where either DNA or cDNA is derived from
diseased tissue hybridized to the target DNA.
YELLOW represents a combination of Control and Sample DNA, where
both hybridized equally to the target DNA.
BLACK represents areas where neither the Control nor Sample DNA
hybridized to the target DNA.
Each spot on an array is associated with a particular gene. Each color in
an array represents either healthy (control) or diseased (sample) tissue.
Depending on the type of array used, the location and intensity of a color
will tell us whether the gene, or mutation, is present in either the control
and/or sample DNA. It will also provide an estimate of the expression
level of the gene(s) in the sample and control DNA.

17. - Clustering
Idea: Groups of genes that share similar function have similar expression
patterns
 Hierarchical clustering
 k-means
 Bayesian approaches
 Projection techniques
 Principal Component Analysis
 Independent Component Analysis
- Classification
Idea: A cell can be in one of several states
(Diseased vs. Healthy, Cancer X vs. Cancer Y vs. Normal)
 Can we train an algorithm to use the gene expression patterns to
determine which state a cell is in?
 Support Vector Machines
 Decision Trees
 Neural Networks
 K-Nearest Neighbors

18. Of MicroarrayApplications
GENE EXPRESSION
DISEASE DIAGNOSIS
DRUG DISCOVERY
TOXICOLOGICAL RESEARCH

19. MICROARRAY AS A GENE EXPRESSION
PROFILING TOOL
 The principle aim of using microarray technology as a
gene expression profiling tool is to answer some of the
fundamental questions in biology such as "when,
where, and to what magnitude genes of interest are
expressed.
 Microarray analysis measure changes in the multigene
patterns of expression to better understand about
regulatory mechanisms and broader bioactivity
functions of genes.

20. Gene expression Profiling
• The expression
levels of
thousands of
genes are
simultaneously
monitored to
study the effects
of certain
treatments,
diseases , and
developmental
stages on gene
expression.
Conditions
Genes
How experimental conditions influenced production
(expression) of mRNA for a set of genes. Green indicates
reduced expression. Cluster analysis has placed a group of
down regulated genes in the upper left corner.

21. MICROARRAY AS A COMPARATIVE
GENOMICS TOOL
 Microarray technology have widespread use in
comparative gene mutation analysis to analyse
genomic alterations such as sequence and single
nucleotide polymorphisms.
 In microbiology microarray gene mutation
analysis is directed to characterisation of genetic
differences among microbial isolates,
particularly closely related species.

22. DISEASE DIAGNOSIS
 Different types of cancer have been classified on the
basis of the organs in which the tumors develop.
 Now, with the evolution of microarray technology, it
will be possible for the researchers to further classify
the types of cancer on the basis of the patterns of gene
activity in the tumor cells.
• Use in diagnosis (presence)
• Example: characterizing acute lymphoblastic leukemia. Also
breast cancer.
• Use in prognosis
• Example: assessing the likelihood of metastasis in
medulloblastoma (brain tumor in children)

23. TOXICOLOGICAL RESEARCH
 Microarray technology provides a robust platform for
the research of the impact of toxins on the cells and
their passing on to the progeny.
 Toxicogenomics establishes correlation between
responses to toxicants and the changes in the genetic
profiles of the cells exposed to such toxicants.
 The microarray permits researchers to examine
thousands of different genes in the same experiment
and thus to obtain a good understanding of the
relative levels of expression between different genes in
an organism.

24. Advantages of DNA Microarrays.…
DNA microarrays are better than other profiling
methods ,it has features such as :
 Easier to use
 Are high-throughput (can analyze thousands of genes
or markers at a time)
 Generate large amounts of data in little time
 Do not require large-scale sequencing
 - Allow the quantitation of thousands of genes from
many samples

25. Limitations of array.…
• Do not necessarily reflect true levels of
proteins - protein levels are regulated by
translation initiation & degradation as well
• The production of too many results at a
time requires long time for analysis, which
is quite complex in nature.
• Expensive! $20-$100K to make your own /
buy enough to get publishable data
• The DNA chips do not have very long shelf
life, which proves to be another major
disadvantage of the technology.

26. Thank you