Microarray introduction
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DNA Microarray Introduction
Huai-Kuang Tsai
Department of Computer Science &
Information Engineering
National Taiwan University
d7526010@csie.ntu.edu.tw
2002.03.28
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Contents
Introduction to Microarray
Gene-wide cluster analysis
Software demo
Classification (If we have time)
Genetic network (Optional)
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Introduction to Microarray
What Is microarray
Instruments
Life Cycle
Applications
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What Is Microarray
A new powerful technology for biological exploration which enable one to simultaneously measure the level of activity of up to 60,000 genes. In particular, the amount of mRNA for each gene in a given sample (or a pair of samples) is measured
Parallel
High-throughput
Large-scale
Genomic scale
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Basic Idea
Central dogma
Complementary hybridization
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ATATCGGCATCAGTCGATCGATCATCGATCGAT
UAUAGCCGUAGUCAGCUAGCUAGUAGCUAGCUA
ATATCGGCATCAGTCGATCGATCATCGATCGAT
DNA
mRNA
cDNA
Central Dogma
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What Is Microarray
Different Approaches
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Stanford Approach
Use robot to spot glass slides
Able to measure qualitatively relative expression levels of genes
Differential expression by use of simultaneous, two-color fluorescence hybridisation
Cheaper with DIY ($60,000)
Also called home-made system
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Affymetrix
Probe Array (Photolithography)
Synthesis of probe




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Instruments
Arrayer
Scanner
Laser Confocal Microscope
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Arrayer
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Scanner
GenPix 4000
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Life Cycle
Biological
Question
Sample
Preparation
Microarray
Reaction
Microarray
Detection
Data Analysis
& Modeling
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Life cycle
Cy3
(green)
Cy5
(red)
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Procedures
Preparation
Target DNA (reference and test samples)
Slides
Reaction(Droplet or Pin Spotting)
Hybridization
Scanning
Analysis
Image processing
Data mining
Modeling
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Applications
Gene expression studies
Gene function for cell state change in various conditions (clustering, classification)
Disease diagnosis (classification)
Inferring regulatory networks
Pathogen analysis
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Applications(Cont.)
Drug Discovery
identify appropriate molecular targets for therapeutic intervention
monitor changes in gene expression in response to drug treatments
Targeted Drug Treatment
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The Basic System Computational Tasks
Gene set selection
Probe design
Image analysis
Normalization of chip, sample….
…more….
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The Analysis
Computational Tasks
Clustering genes: which genes seem to be regulated together
Classifying genes: which functional class does a given gene fall into
Classifying cell samples: does this patient have ALL or AML
Inferring regulatory networks: what is the “circuitry” of the cell
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Probe design system(一)
A method of hybridization of short synthetic oligonucleotide probes to cloned DNA sequences to derive genetic sequence information.
Application field
oligonucleotide array
Polymerase Chain Reaction : primer design
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Probe design system(二)
Probe design issue
Unique probe for each gene
Different probe sets for each genes : fingerprints
Probes (or a unique probe) of each gene should have the ability of representing the gene.
The similarities between probes should very low.