What Is Microarray A new powerful technology for

biological exploration Parallel High-throughput Large-scale Genomic scale

Microarray

ATATCGGCATCAGTCGATCGATCATCGATCGAT

UAUAGCCGUAGUCAGCUAGCUAGUAGCUAGCUA

ATATCGGCATCAGTCGATCGATCATCGATCGAT

DNA

mRNA

cDNA

DNA RNA Protein

Transcription

Reverse transcription

TranslationReplication

What Is Microarray Different Approaches

Stanford/Synteni

Affymetrix

How DNA sequences are laid down

Spotting Photolithography

Length of DNA sequences

cDNA(Complete sequences)

Oligonucleotides

Affymetrix Probe Array (Photolithography)

Synthesis of probe

Hybridization

Stanford Approach Use robot to spot glass slides Able to measure qualitatively relative

expression levels of genes Differential expression by use of simultan

eous, two-color fluorescence hybridisation

Cheaper with DIY ($60,000) Also called home-made system

Life Cycle(cont.)

Cy3(green)

Cy5(red)

Procedures Preparation

Target DNA (reference and test samples) Slides

Reaction(Droplet or Pin Spotting) Hybridization

Scanning Analysis

Image processing Data mining Modeling

ArrayerScanner

Hardware

Software

Instruments Arrayer Scanner

Laser Confocal Microscope

Arrayer

Scanner GenPix 4000

Problems – by direct view

Anti-probe Locally high background Spot overlap

Precipitate Locally low signal Comet-tails (donut hole)

Problems –related wit IP Local problems

Spot position variation Spot shape and size irregularity Spot Overlapping

Global problems High background Low signal White-noise/Speckle effect

(Contamination)

Array Alignment

Good Alignment Bad Alignment

Spot Finding Grid System Determination

Manual Semiautomatic Automatic

Spot Segmentation Space-based Intensity-based Frequency-based Hybrid approach

Grid System Determination

Spot Segmentation

Spot Segmentation(cont.)

Applications Gene expression studies

Gene function for cell state change in various conditions

Disease Diagnosis Pathogen Analysis

Applications(Cont.) Drug Discovery

identify appropriate molecular targets for therapeutic intervention

monitor changes in gene expression in response to drug treatments

Trageted Drug Treatment

Example Images – E. Coli

Example Images – C. Elegan

1.75

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Log(R/G)

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Gene index

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Log(R/G)

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Log(R/G)

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Log(R/G)

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N gene

M experiments

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