what is microarray a new powerful technology for biological exploration parallel high-throughput...
TRANSCRIPT
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What Is Microarray A new powerful technology for
biological exploration Parallel High-throughput Large-scale Genomic scale
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Microarray
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ATATCGGCATCAGTCGATCGATCATCGATCGAT
UAUAGCCGUAGUCAGCUAGCUAGUAGCUAGCUA
ATATCGGCATCAGTCGATCGATCATCGATCGAT
DNA
mRNA
cDNA
DNA RNA Protein
Transcription
Reverse transcription
TranslationReplication
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What Is Microarray Different Approaches
Stanford/Synteni
Affymetrix
How DNA sequences are laid down
Spotting Photolithography
Length of DNA sequences
cDNA(Complete sequences)
Oligonucleotides
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Affymetrix Probe Array (Photolithography)
Synthesis of probe
Hybridization
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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 simultan
eous, two-color fluorescence hybridisation
Cheaper with DIY ($60,000) Also called home-made system
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Life Cycle(cont.)
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
ArrayerScanner
Hardware
Software
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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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Problems – by direct view
Anti-probe Locally high background Spot overlap
Precipitate Locally low signal Comet-tails (donut hole)
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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)
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Array Alignment
Good Alignment Bad Alignment
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Spot Finding Grid System Determination
Manual Semiautomatic Automatic
Spot Segmentation Space-based Intensity-based Frequency-based Hybrid approach
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Grid System Determination
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Spot Segmentation
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Spot Segmentation(cont.)
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Applications Gene expression studies
Gene function for cell state change in various conditions
Disease Diagnosis 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
Trageted Drug Treatment
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Example Images – E. Coli
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Example Images – C. Elegan
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1.75
…..
Log(R/G)
…..
Gene index
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…..
Log(R/G)
…..
…..
Log(R/G)
…..
…..
Log(R/G)
…..
…
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N gene
M experiments
…..
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