DNA Microarray Image Analysis - University of Illinois at Urbana ...
DNA Microarray Image Analysis - University of Illinois at Urbana ... DNA Microarray Image Analysis - University of Illinois at Urbana ...
DNA Microarray Preparation • DNA microarrays are typically composed of thousands of DNA sequences, called probes, fixed to a glass or silicon substrate. The DNA sequences can be long (500-1500bp) cDNA sequences or shorter (25-70 mer) oligonucleotide sequences. Oligonucleotide sequences can be presynthesized and deposited with a pin or piezoelectric spray or synthesized in situ by photolithographic or ink-jet technologies. • Relative quantitative detection of gene expression or gene copy number can be carried out between two samples on one array or by single samples comparing multiple arrays. • Double-fluorescent technique uses samples from two sources that are labeled with different fluorescent molecules (Cy3 and Cy5, or Alexa 555 and Alexa 647) and hybridized together on the same array. 6
Input and Output of Microarray Data Analysis • Input: Laser image scans (data) and underlying experiment hypotheses or experiment designs (prior knowledge) • Output: — Conclusions about the input hypotheses or knowledge about statistical behavior of measurements 7 — The theory of biological systems learnt automatically from data (machine learning perspective) – Model fitting, Inference process
- Page 1 and 2: February 4, 2005 DNA Microarray Ima
- Page 3 and 4: Publications • Journals: — Bajc
- Page 5: Microarray Problem: Major Objective
- Page 9 and 10: Types of Expected Microarray Data M
- Page 11 and 12: 11 Microarray Data Processing Workf
- Page 13 and 14: DNA Microarray Image Analysis • T
- Page 15 and 16: Ideal Microarray Image? 1. Ideal cD
- Page 17 and 18: Microarray Image Technologies • A
- Page 19 and 20: Variations of Grid Geometry • Rot
- Page 21 and 22: Variation of Spot Morphology • Sp
- Page 23 and 24: Examples: Spatially Varying Backgro
- Page 25 and 26: 25 Examples: Spatial Resolution, Li
- Page 27 and 28: IMAGE ANALYSIS: MICROARRAY GRID ALI
- Page 29 and 30: Grid Alignment: Application Domains
- Page 31 and 32: 31 Microarray Grid Alignment: Previ
- Page 33 and 34: Microarray Grid Alignment: Previous
- Page 35 and 36: 35 Grid Alignment Algorithm Overvie
- Page 37 and 38: Image Down-Sampling • Design of r
- Page 39 and 40: Vertical and Horizontal Line Score
- Page 41 and 42: Optional Regularity Enforcement •
- Page 43 and 44: Processing Multiple Grids Line Disc
- Page 45 and 46: Spot Size & Spot Density 45 •Radi
- Page 47 and 48: Missing Spots The fewer the spots i
- Page 49 and 50: Down-sampling •Experimental resul
- Page 51 and 52: Grid Alignment Properties Color Inv
- Page 53 and 54: Multiple Grids: Semi-Automated vs.
- Page 55 and 56: 55 MICROARRAY FOREGROUND SEPARATION
<strong>DNA</strong> <strong>Microarray</strong> Prepar<strong>at</strong>ion<br />
• <strong>DNA</strong> microarrays are typically composed <strong>of</strong><br />
thousands <strong>of</strong> <strong>DNA</strong> sequences, called probes,<br />
fixed to a glass or silicon substr<strong>at</strong>e. The <strong>DNA</strong><br />
sequences can be long (500-1500bp) c<strong>DNA</strong><br />
sequences or shorter (25-70 mer)<br />
oligonucleotide sequences. Oligonucleotide<br />
sequences can be presynthesized and<br />
deposited with a pin or piezoelectric spray or<br />
synthesized in situ by photolithographic or<br />
ink-jet technologies.<br />
• Rel<strong>at</strong>ive quantit<strong>at</strong>ive detection <strong>of</strong> gene<br />
expression or gene copy number can be<br />
carried out between two samples on one array<br />
or by single samples comparing multiple<br />
arrays.<br />
• Double-fluorescent technique uses samples<br />
from two sources th<strong>at</strong> are labeled with<br />
different fluorescent molecules (Cy3 and Cy5,<br />
or Alexa 555 and Alexa 647) and hybridized<br />
together on the same array.<br />
6
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