Lecture on microarray hybridization technologies, including Affymetrix, spotted arrays and printed oligo arrays, and a survey of some open source and commercial microarray analysis tools.

Organizers: Agnes Viale (GCL, MSKCC), Piali Mukherjee (ICB, WMC)

Size: 50

Module A: Approaches to Microarray-based Studies (day 1: 2 hours)

Part 1: General introduction and potential applications of array platform

1. Expression profiling
2. Chromosomal abnormality
3. Proteomics
4. Transcription factor binding site analysis
5. Other applications

Part 2: Overview of existing platforms

1. Affymetrix platform: technology, principle, pros and cons
2. Spotted array platform: fabrication process, principle, pros and cons
3. Other commercially available platforms

Part 3: Experimental design

1. Types of projects that can benefit from array technology: molecular classification, fishing, others
2. Technical limitations: starting amount of material, purity of sample
3. Financial considerations

Part 4: Steps involved in data analysis

1. Data set QC
2. Normalization
3. Feature (gene) filtering
4. Replicate analysis
5. Clustering
6. Statistical tests
7. Pathways

Part 5: Validation

1. Real time PCR
2. Northern blot
3. RNAse Protection assay

Module B: Survey of Microarray Analysis Tools (day 2: 2 hours)

Part 1: Open-source Tools

1. Cluster (XCluster) / TreeView
2. CAGED
3. D-Chip
4. Bioconductor (R, S-plus)
5. Web-based tools (CYBER-T, SNOMAD)

Part 2: Commercial Tools

1. Genespring
2. GCOS

Part 3: Introduction to Functional Interpretation of High-throughput Data