Affymetrix User’s Group Meeting Boston, MA May 2005 Keynote Topics: 1. Human genome annotations: emergence of non-coding transcripts -tiling arrays: study.

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Presentation transcript:

Affymetrix User’s Group Meeting Boston, MA May 2005 Keynote Topics: 1. Human genome annotations: emergence of non-coding transcripts -tiling arrays: study gene regulation (complement expression arrays), explore genome functions including: DNA methylation, origins of replication, mapping sites of TF binding 2. mRNA transcript variation across ‘druggable’ genome: novel targets from exon array data - exon arrays: study alternative splicing, explore transcript based pathways vs gene based pathways 3. Enabling microarrays for routine clinical use -personalized medicine -example = SNP chips (mapping & linkage analysis) -10K, 100K & 500K SNP chips - Serono Identifies 80 genes involved in MS using 100K SNPs

Data Analysis Track: 1. Microarray Expts: Conceptual view & Practical Considerations - Experiment design-begin w/end in mind, focus on questions seeking to be addressed & have specific goals (i.e. transcriptional changes vs cluster analysis) - Replicates: biological vs technical, no need for technical replicates if sample preparation, etc is done consistently, # of biological replicates depends on focus of experiment, pooling – suppresses changes - data analysis: 1) look at the data statistically 2) look at the data biologically 2. Plier algorithm: higher differential sensitivity for low expressors - signal detection algorithm - normalization - background correction (PM-MM) 3. Statistical tools & data visualization - RMA = robust multi-chip average - T-test (ANOVA) – compare signal across biological replicates - software

Software Affy Array Assist Lite (Stratagene) – download for free off Affymetrix website ( Poster Effects of RNA Degradation on Gene Expression Analysis of Human Post- mortem Tissues – Jerry Lee, Dept of Molecular Medicine, Neurocrine Biosciences, Inc., San Diego, CA - Summary: RNA from Human Brain (and other tissues) & RNA from Rat duodenum was used to address how RNA quality affects gene expression data generated using Affy chips – Conclusion: Degraded RNA gave comparable signal to “good quality” RNA

Effects of Exercise on Gene Expression in Bone & Brain Tissues from different strains and sexes of mice Updates: 1. Exercise Program (sufficient to produce significant changes in skeletal system) -mice ~6 months old (growth should have stopped) -mice randomly selected to exercise -10 degree incline (treadmill design) -exercise during dark cycle (when mice naturally more active) -30 min/day, 5 days/wk, 6 wks total 2. Experimental Considerations a. RNA quality b. # of replicates/pooling c. chip array type? ($175 price difference) A $350/chip, 14,000 genes $525/chip, 39,000 transcripts