Uses of Microarrays in Research.pptVIP

Uses of Microarrays in Research Anne Rosenwald Georgetown University Microarrays in Research:A Survey of PubMed Recent Microarray Papers: I. New Techniques/Applications Transcriptional regulatory networks in Saccharomyces cerevisiae Lee et al. (2002) Science 298 799-804 “ChIP-on-chip” Recent Microarray Papers: I. New Techniques/Applications 5,000 RNAi experiments on a chip Lehner and Fraser (2004) Nat Methods 1, 103 RNA living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells Wheeler et al. (2004) Nat Methods 1, 127 Spots on chip contain dsRNA Chip incubated with Drosophila cells Cells induced to “take-up” RNA Are cells alive or dead? Do cells have phosphorylated Akt? Do cells have altered actin fibrils? Recent Microarray Papers: II. Improved Methods for Analysis/Access Reproducibility and statistical rigor outbred organisms (i.e. humans) do different platforms give the same answers? Tools for analysis MAGIC Tool! (many others….) Recent Microarray Papers: II. Improved Methods for Analysis/Access Tools for access and annotation GeneCruiser /cancer/genecruiser Liefeld et al. Bioinformatics (2005) 21, 3681 Uses Affymetrix-generated data incorporates GO terms and links info with SwissProt, RefSeq, LocusLink, etc. Primarily for mouse and human data GEO (Gene Expression Omnibus) /geo/ Barrett et al. (2007) NAR 35, D760 Also heavily weighted to mouse and human data Recent Microarray Papers: II. Improved Methods for Analysis/Access Tools for access and annotation (cont). Stanford Microarray Database / Links to Caryoscope – a way to look at gene expression data in a whole genome context :8080/caryoscope/index.html Recent Microarray Papers: III. Scientific Endeavors Mutational change: compare “wild type” to mutant Tissue-specific gene expression Environmental change: compare same organism in two different environments Development: compare different stages along a particular lineage Therapeutics: compare in cells/tissu