《生物信息学》教学课件 Sakai_uarray_.ppt

Gene expression:Microarray data analysis1 Outline: microarray data analysisGene expressionMicroarraysPreprocessing normalization scatter plotsInferential statistics t-test ANOVAExploratory (descriptive) statistics distances clustering principal components analysis (PCA)2 Outline of Chapter 8: Bioinformatic approaches to RNANoncoding RNA (p. 282) Rfam database (p. 283) transfer RNA (p. 283) ribosomal RNA (p. 288) microRNA, other noncoding RNA UCSC Genome Browser (p. 294)Messenger RNA (mRNA)(p. 296)Microarrays (p. 312)Interpretation of RNA (p. 320)Our topic tonight3 4 5 6 7 Compare gene expression in this cell type……after drug treatment…at a later developmental time…in a different body region…after viral infection…in samplesfrom patients…relative to a knockout8 ? by region (e.g. brain versus kidney)? in development (e.g. fetal versus adult tissue)? in dynamic response to environmental signals (e.g. immediate-early response genes) in disease states by gene activityGene expression is context-dependent,and is regulated in several basic waysPage 2979 DNARNAcDNAproteinDNARNAcDNAproteinUniGeneSAGEmicroarrayFig. 8.10Page 299next-generation sequencing!!!10 UniGene: unique genes via ESTs? Find UniGene at NCBI: /UniGene UniGene clusters contain many ESTs? UniGene data come from many cDNA libraries. Thus, when you look up a gene in UniGene you get information on its abundance and its regional distribution.Page 30211 Outline: microarray data analysisGene expressionMicroarraysPreprocessing normalization scatter plotsInferential statistics t-test ANOVAExploratory (descriptive) statistics distances clustering principal components analysis (PCA)12 Microarrays: tools for gene expressionA microarray is a solid support (such as a membraneor glass microscope slide) on which DNA of knownsequence is deposited in a grid-like array.Page 31213 Microarrays: tools for gene expressionThe most common form of microarray is used to measure gene expression. RNA is isolated from matched samp