Gene Regulation and MicroarraysOverviewCells respond to environmentGenome is fixed – Cells are dynamicWhere gene regulation takes placeTranscriptional RegulationTranscription Factors Binding to DNAPromoter and EnhancersGene Regulation with TFsSlide 10Slide 11Slide 12Slide 13Example: A Human heat shock proteinThe Cell as a Regulatory NetworkThe Cell as a Regulatory Network (2)DNA MicroarraysWhat is a microarraySlide 19Goal of Microarray ExperimentsClustering vs. ClassificationClustering AlgorithmsHierarchical clusteringDistance between clustersResults of Clustering Gene ExpressionK-Means Clustering AlgorithmK-Means AlgorithmSlide 28Slide 29Slide 30Slide 31Slide 32Slide 33Mixture of Gaussians – Probabilistic K-meansAnalysis of Clustering DataEvaluating clusters – Hypergeometric DistributionFinding Regulatory MotifsRegulatory Motif DiscoveryCharacteristics of Regulatory MotifsSequence LogosProblem DefinitionDiscrete Approaches to Motif FindingDiscrete FormulationsExhaustive SearchesSlide 45MULTIPROFILERSlide 47Slide 48Expectation Maximization in Motif FindingExpectation MaximizationSlide 51Slide 52Slide 53Slide 54Expectation Maximization: E-stepExpectation Maximization: M-stepSlide 57Initial Parameters Matter!Overview of EM AlgorithmGibbs Sampling in Motif FindingGibbs SamplingSlide 62Slide 63Slide 64Slide 65Slide 66Advantages / DisadvantagesRepeats, and a Better Background ModelLimits of Motif FindersExample Application: Motifs in YeastMotifs in Periodic ClustersMotifs in Non-periodic ClustersSlide 73Comparison-based Regulatory Motif DiscoveryKnown motifs are frequently conservedFinding conserved motifs in whole genomes M. Kellis PhD Thesis on yeasts, X. Xie & M. Kellis on mammalsTest 1: Intergenic conservationTest 2: Intergenic vs. CodingTest 3: Upstream vs. DownstreamConstructing full motifsSummary for promoter motifsCS262 Lecture 17, Win07, BatzoglouGene Regulation and Gene Regulation and MicroarraysMicroarraysCS262 Lecture 17, Win07, BatzoglouOverview•A. Gene Expression and Regulation•B. Measuring Gene Expression: Microarrays•C. Finding Regulatory MotifsCS262 Lecture 17, Win07, BatzoglouCells respond to environmentCell responds toenvironment—various external messagesCS262 Lecture 17, Win07, BatzoglouGenome is fixed – Cells are dynamic•A genome is staticEvery cell in our body has a copy of same genome•A cell is dynamicResponds to external conditionsMost cells follow a cell cycle of division•Cells differentiate during development•Gene expression varies according to:Cell typeCell cycleExternal conditionsLocationslide credits: M. KellisCS262 Lecture 17, Win07, BatzoglouWhere gene regulation takes place•Opening of chromatin•Transcription•Translation•Protein stability•Protein modificationsCS262 Lecture 17, Win07, BatzoglouTranscriptional Regulation•Efficient place to regulate: No energy wasted making intermediate products•However, slowest response timeAfter a receptor notices a change:1. Cascade message to nucleus2. Open chromatin & bind transcription factors3. Recruit RNA polymerase and transcribe4. Splice mRNA and send to cytoplasm5. Translate into proteinCS262 Lecture 17, Win07, BatzoglouTranscription Factors Binding to DNATranscription regulation:•Transcription factors bind DNA•Binding recognizes DNA substrings:•Regulatory motifsCS262 Lecture 17, Win07, BatzoglouPromoter and Enhancers•Promoter necessary to start transcription•Enhancers can affect transcription from afarCS262 Lecture 17, Win07, Batzoglou Transcription Factor(Protein)DNAGene Regulation with TFsRegulatory ElementGeneRNA polymeraseCS262 Lecture 17, Win07, Batzoglou GeneRNA polymeraseTranscription Factor(Protein)Regulatory ElementDNAGene Regulation with TFsCS262 Lecture 17, Win07, Batzoglou DNANew proteinGene Regulation with TFsTranscription Factor(Protein)Regulatory ElementGeneRNA
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