生物信息学课件英文原版课件 (153)

August 29, 2002,InforMax Confidential,1,Vector XpressionProduct Overview,August 29, 2002,InforMax Confidential,2,Agenda,Introduction to Vector XpressionProduct Features and BenefitsFuture Direction,August 29, 2002,InforMax Confidential,3,Agenda,Introduction to Vector XpressionProduct Features and BenefitsFuture Direction,August 29, 2002,InforMax Confidential,4,Source: BioInformatics LLC Survey 2002, InforMax Research,What do Customers Want?,When considering bioinformatics software what do Life Sciences Researchers care about most?Intuitive and easy to useEasy to link to external dataStrong scientific and technical support,August 29, 2002,InforMax Confidential,5,Vector Family of Products,Vector PathBlazer,Vector Xpression,Work with RNA quantitationWhich genes are turned on or off under conditions of interestGene and sample profiling,Work with biological pathways and protein-protein interactionsAdd your own data to curated data,Work with gene and protein sequenceUnderstand sequenceClassify genes based on sequence similarityDesign sequences for wet lab experiments,VectorNTI,August 29, 2002,InforMax Confidential,6,High Quality Expression Results,Vector Xpression Data AnalysisAnd Mining,INPUTS,RESULTS,PROCESSING,InforMax Vector Xpression leverages your investment in inputs and processing to deliver to sophisticated analysis and high quality results.,ImageAnalysis,Imaging,Fluidics,Chips,Samples,August 29, 2002,InforMax Confidential,7,Extracting biologically meaningful information from microarray data requires sophisticated data analysis, mining, and exploration.,Sophisticated Analysis and Mining,August 29, 2002,InforMax Confidential,8,Vector Xpression,Vector Xpression is a powerful, easy to use and flexible application for microarray expression data analysisVector Xpression makes complicated, peer-reviewed workflows easy and accessible to users of all experience levelsVector Xpression contains a robust set of peer-reviewed microarray gene expression analysis toolsVector Xpression is supported by experienced bioinformaticists, industry leading technical support and tutorialsVector Xpression is the best available software solution for both beginners and experts in the field of microarray gene expression analysis,August 29, 2002,InforMax Confidential,9,Vector Xpression,Powerful Features Easy data import wizard accommodates almost any formatLocal storage and management of microarray expression dataData analysis using a comprehensive set of state of the art, peer-reviewed methodsFocused on User NeedsEase of use (intuitive GUI, tutorials and industry leading support)Compelling core functionality (sophisticated, peer reviewed, data processing and analysis methods)Links with other applications (Sequence and Pathways)Configurable links to biological databases and GO annotationsBacked by InforMax Global Services and Technical Support,August 29, 2002,InforMax Confidential,10,Agenda,Introduction to Vector XpressionProduct Features and BenefitsFuture Direction,August 29, 2002,InforMax Confidential,11,Powerful, Intuitive, Flexible,Simple wizard to import data in any formatUser defined fields to extend data modelEasy background correction and log ratio transformationVariety of ways to filter and sort data. Gene profiling and statistical validation for differential gene expressionComprehensive set of advanced, peer reviewed statistical methods and clustering algorithms with choice of several distance metric comparison options and cluster validationEasy link to sequence analysis application (Vector NTI) and pathways application (Vector PathBlazer)Import and incorporate annotations from GO consortiumEasily configurable external links to biological databases,August 29, 2002,InforMax Confidential,12,Product Features and Functions,Data Import and StorageData ProcessingData Mining and VisualizationLink to Sequence and Pathways,August 29, 2002,InforMax Confidential,13,Product Features and Functions,Data Import and StorageData ProcessingData Mining and VisualizationLink to Sequence and Pathways,August 29, 2002,InforMax Confidential,14,Database Objects,Expression Genes (Probes)Expression runs (Hybridizations)Expression Targets (Samples)Experiments (related hybridizations)Physical Chips (Chip layout)Run Projects (organize experiments to be analyzed)Raw data (original data from image analysis),August 29, 2002,InforMax Confidential,15,Easy Database Management,UtilitiesSelect DatabaseOpens an Expression database other than the default. This allows you to have several different databases to work with and to alternately view those databases.Database CompactRemoves from the data files and database tables any unnecessary data that may accumulate from extensive creation and deletion of database objects. New Empty DatabaseCreates a new and empty expression database. This option is useful when your current database become very large, or when you have a large number of database objects in a specific project.,August 29, 2002,InforMax Confidential,16,Import data easily and quickly using Import Wizard,Data in known formats imported automatically,Data Import Wizard,If unknown format, wizard quickly guides import,August 29, 2002,InforMax Confidential,17,Create links to external web sites using User Defined Fields,User Defined Fields,Easily create and populate User Defined Fields,August 29, 2002,InforMax Confidential,18,Supports:wildcard boolean user defined fields,Database Search Utility,August 29, 2002,InforMax Confidential,19,Easily import, assign and manage annotations based on classificationsfrom Gene Ontology Consortium,Annotate Genes,August 29, 2002,InforMax Confidential,20,Product Features and Functions,Data Import and StorageData ProcessingData Mining and VisualizationLink to Sequence and Pathways,August 29, 2002,InforMax Confidential,21,Easy Data Processing,Easy to Use Data Processing OptionsSubtract BackgroundCarry out Log 2 TransformationsNormalization FilteringSorting,August 29, 2002,InforMax Confidential,22,State of the art, peer reviewed statistical methods for normalizationGlobal Control based methodsMA- PlotLowess Smoothing (global, print tip, user defined block patterns),Pre,Post,Normalization,August 29, 2002,InforMax Confidential,23,Filter in many ways using easy pull down menu and dialog boxes,Filter Options,August 29, 2002,InforMax Confidential,24,Sort in many ways using easy pull down menu and dialog boxes,Sorting Options,August 29, 2002,InforMax Confidential,25,Product Features and Functions,Data Import and StorageData ProcessingData Mining and VisualizationLink to Sequence and Pathways,August 29, 2002,InforMax Confidential,26,Visualization Options,GraphicsScatter plotHistogramMA-plotQuartile plotBootstrap confidence plotSeveral model checking plotsHierachical biclustering (simultaneous view of clustering of samples and genes),August 29, 2002,InforMax Confidential,27,Easily modify appearance of graphics,Customize Appearance,August 29, 2002,InforMax Confidential,28,Convenient layout for visualizing and analyzing expression values,Expression Data Viewer,August 29, 2002,InforMax Confidential,29,Scatter Plot for easy comparison of two samples,Scatter Plot,August 29, 2002,InforMax Confidential,30,Easily carry out clustering analysis using several options and Cluster Validation tool,Clustering,August 29, 2002,InforMax Confidential,31,Convenient view and manipulation of cluster dendrogram including hierarchical two-way cluster view,Two-way Clustering,August 29, 2002,InforMax Confidential,32,Easily show and create a gene profile.,Gene Profile,August 29, 2002,InforMax Confidential,33,Differential Gene Expression,State of the art and peer-reviewed methods for validationt- test statistic Step down method for Multiple testingLatin Squares (ANOVA) / Dye swap,August 29, 2002,InforMax Confidential,34,Easily tag genes of interest to follow through analysis,Tag Genes of Interest,August 29, 2002,InforMax Confidential,35,View history of analysis steps performed,Session History,August 29, 2002,InforMax Confidential,36,Product Features and Functions,Data Import and StorageData ProcessingData Mining and VisualizationLink to Sequence and Pathways,August 29, 2002,InforMax Confidential,37,Link to Pathways,Use Vector Pathblazer to view expression results and clusters in context of pathways, protein-protein interactions,“When you find a coincidence between RNAs that co-cluster and proteins that interact, it . reinforces your confidence that theyre both correct.George Church, Harvard Medical School, The Scientist,August 29, 2002,InforMax Confidential,38,Link to sequence analysis,Use Vector NTI to view sequence record of gene and run sequence analysis tools,August 29, 2002,InforMax Confidential,39,Easily export data to applications like Excel, MatLab,Data Export,August 29, 2002,InforMax Confidential,40,Agenda,Introduction to Vector XpressionProduct Features and BenefitsFuture Direction,August 29, 2002,InforMax Confidential,41,Continuous Improvement,Powerful, Intuitive, FlexibleWizard based workflow guides based on popular peer reviewed papersCollaborative data sharing (workgroup)Scriptability and automationAbility to call plug-ins written in commonly used scripting languagesOpen architecture allowing easy customizationKeep up