1、实习三：实习三：芯片数据的基本处理和分析芯片数据的基本处理和分析 实习一实习一基因组数据注释和功能分析基因组数据注释和功能分析实习二实习二核苷酸序列分析核苷酸序列分析实习三实习三芯片数据的基本处理和分析芯片数据的基本处理和分析实习四实习四蛋白质结构与功能分析蛋白质结构与功能分析实习五实习五蛋白质组学数据分析蛋白质组学数据分析实习六实习六系统生物学软件实习系统生物学软件实习 区块区块(block)背景背景A package of Open Source software programs for Microarray analysis 芯片数据采集（读取扫描图）芯片数据采集（读取扫描图）数据基本
2、处理数据基本处理存储整理芯片数据（数据库）存储整理芯片数据（数据库）芯片数据分析结果的图形显示芯片数据分析结果的图形显示（ ）inputoutput程序运行前程序运行前程序运行结果程序运行结果 由于样本差异、荧光标记效率和检出率的不平衡等因素，需对cy3和cy5的原始提取信号进行均衡和修正才能进一步分析实验数据，Normalization正是基于此种目的。Total Intensity normalizationInvalid-intensity checkingLOWESS (Locfit) normalizationIterative linear regression normaliza
3、tionIterative log mean centering normalizationRatio Statistics normalizationLow intensity filterStandard deviation regularizationSlice analysis (non-statistical)In-slide replicates analysisFlip-dye consistency checkingRatio Statistics confidence interval checkingSignal/Noise checkingCross-file-trimS
4、pot QC flag checkingMA-ANOVACross-slide replicates t-test (statistical)Cross-slide one-class SAM (statistical)MA plotIn many microarray gene expression experiments, the general assumption is that most of the genes would not see any change in their expression. Therefore the majority of the points on
5、the y axis (M) would be located at 0, since log(1) is 0.M=log2(R/G)A=log2R*GMIDAS 程序主界面可选的数据处理步骤数据分析流程设计各个处理步骤的相应参数程序运行状况显示log-ratios histogram(.his)Box plot (.box)Intensity plot (.ity)R-I (.prc)Intensity plot (.lty)常用工具栏常用工具栏导航栏导航栏结果界面结果界面1 选择选择“FileLoad Data”弹出导弹出导入数据对话框入数据对话框数据起始位置数据起始位置Why Pathw
6、ay Analysis?Intuitive to BiologistsProvide a biological context for resultsMore efficient than searching databases gene-by-geneIntuitive data display for sharing data Computation on Pathway ContentAnalyze over-representation of changed genes on pathways and ontologiesGenerate and compare pathway sig
7、natures between modelsSupported SpeciesFruit flyHumanMouseRatWormYeastZebrafishChicken DogCowMosquitoBy request:Any Ensembl speciesDatabases by other groups:Fission yeastE. coliSoon: Arabidopsis心肌炎患者数据心肌炎患者数据-脂肪酸降解途径脂肪酸降解途径ID System (Species)System CodeAffymetrix Probe Set IDXPDBPdEMBLEmPfamPfEnsemb
8、lEnRefSeqQ Entrez GeneLRGD (R. norvegicus)RFlyBase (D. melanogaster)FSGD (S.cerevisiae)DGene OntologyTUniProt/TrEMBLSHUGOHUniGeneUInterProIWormBase (C. elegans)WMGI (M. musculus)MZFIN (D. rerio)ZOMIMOmOtherOMicroarray Data FlowImage AnalysisDatabaseAGEDDatabaseOthersDatabaseMADRaw Gene Expression Da
9、taNormalized Data with Gene AnnotationInterpretation of Analysis Results.tiff Image FileGene AnnotationScannerPrinterNormalization / FilteringExpression AnalysisData Entry / ManagementGenMAPP 流程流程导入数据导入数据设置和应用颜色集设置和应用颜色集数据在代谢途径中图形化显示数据在代谢途径中图形化显示原始数据的处理和准备原始数据的处理和准备选定相应的代谢途径选定相应的代谢途径代谢途径全局分析代谢途径全局分析个别基因分析个别基因分析浙江加州国际纳米技术研究院
