系统生物学软件（王栋）系统生物学软件-2.pptVIP

系统生物学软件 王 栋 wangdong@ BRB-ArrayTools Overview of the software’s capabilities Importing data Gene annotations Filtering, normalization Hierarchical cluster analysis of genes Hierarchical cluster analysis of experiments Survival analysis Class comparison between groups of arrays Significance Analysis of Microarrays Processing expression data from multiple experiments, visualization of data, multidimensional scaling, clustering of genes and samples, and classification and prediction of samples. Single-channel and dual-channel experiments. Implemented as an Excel add-in so that it has an interface that is familiar to biologists.  Spotted cDNA arrays| Affymetrix arrays 问题： Affymetrix GeneChip 原理？ 独特的PM-MM探针设计 ？ A probe set = 11-20 PM, MM pairs Single-channel experiments GEO: GSE19188 91 tumor and 65 adjacent normal lung tissue samples Affymetrix Human Genome U133 Plus 2.0 Array Due-channel experiments Chen X, et al. (2004) Mod Pathol 17(10):1198-210 Gene expression patterns in human liver cancers Spot filters For single-channel data, a spot on any array, which has a signal intensity less than the specified minimum, may either be filtered out or thresholded on the filtered log intensity worksheet. Normalization by reference array The normalization is performed by computing a gene-by-gene difference between each array and the reference array, and subtracting the median difference from the log-intensities on that array, so that the gene-by-gene difference between the normalized array and the reference array is 0. Single-channel experiments GEO: GSE19188 91 tumor and 65 adjacent normal lung tissue samples Affymetrix Human Genome U133 Plus 2.0 Array Due-channel experiments Chen X, et al. (2004) Mod Pathol 17(10):1198-210 Gene expression patterns in human liver cancers * * BRB-ArrayTools is an integrated software package for the