Information Encoding in Biological Molecules DNA and ：生物分子DNA编码的信息.ppt

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Information Encoding in Biological Molecules DNA and ：生物分子DNA编码的信息.ppt

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Information Encoding in Biological Molecules DNA and ：生物分子DNA编码的信息

(c) CGDN August 17, 2004 Ben Bolstad (c) 2004 CGDN Microarray Data Analysis Class discovery and Class prediction: Clustering and Discrimination Gene expression profiles Many genes show definite changes of expression between conditions These patterns are called gene profiles Motivation (1): The problem of finding patterns It is common to have hybridizations where conditions reflect temporal or spatial aspects. Yeast cycle data Tumor data evolution after chemotherapy CNS data in different part of brain Interesting genes may be those showing patterns associated with changes. Our problem seems to be distinguishing interesting or real patterns from meaningless variation, at the level of the gene Finding patterns: Two approaches If patterns already exist ? Profile comparison (Distance analysis) Find the genes whose expression fits specific, predefined patterns. Find the genes whose expression follows the pattern of predefined gene or set of genes. If we wish to discover new patterns ?Cluster analysis (class discovery) Carry out some kind of exploratory analysis to see what expression patterns emerge; Motivation (2): Tumor classification A reliable and precise classification of tumours is essential for successful diagnosis and treatment of cancer. Current methods for classifying human malignancies rely on a variety of morphological, clinical, and molecular variables. In spite of recent progress, there are still uncertainties in diagnosis. Also, it is likely that the existing classes are heterogeneous. DNA microarrays may be used to characterize the molecular variations among tumours by monitoring gene expression on a genomic scale. This may lead to a more reliable classification of tumours. Tumor classification, cont There are three main types of statistical problems associated with tumor classification: The identification of new/unknown tumor classes using gene expression profiles - cluster analysis; The classification of malignancies into known classes - discri