ClusteringShortGeneExpressionProfiles基因表达谱聚类的短裤.pptVIP

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ClusteringShortGeneExpressionProfiles基因表达谱聚类的短裤.ppt

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ClusteringShortGeneExpressionProfiles基因表达谱聚类的短裤

* * * * * * * * * Abdullah Mueen Clustering Short Gene Expression Profiles Ling Wang Marco RamoniPaolo Sebastiani Abdullah Mueen * The Problem: Input Gene Symbol 0h 0.5h 3h 6h 12h 1 ZFX -0.027 0.158 0.169 0.193 -0.165 2 ZNF133 0.183 -0.068 -0.134 -0.252 0.177 3 USP2 -0.67 -0.709 -0.347 -0.779 -0.403 4 DSCR1L1 -0.923 -0.51 -0.718 -0.512 -0.668 5 WNT5A -0.471 -0.264 -0.269 -0.154 -0.254 . . . . . . . . . . . . . . . . . . . . . 24180 0.983 1.55 2.541 2.187 0.147 Abdullah Mueen * Gene expression profiles for J genes from microarray experiments [1] The Problem: Output A clustering of the genes that groups functionally related genes in the same cluster. Abdullah Mueen * Previous Works Hierarchical Clustering (Eisen et al., 1998) K-means and self organizing maps (Tamayo et al, 1999) Standard measures : Euclidian Distance, Correlation coefficient. Problem Ignores the sequential nature of the profiles. Different pairs of time series can have same measure. Abdullah Mueen * [3] Previous Works Continuous representation of the profile using Autoregressive Models. Hidden Markov Models. Advantages: Count the temporal information Good for long profiles ( 10 points or more ) Easily go with Bayesian Clustering. Abdullah Mueen * [3] Autoregressive Model: Definition Each time point is correlated with p previous time points. Combining the models of all the time points for a gene Xj is the regression matrix of size (n-p)x(p+1) and βj is the coefficient matrix. Abdullah Mueen * [2] Autoregressive Model: Problems Problems AR model is for stationary time series. Interval between time points are ignored. For short gene expression profiles (5 time points) the regression order can not be large. For a large number of genes with short expression profiles, there may be random patterns. AR model overfit these random patterns. Abdullah Mueen * The Algorithm The algorithm has three components A model describing the dynamics of gene expression temporal profiles. A probabilist