lecture_10pt1

lecture_10pt1 - An Example of Clustering Expression Data...

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An Example of Clustering Expression Data 6.874 / 7.90 Computational Functional Genomics Spring 2005
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Input Optimal ordering Hierarchical clustering Input Hierarchical clustering Optimal ordering Results – hand generated data
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Problem definition Denote by Φ the space of the possible linear orderings consistent with the tree. Denote by v 1 …v n the tree leaves. Our goal is to find an ordering that maximizes the similarity of adjacent elements: ) , ( 1 1 1 max v v i n i i S φ + = Φ where S is the similarity matrix
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59 experiments, combining cdc15, cdc28 and α factor arrest
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Discovering new types of cancer Alizadeh, A., Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling, Nature 403, pp. 503- 511 (February 3, 2000) (Does not use optimal ordering)
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Goal • Discover cause for different disease courses for diffuse large B-cell lymphoma (DLBCL) – 40% of patients respond to therapy – 60% succumb to disease • Provide diagnostic / prognostic tool • DLBCL is most common subtype of non- Hodgkin’s lymphoma
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lecture_10pt1 - An Example of Clustering Expression Data...

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