Stats254_Ch3_Sequence_6

Stats254_Ch3_Sequence_6 - 3.2 Discovery of cis-regulatory...

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± 3.2 Discovery of cis -regulatory modules References of this section: Zhou and Wong (2004) PNAS 101: 12114-12119. Johnson et al. (2005) Genome Res. 15: 1315-1324. Zhou and Wong (2007) Annals of Applied Statistics 1: 36-65. Cis -regulatory modules Combinatorial control of genes: cis-regulatory modules module module
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± Modeling module structure Module structure: consider co-localization of motif sites. Motif 1 Motif 2 Motif 3 Hierarchical Mixture modeling K : # of motifs B M S Parameters and missing data Missing data problem. K # of motifs l Module length S Set of sequences M Indicators for a module start A Indicators for a motif site start Background model Weight matrices for motifs W Motif widths r Probability of a module start q Probability of starting a motif site Given Observed data Missing data Parameters Ψ
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± Bayesian inference by posterior sampling Module-motif detection Given Θ , r , q, and W, 1) Sample modules: 2) Within each module, sample motif sites:
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This note was uploaded on 11/24/2010 for the course STAT 201a taught by Professor Wu during the Spring '10 term at Pasadena City College.

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Stats254_Ch3_Sequence_6 - 3.2 Discovery of cis-regulatory...

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