Chen2008

CREATED: 200701030719 LINK: url:~/Modules/Literature/Chen2008.pdf ** Motif discovery

cluster coregulated genes

** gene annotation ** gene expression ** ChIP-ChIP ** phylogenetic footprinting

find DNA patterns that are enriched

** Finding motifs

• How to select cutoff?
• combinatorial, word statistics
• probabilistic, local MSA

** Gibbs sampler

• special case of Metropolis-Hasting sampling
• related work: KIMONO, REDUCE, GMEP, MDScan, Motif Repressor, EBMF

** Sequence weighting

• highly expressed genes should be given more weight in PWM
• present cutoff not needed since they will have small weight