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lect 04 signal sensor, pwm

lect 04 signal sensor, pwm - BIOC 2808 Lecture 4 Signal...

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Click to edit Master subtitle style 7/29/10 BIOC 2808 Lecture 4 Signal sensor, PWM, and Motif discovery Instructor Dr. Junwen Wang
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7/29/10 Signal sensor A feature is any DNA subsequence of biological significance . For practical reasons, we recognize two broad classes of features: signals short, fixed-length features such as regulatory elements, start codons, stop codons, or splice sites content regions variable-length features such as exons or introns
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7/29/10 Gene Structure
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7/29/10 Today’s topics What are cis- and trans- elements (transcription factor and its binding sites) Position Weight Matrix(PWM) and TFBS representation Motif discovery by EM algorithm
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7/29/10 Transcriptional Regulation TF-DNA binding Interactions and Modules
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Picture from http://weblogo.berkeley.edu/
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Click to edit Master subtitle style 7/29/10 Application of motif finding
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7/29/10 Clustering of Genes Find binding sites responsible for common expression patterns
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7/29/10 Chromatin Immunoprecipitation Microarray Chip “ChIP-chip”
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7/29/10 Finding Regulatory Motifs Given a collection of genes with common expression, Find the TF-binding motif in common . . .
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Click to edit Master subtitle style 7/29/10 Finding know TFBS
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7/29/10 Representing motif by PWM AATTGTGGTTA ATCTGTGGTTA AATTGTGGTAA TTCTGCGGTTA AATTGCGGTAA 12345678901 WWYTGYGGTWA A C G T 1 4 1 2 3 2 3 2 3 4 5 5 5 6 2 3 7 5 8 5 9 5 10 2 3 11 5 A C G T 1 4 0.1 0.1 1 2 3 0.1 0.1 2 3 0.1 2 0.1 3 4 0.1 0.1 0.1 5 5 0.1 0.1 5 0.1 6 0.1 2 0.1 3 7 0.1 0.1 5 0.1 8 0.1 0.1 5 0.1 9 0.1 0.1 0.1 5 10 2 0.1 0.1 3 11 5 0.1 0.1 0.1
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7/29/10 Normalization and log transformation A C G T base compos 0.3 0.2 0.2 0.3 expected ct 1.5 1 1 1.5 Pos A C G T Con 1 2.67 0.1 0.1 0.67 A 2 2 0.1 0.1 1.33 A 3 0.07 2 0.1 2 T 4 0.07 0.1 0.1 3.33 T 5 0.07 0.1 5 0.07 G 6 0.07 2 0.1 2 T 7 0.07 0.1 5 0.07 G 8 0.07 0.1 5 0.07 G 9 0.07 0.1 0.1 3.33 T 10 1.33 0.1 0.1 2 T 11 3.33 0.1 0.1 0.07 A Pos A C G T Con 1 4 0.1 0.1 1 A 2 3 0.1 0.1 2 A 3 0.1 2 0.1 3 T 4 0.1 0.1 0.1 5 T 5 0.1 0.1 5 0.1 G 6 0.1 2 0.1 3 T 7 0.1 0.1 5 0.1 G 8 0.1 0.1 5 0.1 G 9 0.1 0.1 0.1 5 T 10 2 0.1 0.1 3 T 11 5 0.1 0.1 0.1 A Pos A C G T Con 1 0.43 -1 -1 -0.2 A 2 0.3 -1 -1 0.12 A 3 -1.2 0.3 -1 0.3 T 4 -1.2 -1 -1 0.52 T 5 -1.2 -1 0.7 -1.2 G 6 -1.2 0.3 -1 0.3 T 7 -1.2 -1 0.7 -1.2 G 8 -1.2 -1 0.7 -1.2 G 9 -1.2 -1 -1 0.52 T 10 0.12 -1 -1 0.3 T 11 0.52 -1 -1 -1.2 A Matrix Normalization Log transformation
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7/29/10 Relative Entropy A,T,C,G are not equally likely distributed in Genome. Ex: %A/T=60%, %C/G=40% Then relative entropy at a position i is defined as where Q is the background distribution Relative distance of two distribution
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  • Fall '09
  • DR.JJWANG
  • probability density function, Maximum likelihood, Estimation theory, Likelihood function, Expectation-maximization algorithm

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