Utilizing promoter pair orientations for HMM-based analysis of ChIP-chip data





Fig.1: Exemplary Hidden Markov Model with scaled transition matrices (SHMM) for the analysis of ChIP-chip profiles. The two states + and - model the potenial of a promoter to be a target (+) or not to be a target (-) of the studied transcription factor. Each state is characterized by its Gaussian emission distribution. The arrows represent transitions between the ChIP-chip measurements of adjacent promoters on the DNA. Thick arrows characterize adjacent promoters in head-head orientation, and thin arrows model adjacent promoters that are not in head-head orientation.

Overview

Motivation

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Case Study

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Log-Fold-Change Analysis

Standard HMMs

SHMMs

General Usage

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ID

Chr

Start

End

Strand

NextIsDirectNeighbor

Log-Ratio

A

1

10

12

1

FALSE

1.87

B

1

15

16

-1

TRUE

-0.93

C

1

18

20

1

FALSE

-0.88

D

2

12

20

-1

TRUE

2.72

E

2

26

54

-1

FALSE

0.03

F

5

13

27

1

FALSE

1.41


© Michael Seifert July 2008