Sanger ChIP Hits Track Settings
 
Sanger ChIP-chip Hits and Peak Centers   (Sanger ChIP-chip)

This track is part of a parent called 'Sanger ChIP-chip'. To show other tracks of this parent, go to the Sanger ChIP-chip configuration page.

Display mode:       Reset to defaults

Type of graph:
Track height: pixels (range: 16 to 128)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 49.45)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
Select subtracks:
    All                    
    Data_Type
            Hit
            Peak_Center
    Cell_Type
            GM06990
            HeLa
            K562
    Factor
            H3K4me1
            H3K4me2
            H3K4me3
            H3ac
            H4ac
List subtracks: only selected/visible    all    ()  
dense
 SI H3K4m1 GM6990  Sanger Institute ChIP-chip Hits (H3K4me1 ab, GM06990 cells)   schema 
dense
 SI H3K4m2 GM6990  Sanger Institute ChIP-chip Hits (H3K4me2 ab, GM06990 cells)   schema 
dense
 SI H3K4m3 GM6990  Sanger Institute ChIP-chip (H3K4me3 ab, GM06990 cells)   schema 
dense
 SI H3ac GM06990  Sanger Institute ChIP-chip Hits (H3ac ab, GM06990 cells)   schema 
dense
 SI H4ac GM06990  Sanger Institute ChIP-chip Hits (H4ac ab, GM06990 cells)   schema 
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 SI H3K4me2 K562  Sanger Institute ChIP-chip Hits (H3K4me2 ab, K562 cells)   schema 
dense
 SI H3K4me3 K562  Sanger Institute ChIP-chip Hits (H3K4me3 ab, K562 cells)   schema 
dense
 SI H3ac K562  Sanger Institute ChIP-chip Hits (H3ac ab, K562 cells)   schema 
dense
 SI H4ac K562  Sanger Institute ChIP-chip Hits (H4ac ab, K562 cells)   schema 
dense
 SI H3K4me1 HeLa  Sanger Institute ChIP-chip Hits (H3K4me1 ab, HeLa cells)   schema 
dense
 SI H3K4me2 HeLa  Sanger Institute ChIP-chip Hits (H3K4me2 ab, HeLa cells)   schema 
dense
 SI H3K4me3 HeLa  Sanger Institute ChIP-chip Hits (H3K4me3 ab, HeLa cells)   schema 
dense
 SI H3ac HeLa  Sanger Institute ChIP-chip Hits (H3ac ab, HeLa cells)   schema 
dense
 SI H4ac HeLa  Sanger Institute ChIP-chip Hits (H4ac ab, HeLa cells)   schema 
dense
 SI H3K4m1 GM6990  Sanger Institute ChIP-chip Peak Centers (H3K4me1 ab, GM06990 cells)   schema 
dense
 SI H3K4m2 GM6990  Sanger Institute ChIP-chip Peak Centers(H3K4me2 ab, GM06990 cells)   schema 
dense
 SI H3K4m3 GM6990  Sanger Institute ChIP-chip Peak Centers(H3K4me3 ab, GM06990 cells)   schema 
dense
 SI H3ac GM06990  Sanger Institute ChIP-chip Peak Centers (H3ac ab, GM06990 cells)   schema 
dense
 SI H4ac GM06990  Sanger Institute ChIP-chip Peak Centers (H4ac ab, GM06990 cells)   schema 
dense
 SI H3K4me2 K562  Sanger Institute ChIP-chip Peak Centers (H3K4me2 ab, K562 cells)   schema 
dense
 SI H3K4me3 K562  Sanger Institute ChIP-chip Peak Centers (H3K4me3 ab, K562 cells)   schema 
dense
 SI H3ac K562  Sanger Institute ChIP-chip Peak Centers (H3ac ab, K562 cells)   schema 
dense
 SI H4ac K562  Sanger Institute ChIP-chip Peak Centers (H4ac ab, K562 cells)   schema 
dense
 SI H3K4me1 HeLa  Sanger Institute ChIP-chip Peak Centers (H3K4me1 ab, HeLa cells)   schema 
dense
 SI H3K4me2 HeLa  Sanger Institute ChIP-chip Peak Centers (H3K4me2 ab, HeLa cells)   schema 
dense
 SI H3K4me3 HeLa  Sanger Institute ChIP-chip Peak Centers (H3K4me3 ab, HeLa cells)   schema 
dense
 SI H3ac HeLa  Sanger Institute ChIP-chip Peak Centers (H3ac ab, HeLa cells)   schema 
dense
 SI H4ac HeLa  Sanger Institute ChIP-chip Peak Centers (H4ac ab, HeLa cells)   schema 
    
Data version: ENCODE Oct 2005 Freeze
Data coordinates converted via liftOver from: May 2004 (NCBI35/hg17)

Description

This track displays hit regions and peak centers for Sanger ChIP-chip data, as identified by hidden Markov model (HMM) analysis.

Display Conventions and Configuration

This annotation follows the display conventions for composite tracks. The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.

Methods

Data for each replicate was normalized with the Tukey-Biweight Method using R (as recommended by NimbleGen). The log base 2 ratio of the normalized intensities was used for downstream data processing.

A two-state HMM was used to analyze the data. The states of the HMM represent regions of the tile path corresponding to antibody binding locations. State emission probabilities were determined by comparing the cumulative distribution of the experimental data for each replicate on each ENCODE region to a fitted cumulative normal distribution. The fitted distribution was calculated using the Levenberg-Marquart curve-fitting technique and six fitting points ranging from 0.05 to 0.45 of the cumulative distribution. Initial fitting parameters were set from the experimental data. This model is robust through a range of sensible transition probabilities.

Bound regions were identified by finding the optimal state sequence from the HMM using the Viterbi algorithm, and the resulting region data was post-processed to develop the hit list. Hits were defined as contiguous portions of the tile path identified as bound by the HMM. The score of a hit was determined by taking the summation of the median enrichment values of the tiles in the contiguous portions (i.e. the area under the peak). For the purpose of this analysis, hits that were within 1000 base pairs of adjacent hits were combined into hit regions.

The start position of the oligo with the highest enrichment value in the hit region was deemed the center of the peak. The ranking of hits was based on the total score of all hits in a hit region. It is recommended that analysis based on this data use the peak centers expanded to a convenient size for the analysis.

Credits

The ChIP-chip data were generated by Ian Dunham's lab at the Sanger Institute. Contacts: Ian Dunham and Christoph Koch.

The HMM analysis was performed at the EBI by Paul Flicek.

Raw data may be downloaded from the Sanger Institute website at ftp://ftp.sanger.ac.uk/pub/encode.