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Figure 2 | BMC Genomics

Figure 2

From: T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets

Figure 2

A schematic overview of T-KDE.As input, T-KDE uses the locations of peak centers (defined by chromosome and coordinate), not the sequence reads. Step 1: order the peak centers for a TF from all cell lines together and partition them into subsets (terminal nodes) using a binary range tree algorithm. Solid circles indicate terminal nodes. Step 2: apply KDE to estimate a density function for each terminal node. Horizontal lines represent ChIP-seq peaks with dots indicating their centers. The blue curve is the estimated density function. Step 3: apply a mode finding algorithm to each terminal node’s density estimate to identify the modal regions associated with each local maximum. The density function shown has four local maxima (the rightmost two almost coincide); a horizontal red bar marks the constitutive modal region and seven vertical lines mark boundaries of the modal regions.

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