Computational and Mathematical Methods in Medicine / 2012 / Article / Tab 2

Research Article

Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data

Table 2

An overview of the characteristics of different Chip-Seq peak detection algorithm.

AlgorithmProfileBackground modelControl sampleUse control to compute FDR

F-SeqKernel density estimation (KDE)
FindPeaksAggregation of overlapped tagsMonte Carlo
SISSRsWindow scanPoisson
QuESTKernel density estimation (KDE)
MACSTags shifted then window scandynamic Poisson
CisGenomeStrand-specific window scanNegative binomial