Table 2

Genome-wide correlation coefficients between experimental nucleosome occupancies and nucleosome occupancies predicted by different models

Prediction models

Features used in a model

Pearson correlation


In vitro [9]

In vivo [45]


Our integrated model (this paper)

12 structural features in a linear model

0.88

0.42


Xi et al., 2010 [54]

Position-dependant k-mer preferences (k up to 5)

0.618

0.34


Kaplan et al., 2009 [9]

Position-dependant 5-mer preferences and periodic dinucleotide

0.89

0.34


Tillo and Hughes, 2009 [10]

A linear model combining G + C content, propeller twist, slide and several 4-mer occurrence

0.86

0.38


Yuan and Liu, 2008 [14]

Periodic dinucleotide signals of linker and nucleosomal sequence

0.35

0.27


Gabdank et al.,2010 [24]

Uses DNA bendability matrix

0.41

0.25


Miele et al., 2008 [20]

Sequence-dependant free energy of nucleosome formation

0.38

0.22


Field et al., 2008 [2]

Uses 5-mer preferences and periodic dinucleotide

0.74

0.39


Lee et al., 2007 [45]

G + C content, 4-mer occurrence, TFBSs and several structural features

0.63

0.42


Gan et al. BMC Bioinformatics 2012 13:49   doi:10.1186/1471-2105-13-49

Open Data