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Table 2 Genome-wide correlation coefficients between experimental nucleosome occupancies and nucleosome occupancies predicted by different models

From: Structural features based genome-wide characterization and prediction of nucleosome organization

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