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 | |
|---|---|---|---|
| Â | Â | 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 |