Table 2

Top features in CoreBoost

Classifier type

Features

CpG

P versus U

Log-likelihood ratios from third order Markov chain, log-likelihood ratios from TSS weight matrix

GC-box score, weighted score of transcription factor NFY, weighted energy score at position +1

Weighted score of transcription factor YY1, TATA score, weighted score of transcription factor ELK1

MTE score, weighted score of transcription factor CREB

P versus D

Log-likelihood ratios from third order Markov chain, GC-box score

Weighted score of transcription factor NFY

Log-likelihood ratios from TSS weight matrix

Difference between the energy score around positions -25 and +1 and the average from surroundings

Log-likelihood ratios from transcription factor ELK1, frequency of G+C

Log-likelihood ratios from transcription factor YY1, TATA score, frequency of G

Non-CpG

P versus U

Correlation between vector of energy scores and empirical average energy profile

Log-likelihood ratios from third order Markov chain, TATA score

Difference between the energy score around positions -25 and +1 and the average from surroundings

Weighted energy at position +1

Proportion of Inr and GC-box pair within 10 bp of observed distance, Inr score.

P versus D

Correlation between vector of energy scores and empirical average energy profile, TATA score

Log-likelihood ratios from third order Markov chain

Weighted energy at position +1

Correlation between vector of flexibility scores and empirical average flexibility profile, Inr score

Difference between the flexibility score around position +1 and the average from surroundings, GC-box score

bp, base pairs; D, immediate downstream sequence; P, promoter; TSS, transcription start site; U, immediate upstream sequence.

Zhao et al. Genome Biology 2007 8:R17   doi:10.1186/gb-2007-8-2-r17