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Table 2 Top features in CoreBoost

From: Boosting with stumps for predicting transcription start sites

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

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