Skip to main content

Advertisement

Table 2 Number of features in each category and information resource for the feature extraction.

From: CpGIMethPred: computational model for predicting methylation status of CpG islands in human genome

Category # Features Resource
General attributes 3 Gardiner-Garden criteria [19], obtained from UCSC Genome Browser
DNA sequence composition tetramer frequency 256 calculated by in-house code based on definition
  tetramer z-score 256 calculated by in-house code based on formula (1)-(3)
Conserved TFBS's/elements conserved TFBS's 230 calculated by in-house code based on UCSC information [24]
  conserved elements 2 calculated by in-house code based on conserved elements [15] from UCSC
Structural properties DNA 3-D conformation 6 calculated by in-house code based on formula [25]
  nucleosome positioning propensity 4 calculated by in-house code using nucleosome organization map [27]
Functional roles of nearby genes 2 calculated by in-house code for enrichment analysis
Histone modifications histone methylation 46 calculated by in-house code based on the data set from [31]
  histone acetylation 36 calculated by in-house code based on the data set from [33]