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] |