Table 2

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

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]


Zheng et al. BMC Medical Genomics 2013 6(Suppl 1):S13   doi:10.1186/1755-8794-6-S1-S13

Open Data