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Table 1 List of default attributes included in EpiGRAPH

From: EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data

  Total number of attributes  
Attribute groups hg18 hg17 mm9 panTro2 galGal3 Attributes (examples)
DNA sequence 178 178 178 178 178 Frequency of 'TATA' pattern, cytosine content, CpG frequency
DNA structure 21 21 21 21 21 Predicted DNA helix twist, predicted solvent accessibility
Repetitive DNA 95 95 91 94 94 Overlap with Alu elements, LINEs and tandem repeats
Chromosome organization 18 29 15 - - Overlap with chromosomal bands and isochors
Evolutionary history 94 101 - - 86 Overlap with evolutionarily conserved regions
Population variation 75 75 - - - SNP density and overlap with specific SNP types (for example, non-synonymous exonic or splice site)
Genes 37 60 20 10 10 Overlap with annotated genes, pseudogenes and predicted microRNA genes
Regulatory regions 249 259 5 5 5 Overlap with CpG islands and predicted transcription factor binding sites
Transcriptome 49 65 9 9 9 Overlap with ESTs and mRNA sequences
Epigenome and chromatin structure 80 17 114 - - Overlap with ChIP-seq tags indicating enrichment for specific histone modifications
Sum 896 900 453 317 403  
  1. This table summarizes the collection of default attributes that are currently included in EpiGRAPH. Due to different degrees of annotation, the numbers differ between the genomes of human (hg18 and hg17), mouse (mm9), chimp (panTro2) and chicken (galGal3). EST, expressed sequence tag; SNP, single nucleotide polymorphism.