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 | |