Table 1 |
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|
List of default attributes included in EpiGRAPH |
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|
Total number of attributes |
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|
|
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|
Attribute groups |
hg18 |
hg17 |
mm9 |
panTro2 |
galGal3 |
Attributes (examples) |
|
|
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|
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 |
|
|
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|
Sum |
896 |
900 |
453 |
317 |
403 |
|
|
|
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|
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. |
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|
Bock et al. Genome Biology 2009 10:R14 doi:10.1186/gb-2009-10-2-r14 |
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