Schema for Neandertal Methyl - Neandertal Reconstructed DNA Methylation Map
Database: hg19 Primary Table: neandertalMethylation Row Count: 26,681,234   Data last updated: 2014-08-28|
Format description: Browser extensible data
|field||example||SQL type ||description |
|bin ||585||smallint(5) unsigned ||Indexing field to speed chromosome range queries.|
|chrom ||chr1||varchar(255) ||Reference sequence chromosome or scaffold|
|chromStart ||10469||int(10) unsigned ||Start position in chromosome|
|chromEnd ||10470||int(10) unsigned ||End position in chromosome|
|name ||48.9178||varchar(255) ||Name of item|
|score ||489||int(10) unsigned ||Optional score, nominal range 0-1000|
|strand ||+||char(1) ||+ or -|
|thickStart ||10469||int(10) unsigned ||Start of where display should be thick (start codon)|
|thickEnd ||10470||int(10) unsigned ||End of where display should be thick (stop codon)|
|itemRgb ||16776960||int(10) unsigned ||Used as itemRgb as of 2004-11-22|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
Neandertal Methyl (neandertalMethylation) Track Description
This track shows the reconstructed DNA methylation map of the Neandertal genome,
derived from bone tissues.
Display conventions and configuration
Green to red scaling is used as a rough indicator of methylation.
Values range from 0% (green, unmethylated) to 100% (red, methylated).
Data are displayed for CpG positions across the genome.
Gokhman et al. reconstructed the DNA methylation maps of two archaic humans,
the Neandertal and the Denisovan, based on the natural deamination of cytosines
in ancient DNA. With time, cytosines (C's) in post-mortem DNA lose their amine
group (deamination). However, deamination of methylated vs. unmethylated C's
results in different products - Methylated C's are deaminated with time to T's,
whereas unmethylated C's are deaminated to U's.
The U's are later removed during ancient DNA library preparation and as a result,
a distinct pattern is observed: methylated regions in the genome display high C-->T
conversion rate, whereas unmethylated regions display a low C-->T conversion rate.
These patterns were used to reconstruct the full DNA methylation maps of the archaic humans.
This track was produced at UCSC using data generated by Gokhman et al
Gokhman D, Lavi E, Prüfer K, Fraga MF, Riancho JA, Kelso J, Pääbo S, Meshorer E,
Reconstructing the DNA methylation maps of the Neandertal and the Denisovan.
Science. 2014 May 2;344(6183):523-7.