Tracks and Tables

Methylation Data

Methylation Data was exported to the following formats:

Sample summary

This section contains summary metrics for each sample as well as links to exported files. The summary table below contains the following metrics. It is also available as csv file.

Bed files for each sample contain the locations of methylation sites and regions the methylation level (in the score column). The following table links to the files. The files can be quite large in size, so you might want to consider using the "save as" option instead of opening the links directly.

sampleName sites_bigBedFile sites_bedFile sites_num tiling_num tiling_numSitesMean tiling_numSitesMedian tiling_numSites2 tiling_numSites5 tiling_numSites10 tiling_numSites20 genes_num genes_numSitesMean genes_numSitesMedian genes_numSites2 genes_numSites5 genes_numSites10 genes_numSites20 promoters_num promoters_numSitesMean promoters_numSitesMedian promoters_numSites2 promoters_numSites5 promoters_numSites10 promoters_numSites20 cpgislands_num cpgislands_numSitesMean cpgislands_numSitesMedian cpgislands_numSites2 cpgislands_numSites5 cpgislands_numSites10 cpgislands_numSites20
1 bigBed bed 471548 133950 3.52108249346771 1 63024 32168 14077 1204 30784 12.7912551975052 8 26434 20474 13016 5460 30969 6.71826665375052 6 26213 18916 8552 353 26610 5.56136790680195 4 25467 12135 3704 271
2 bigBed bed 471549 133950 3.5210899589399 1 63024 32168 14077 1204 30784 12.7912876819127 8 26434 20474 13016 5460 30969 6.7182989441054 6 26213 18916 8552 353 26610 5.56140548665915 4 25467 12135 3704 271
3 bigBed bed 471546 133950 3.52106756252333 1 63024 32167 14077 1204 30784 12.7912227130977 8 26434 20474 13016 5460 30969 6.71823436339565 6 26213 18915 8552 353 26610 5.56133032694476 4 25467 12135 3704 271
4 bigBed bed 471547 133950 3.52107502799552 1 63024 32167 14077 1204 30784 12.7912227130977 8 26434 20474 13016 5460 30969 6.71820207304078 6 26213 18916 8552 353 26610 5.56133032694476 4 25467 12135 3704 271
5 bigBed bed 471549 133950 3.5210899589399 1 63024 32168 14077 1204 30784 12.7912876819127 8 26434 20474 13016 5460 30969 6.7182989441054 6 26213 18916 8552 353 26610 5.56140548665915 4 25467 12135 3704 271
6 bigBed bed 471547 133950 3.52107502799552 1 63024 32168 14077 1204 30784 12.7912551975052 8 26434 20474 13016 5460 30969 6.71823436339565 6 26213 18916 8551 353 26610 5.56133032694476 4 25467 12135 3704 271
7 bigBed bed 471547 133950 3.52107502799552 1 63024 32168 14077 1204 30784 12.7912551975052 8 26434 20474 13016 5460 30969 6.7182989441054 6 26213 18916 8552 353 26610 5.56140548665915 4 25467 12135 3704 271
8 bigBed bed 471548 133950 3.52108249346771 1 63024 32168 14077 1204 30784 12.7912876819127 8 26434 20474 13016 5460 30969 6.7182989441054 6 26213 18916 8552 353 26610 5.56136790680195 4 25467 12135 3704 271
9 bigBed bed 471548 133950 3.52108249346771 1 63024 32168 14077 1204 30784 12.7912551975052 8 26434 20474 13016 5460 30969 6.7182989441054 6 26213 18916 8552 353 26610 5.56140548665915 4 25467 12135 3704 271
10 bigBed bed 471548 133950 3.52108249346771 1 63024 32168 14077 1204 30784 12.7912227130977 8 26434 20474 13016 5460 30969 6.71823436339565 6 26213 18916 8551 353 26610 5.56136790680195 4 25467 12134 3704 271
11 bigBed bed 471548 133950 3.52108249346771 1 63024 32168 14077 1204 30784 12.7912551975052 8 26434 20474 13016 5460 30969 6.7182989441054 6 26213 18916 8552 353 26610 5.56140548665915 4 25467 12135 3704 271
12 bigBed bed 471548 133950 3.52108249346771 1 63024 32168 14077 1204 30784 12.7912551975052 8 26434 20474 13016 5460 30969 6.7182989441054 6 26213 18916 8552 353 26610 5.56136790680195 4 25467 12134 3704 271

Tracks Hubs

Track Hub data was generated for export to various genome browsers. Note that you need a server that is capable of serving the tracks to the genome browser via URL. Below, instructions are provided to view the tracks in the UCSC genome browser. Of course the files can also be viewed in other browsers such as the Ensembl genome browser.

  1. Make sure you are viewing this report via the internet and not locally (simply look at the URL in the address line of your browser). If this is not the case, copy the files belonging to this report to a directory which is accessible via the internet and enter the corresponding URL in your browser. If you don't want to copy the entire report, it suffices to copy the track hub directories (see table(s) below).
  2. Make sure the hg19 subdirectories in the track hub directory (for its location be referred to the table(s) below) contain all the required bigBed/bigWig files
  3. Go to the UCSC hub connection website to the "My Hubs" tab and add the web-URL of the hub.txt file in the directory you just copied. Hint: You can use the copy link functionality of your browser (right mouse click) on the track hub txt column in the table(s) below. Don't forget to click on "Load Selected Hubs".
  4. Make sure you are looking at the correct genome (hg19). The loaded hubs should now appear below the browsing window where you can modify their display settings.
More information on UCSC track hubs can be found here. Below, you find table(s) containing the directory names for the bed/bedGraph and track hub directories for all exported data, site and region types.

bigBed

bigWig