Three Periods Of Regulatory Innovation: Difference between revisions
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[http://genome.ucsc.edu/cgi-bin/hgTracks?db=gasAcu1&hgt.customText=http://www.stanford.edu/~lowec/data/threePeriods/ThreePeriodsGasAcu1Cnee_track.txt Click here] to load a track with all stickleback CNEEs along with their branch of origin (gasAcu1 assembly) | [http://genome.ucsc.edu/cgi-bin/hgTracks?db=gasAcu1&hgt.customText=http://www.stanford.edu/~lowec/data/threePeriods/ThreePeriodsGasAcu1Cnee_track.txt Click here] to load a track with all stickleback CNEEs along with their branch of origin (gasAcu1 assembly) | ||
[http://genome.ucsc.edu/cgi-bin/hgTracks?db=oryLat2&hgt.customText=http://www.stanford.edu/~lowec/data/threePeriods/ThreePeriodsOryLat2Cnee_track.txt Click here] to load a track with all medaka CNEEs along with their branch of origin ( | [http://genome.ucsc.edu/cgi-bin/hgTracks?db=oryLat2&hgt.customText=http://www.stanford.edu/~lowec/data/threePeriods/ThreePeriodsOryLat2Cnee_track.txt Click here] to load a track with all medaka CNEEs along with their branch of origin (oryLat2 assembly) | ||
==Files To Download== | ==Files To Download== | ||
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==Reference== | ==Reference== | ||
Three Periods of Regulatory Innovation During Vertebrate Evolution.<br> | |||
Craig B. Lowe, Manolis Kellis, Adam Siepel, Brian J. Raney, Michele Clamp, Sofie R. Salama, David M. Kingsley, Kerstin Lindblad-Toh, David Haussler.<br> | |||
Science. 2011 Aug;333(6045):1019-1024. | |||
Revision as of 20:43, 18 August 2011
On-line Supplement: Three Periods Of Regulatory Innovation During Vertebrate Evolution
Genome Browser Tracks
Links in this section will allow you to visualize the sets of CNEEs in the UCSC genome browser. When you click on the link you will be taken to the browser for that species and one of the tracks towards the top titled "Conserved Non-exonic Elements" and subtitled "CNEEs" will show the CNEES we used in this study. If you click on a CNEE in the browser, you will see a number that corresponds to the branch of origin for that CNEE. This image can be used to convert the number to a branch.
Click here to load a track with all human CNEEs along with their branch of origin (hg18 assembly)
Click here to load a track with all human CNEEs along with their branch of origin (mapped to the hg19 assembly)
Click here to load a track with all mouse CNEEs along with their branch of origin (mm9 assembly)
Click here to load a track with all cow CNEEs along with their branch of origin (bosTau4 assembly)
Click here to load a track with all stickleback CNEEs along with their branch of origin (gasAcu1 assembly)
Click here to load a track with all medaka CNEEs along with their branch of origin (oryLat2 assembly)
Files To Download
We realize that along with visualizing data sets in the browser, it can be useful to have raw data files available. These raw data files are in bed format. The "Score" column in the bed file holds a number that represents the inferred branch of origin for that CNEE. This image can be used to convert the number to a branch. The files have been compressed with gzip and are therefore named "exampleName.bed.gz".
Click here to download the human CNEEs as a gzipped bed file (hg18 assembly)
Click here to download the human CNEEs as a gzipped bed file (mapped to the hg19 assembly)
Click here to download the mouse CNEEs as a gzipped bed file (mm9 assembly)
Click here to download the cow CNEEs as a gzipped bed file (bosTau4 assembly)
Click here to download the stickleback CNEEs as a gzipped bed file (gasAcu1 assembly)
Click here to download the medaka CNEEs as a gzipped bed file (oryLat2 assembly)
Reference
Three Periods of Regulatory Innovation During Vertebrate Evolution.
Craig B. Lowe, Manolis Kellis, Adam Siepel, Brian J. Raney, Michele Clamp, Sofie R. Salama, David M. Kingsley, Kerstin Lindblad-Toh, David Haussler.
Science. 2011 Aug;333(6045):1019-1024.
