This directory contains the regPotential7X data values for the March
2006 hg18 human genome assembly. These regulatory potential were generated 
by members of the Comparative Genomics and Bioinformatics Center at Penn 
State University. More information about this research and the collection 
of known regulatory elements used in training the score can be found at the 
website http://www.bx.psu.edu/. 

Please note that the chromosome positions given in these files are 1-based 
positions; in this case, the first base position on a chromosome is "1". In 
this data set, the first location of data on chr1 is given as base position 
1362:

variableStep chrom=chr1
1362    0.0

This differs from our usual BED-format data, in which positions are 0-based,
i.e. the first base position on a chromosome is "0". 

For more information about this data set, see the Genome Browser description 
page for the track labeled "7X Reg Potential". 

(These data were corrected for chroms 3,4,9,10,20,21 to add some missing
data to the end of the chromosomes.  Updated 03 August 2007 in the UCSC
genome browser)

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References:

King DC, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison RC. 
Evaluation of regulatory potential and conservation scores for detecting
cis-regulatory modules in aligned mammalian genome sequences.
(http://www.genome.org/cgi/content/abstract/15/8/1051)
Genome Res. 2005 Aug;15(8):1051-60.

Kolbe D, Taylor J, Elnitski L, Eswara P, Li J, Miller W, Hardison RC and
Chiaromonte F. Regulatory potential scores from genome-wide three-way
alignments of human, mouse, and rat.
(http://www.genome.org/cgi/content/full/14/4/700) 
Genome Res. 2004 Apr;14(4):700-7.

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To download a large file or multiple files from this directory, we recommend 
that you use ftp rather than downloading the files via our website. To do so: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg18/regPotential7X

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

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All the files in this directory are freely available for public use.
For data use restrictions regarding the genome assemblies used in this
annotation, see http://genome.ucsc.edu/goldenPath/credits.html.

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt07-Sep-2007 11:55 2.6K 
[   ]chr1.regPotential7X.hg18.gz13-Jun-2006 10:45 515M 
[   ]chr2.regPotential7X.hg18.gz13-Jun-2006 11:19 526M 
[   ]chr3.regPotential7X.hg18.gz18-Jan-2007 11:21 435M 
[   ]chr4.regPotential7X.hg18.gz18-Jan-2007 12:26 371M 
[   ]chr5.regPotential7X.hg18.gz13-Jun-2006 12:05 386M 
[   ]chr6.regPotential7X.hg18.gz13-Jun-2006 12:09 354M 
[   ]chr7.regPotential7X.hg18.gz13-Jun-2006 12:27 319M 
[   ]chr8.regPotential7X.hg18.gz13-Jun-2006 12:30 292M 
[   ]chr9.regPotential7X.hg18.gz18-Jan-2007 13:06 261M 
[   ]chr10.regPotential7X.hg18.gz18-Jan-2007 13:53 293M 
[   ]chr11.regPotential7X.hg18.gz13-Jun-2006 13:10 298M 
[   ]chr12.regPotential7X.hg18.gz13-Jun-2006 13:12 272M 
[   ]chr13.regPotential7X.hg18.gz13-Jun-2006 13:29 189M 
[   ]chr14.regPotential7X.hg18.gz13-Jun-2006 13:30 196M 
[   ]chr15.regPotential7X.hg18.gz13-Jun-2006 13:43 191M 
[   ]chr16.regPotential7X.hg18.gz13-Jun-2006 13:42 179M 
[   ]chr17.regPotential7X.hg18.gz13-Jun-2006 13:53 180M 
[   ]chr18.regPotential7X.hg18.gz13-Jun-2006 13:53 157M 
[   ]chr19.regPotential7X.hg18.gz13-Jun-2006 13:58 94M 
[   ]chr20.regPotential7X.hg18.gz18-Jan-2007 14:14 139M 
[   ]chr21.regPotential7X.hg18.gz18-Jan-2007 14:26 67M 
[   ]chr22.regPotential7X.hg18.gz13-Jun-2006 14:04 77M 
[   ]chrX.regPotential7X.hg18.gz13-Jun-2006 14:14 246M 
[   ]chrY.regPotential7X.hg18.gz13-Jun-2006 14:05 17M 
[TXT]md5sum.txt07-Sep-2007 12:22 1.5K 

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