03f8972539f5ed48dd9026c8dd95be2764514e3e
jnavarr5
  Mon Sep 30 08:57:51 2019 -0700
Updating http to https for sacCer3, uiLinks cronjob

diff --git src/hg/makeDb/trackDb/sacCer/transRegCode.html src/hg/makeDb/trackDb/sacCer/transRegCode.html
index c515c8f..fdde339 100644
--- src/hg/makeDb/trackDb/sacCer/transRegCode.html
+++ src/hg/makeDb/trackDb/sacCer/transRegCode.html
@@ -1,72 +1,72 @@
 <H2>Description</H2> 
 
 <P>This track shows putative regulatory elements in <I>Saccharomyces
 cerevisiae</I> that are supported by cross-species evidence (Harbison,
 Gordon, <EM>et al</EM>., 2004).  Harbison, Gordon, <EM>et al</EM>. performed a genome-wide
 location analysis with 203 known DNA-binding transcriptional regulators
 (some under multiple environmental conditions) and identified 11,000
 high-confidence interactions between regulators and promoter regions.  They
 then compiled a compendium of motifs for 102 transcriptional regulators
 based on a combination of their experimental results, cross-species
 conservation data for four species of yeast and motifs from the
 literature.  Finally, they mapped these motifs to the
 <I>S. cerevisiae</I> genome.  This track shows positions at which these
 motifs matched the genome with high confidence and at which the
 matching sequence was well conserved across yeast species. </P>
 
 <P>The details page for each putative binding site shows the sequence at
 that site compared to the position-specific probability matrix for the
 associated transcriptional regulator (shown as both a table and a graphical
 logo).  It also indicates whether the binding site is supported by
 experimental (ChIP-chip) results and the number of other yeast species in
 which it is conserved.</P>
 
 <P>See also the "Reg. ChIP-chip" track for additional related information.</P>
 
 <H2>Display Conventions</H2> 
 
 <P>The scoring ranges from 200 to 1000 and is based on the number of lines of 
 evidence that support the motif being active.  Each of the two <I>sensu 
 stricto</I> species in which the motif was conserved counts as a line of 
 evidence.  If the ChIP-chip data showed good (P &le; 0.001) evidence of binding 
 to the transcription factor associated with the motif, that counts as two 
 lines of evidence.  If the ChIP-chip data showed weaker (P &le; 0.005) evidence 
 of binding, that counts as just one line of evidence.  The following table 
 shows the relationship between lines of evidence and score:<P>
 
 <BLOCKQUOTE>
 <TABLE BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD>
 <TABLE BORDER="1" BGCOLOR="#FFFEE8" CELLSPACING="0">
 <BLOCKQUOTE>
   <TR><TH>Evidence</TH><TH>Score</TH></TR>
   <TR><TD>4</TD><TD>1000</TD></TR>
   <TR><TD>3</TD><TD>500</TD></TR>
   <TR><TD>2</TD><TD>333</TD></TR>
   <TR><TD>1</TD><TD>250</TD></TR>
   
   <TR><TD>0</TD><TD>200</TD></TR>
   </BLOCKQUOTE>
   </TABLE>
   </TD></TR></TABLE>
 </BLOCKQUOTE>
 
 <H2>Credits</H2> 
 
 The data for this track was provided by the Young and Fraenkel labs at
 MIT/Whitehead/Broad.  The track was created by Jim Kent.
 
 <H2>References</H2>
 
 Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, MacIsaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J <EM>et al</EM>.  
 <a href="https://www.nature.com/articles/nature02800"
 target=_BLANK>Transcriptional regulatory code of a eukaryotic genome</a>. 
 <em>Nature</em>. 2004 Sep 2;431(7004):99-104.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15343339" target="_blank">15343339</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006441/" target="_blank">PMC3006441</a>
 </p>
 
 Supplementary data at <a href="http://younglab.wi.mit.edu/regulatory_code/"
  target=_BLANK>http://younglab.wi.mit.edu/regulatory_code/</a> and
- <a href="http://fraenkel.mit.edu/Harbison/"
+ <a href="http://younglab.wi.mit.edu/regulatory_code/"
  target=_BLANK>http://fraenkel.mit.edu/Harbison/</a>.
 <BR>