fa272dac584b8d450211f426b50c5e9e6de114c8
mspeir
  Tue Sep 22 08:40:34 2026 -0700
New FAQ page on regulation and cis-regulatory tracks, refs #24610

Adds FAQ/FAQregulation.html, the page requested in this ticket since 2019:
where to find transcription factor binding site data, and how the various
cis-regulatory tracks relate to each other.

The page is organized around the measured vs predicted distinction, which is
what most of the mailing list questions turn on, and then covers which TFBS
tracks to use, what to do when a factor is in none of them, loading ENCODE
portal data through the portal's own Visualize button, promoters, enhancers,
cCREs, restricting to a cell type, and working outward from a gene. It ends
with a summary table of 16 tracks.

Assembly coverage is given per track and every assembly name is a link to
that track's description page on that assembly, since coverage varies a lot
(mm39 carries only three of these tracks, and TFBS Conserved was never built
for hg38).

Also adds the category to FAQ/index.html and a cross-link from the promoter
sequence question in FAQ/FAQdownloads.html.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html
index c177e8038ad..d67dd337145 100755
--- src/hg/htdocs/FAQ/FAQdownloads.html
+++ src/hg/htdocs/FAQ/FAQdownloads.html
@@ -837,30 +837,33 @@
 Browser</a>. Enter the genome, assembly, and select the knownGene table. Paste the gene name or 
 accession number in the identifier field. Choose sequence for the output format type, then click the
 get output button. On the next page, select genomic. On the final page, you will have the 
 opportunity to configure the amount of upstream promoter sequence to fetch, along with several 
 other options. Click Get Sequence when you've finished configuring the output.</p> 
 <p> 
 You can also use the Genome Browser to obtain sequence for a specific gene. Open the Genome Browser 
 window to display the gene in which you're interested. Click the entry for the gene in the RefSeq 
 or Known Genes track, then click the Genomic Sequence link. Alternatively, you can click the DNA 
 link in the top menu bar of the Genome Browser tracks window to access options for displaying the 
 sequence.</p> 
 <p>
 The Stanford Human Promoters track on the 
 <a href="../goldenPath/customTracks/custTracks.html">UCSC Custom Annotation Tracks page</a> shows 
 promoters for some of the human assemblies.</p>
+<p>
+If you want annotated promoter regions rather than upstream sequence, see
+<a href="FAQregulation.html#promoters">Which tracks show promoters?</a> in the regulation FAQ.</p>
 
 <a name="download19"></a>
 <h2>Data from Evolutionary Conservation Score tracks</h2>
 <h6>Where can I download the conservation score data from the Human/Mouse Evolutionary 
 Conservation Score track?</h6>
 <p> 
 The conservation score data are stored in a group of tables in the annotation database downloads 
 directory. The naming conventions of the tables vary among releases. In earlier assemblies, table 
 names are of the form chr<em>N</em>_humMusL, chr<em>N</em>_zoom1_humMusL, and or 
 chr<em>N</em>_zoom2500_humMusL. In later releases, the tables are named using specific release 
 numbers, such as chr<em>N</em>_hg16Mm3. The tables within a given set differ by the number of 
 bases/score interval and are used to generate the browser displays at different zooming levels.</p>
 
 <a name="download20"></a>
 <h2>Minus strand coordinates - axtNet</h2>