b5997c3b91cd3dfa56da7de7e21601b333989773
max
  Tue May 26 08:56:05 2026 -0700
[Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack

512,577 candidate enhancers and 319,322 candidate silencers predicted by the
TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko
2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated
with contributing cell types/tissues/cell lines, colored by dominant sample
category using the Okabe-Ito palette. Tracks live under the new crPred
(Cis-regulatory Predictions) supertrack.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
refs #37631

diff --git src/hg/makeDb/scripts/tredNet/tredNet.as src/hg/makeDb/scripts/tredNet/tredNet.as
new file mode 100644
index 00000000000..af2313ca56d
--- /dev/null
+++ src/hg/makeDb/scripts/tredNet/tredNet.as
@@ -0,0 +1,17 @@
+table tredNet
+"TREDNet candidate regulatory elements (enhancers or silencers)"
+(
+    string  chrom;        "Chromosome"
+    uint    chromStart;   "Start position (0-based)"
+    uint    chromEnd;     "End position"
+    string  name;         "Sample count summary (e.g. '5 tissues')"
+    uint    score;        "Score (0)"
+    char[1] strand;       "Strand"
+    uint    thickStart;   "thickStart (same as chromStart)"
+    uint    thickEnd;     "thickEnd (same as chromEnd)"
+    uint    reserved;     "Color (RGB)"
+    uint    sampleCount;  "Number of samples where this element is predicted|Total count of cell types, tissues, or cell lines"
+    lstring sampleList;   "Sample names|Comma-separated list of all cell types, tissues, or cell lines"
+    lstring mouseOver;    "Mouse-over text|Full sample list (or count summary when list is long)"
+    string  category;     "Dominant sample category|cell_type, tissue, cell_line, or mixed"
+)