2087dbbb5adafd3219e2dfbbbe23d10a758e2828
lrnassar
  Fri May 1 15:48:00 2026 -0700
Update mprabase description page and stanza per QA pass. refs #37359

Description page (mprabase.html): added library-composition framing
(curated union of study-specific libraries, not a uniform enhancer
atlas), element-size note covering 144-200 bp tiles, 354-678 bp Klein
2020 length sub-experiments, and 1 bp SNP-coordinate markers, sharpened
Mattioli mESC cell-line note (mouse orthologous sequence assayed in
mouse cells), cell-line biological-context table, scoring-methodology
paragraph noting that cross-experiment percentile comparisons are
approximate, "Interpreting the raw score" subsection with the log2-to-
fold-change translation, coordinate-provenance sentence, and Arnold
et al. 2013 row in the Experiments table.  References for all seven
source publications added.

trackDb stanza (mpra.ra): HTML mouseOver with bold field names and line
breaks, plus dataVersion "MPRA Base v4.9.3 (Mar 2026)".

Parent superTrack description page (mpra.html) opening paragraph
rewritten to clarify the barcoded reporter-RNA mechanism and fold the
variant-MPRA case in cleanly.

Makedoc (mpra.txt): bundled Mattioli title rebuild ask with AutoSQL
percentile_rank text fix and name disambiguation (149 of 625 unique
names reused across PMIDs); added the open Klein 2020 sub-design
question for Varda; updated Arnold orphan note to reflect Varda's
confirmation that the HeLa STARR-seq element is a valid Stark Lab
proof-of-concept.

diff --git src/hg/makeDb/doc/hg38/mpra.txt src/hg/makeDb/doc/hg38/mpra.txt
index 540e9659792..ee09f197ef3 100644
--- src/hg/makeDb/doc/hg38/mpra.txt
+++ src/hg/makeDb/doc/hg38/mpra.txt
@@ -71,27 +71,47 @@
 #     now store pvalue="nan" instead of "0.0", so untested variants no longer
 #     masquerade as p=0 in the details page and are excluded by the default
 #     filter.fdr / filter.log2FC range sliders.  bedToBigBed accepts the
 #     literal string "nan" in float fields.
 #
 # Pre-rebuild backup preserved at:
 #   /hive/data/genomes/hg38/bed/mpra/mpravardb/mpravardb.bb.preQA-backup
 #
 # Reproduce QA rebuild:
 #   cd /hive/data/genomes/hg38/bed/mpra/mpravardb
 #   python3 ~/kent/src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py
 
 # =============================================================================
 # Known outstanding items (see RM #37359)
 # =============================================================================
-# - mprabase reference field for Mattioli 2020 rows starts with "musculus ..."
-#   (species word merged into title upstream).  Flag to Varda for upstream fix.
-# - mprabase has 1 orphan element (Hela STARR-seq, PMID 23328393, Arnold 2013)
-#   not in the documented experiment table.  Flag to Varda.
+# - mprabase rebuild items to fold into Varda's next bigBed:
+#     * Mattioli 2020 reference field starts with "musculus ..." (species word
+#       merged into title upstream).  Varda confirmed 2026-04-23 she will fix.
+#     * AutoSQL percentile_rank description currently says "Percentile rank
+#       within cell line"; the data is actually computed per (cell_line, assay,
+#       PMID) experiment.  Fix the .as comment to "Percentile rank within
+#       experiment" so the schema page matches the description page.
+#     * Element-name disambiguation: HepG2-XX%-LM and similar auto-generated
+#       names collide across Inoue 2017 and Klein 2020 because both reused the
+#       same ENCODE-derived 171 bp library and produced the same percentile.
+#       Surface: 149 of 625 unique names are reused across multiple PMIDs;
+#       4 are exact (chrom,start,end,name) duplicates.  Encode PMID or short
+#       study tag in the name to disambiguate.
+# - mprabase chr14:69999387-69999388 (HeLa STARR-seq, PMID 23328393, Arnold 2013)
+#   was previously flagged as an orphan.  Varda confirmed (2026-04-23) it is
+#   valid: HeLa was a proof-of-concept in an otherwise Drosophila STARR-seq
+#   paper (Stark Lab).  Row added to the experiments table in mprabase.html.
+# - Klein et al. 2020 (PMID 33046894) is an MPRA-design benchmarking paper
+#   that ran the same 2,440-element library through nine different assays.
+#   The track has three Klein 2020 sub-rows (lentiMPRA, plasmidMPRA, STARR-seq);
+#   confirm with Varda which underlying sub-designs MPRA Base pulled, since
+#   the Klein 2020 authors flag HSS as the worst-correlated of the nine and
+#   recommend pGL4 / ORI / 5'/5' WT.  Description page can be sharpened once
+#   confirmed.
 # - mpraVarDB preserves ~42k (chrom,start,end,name) duplicate rows (same rsID
 #   tested in multiple cells/studies).  Users disambiguate via the
 #   filterValues.cellLine / filterValues.mpraStudy filters in the trackDb.
 # - ~7,400 rows have upstream pvalue=0 and fdr=0 (not NA).  Could be genuine
 #   precision-floor significance or an upstream "not tested" encoding; the
 #   distinction is not recoverable from the CSV.  With pval_to_score returning
 #   0 for p<=0, these no longer dominate score-sorted views but their details
 #   page still reads "pvalue: 0.0".  Upstream clarification needed.