899f9da8129add8c64c86b405c87b3a97738a2ad lrnassar Fri May 1 17:12:18 2026 -0700 Update mpraVarDb description page and trackDb stanza per QA pass. refs #37359 Description page (mpraVarDb.html): - Primary citation corrected from a fabricated "Wang T, Matreyek KA, Yang X." entry to Jin et al., 2024 (PMID 39325859, the actual published Bioinformatics paper for MPRAVarDB). - References for all 18 source studies added. - Studies-table counts corrected to match the data: Tewhey 27,138 to 23,430 (the biggest gap, ~14%), Griesemer 72,588 to 72,546, Abell 29,582 to 29,564, Mouri 14,551 to 14,549, McAfee 10,310 to 10,302, Cooper 5,340 to 5,330, Lu 1,038 to 1,036. - Color counts on Display Conventions corrected to actual post-liftOver values: 22,451 dark red / 17,773 orange / 198,804 grey = 239,028. - "Note on study type" paragraph clarifying that ~41% of variants (Griesemer + Schuster 3'UTR) measure post-transcriptional regulation rather than transcription. - "Cell-type specificity" reminder, "Note on Kircher 2019" saturation- mutagenesis structure, "Interpreting log2FC" subsection with the linear-fold-change translation, and "Significance thresholds across studies" Methods paragraph noting that source studies use a mix of FDR thresholds (0.05/0.10) and that Kircher reports raw regression p-values rather than FDR. - Kircher element list reworded to avoid double-counting UC88 as both a named element and "an ultraconserved enhancer". trackDb stanza (mpra.ra, mpraVarDb subtrack): - filterValues.cellLine fixed: PC3 was hiding 26,546 Schuster rows (data has "PC3 cell"), SF7996 was hiding 3,896 Kircher GBM rows (data has bundled "HEK293T,SF7996"), and SK-MEL-28 (1,510) and K562+GATA1 (31) were missing entirely. Added comma-escape syntax (HEK293T,,SF7996) per slNameListFromCommaEscaped. Recovers ~31,983 hidden rows. - HTML mouseOver with bold field names and line breaks. - urls rsid="https://www.ncbi.nlm.nih.gov/snp/$$" added so rsIDs are clickable linkouts to dbSNP. - dataVersion "MPRAVarDB snapshot 2026-03-10" added. Makedoc (mpra.txt): QA review note added with the trackDb-only fixes and the items punted to upstream / next rebuild for Tao Wang. diff --git src/hg/makeDb/doc/hg38/mpra.txt src/hg/makeDb/doc/hg38/mpra.txt index ee09f197ef3..ed45ad17294 100644 --- src/hg/makeDb/doc/hg38/mpra.txt +++ src/hg/makeDb/doc/hg38/mpra.txt @@ -103,15 +103,61 @@ # - 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. +# +# QA review 2026-05-01 (RM #37359, Lou): +# Found and fixed in trackDb only (no bigBed rebuild this round): +# - filterValues.cellLine had four broken entries hiding ~31,983 rows +# (13% of track): PC3 vs PC3 cell mismatch (26,546 rows), SF7996 needed +# comma-escape syntax for the bundled HEK293T,,SF7996 data value +# (3,896 rows), missing SK-MEL-28 (1,510) and K562+GATA1 (31). All +# four corrected; filter now matches all 32 distinct cellLine values +# in the data. +# - Description page references rebuilt for all 18 source studies plus +# the corrected primary citation (Jin et al. 2024, PMID 39325859 in +# Bioinformatics; the previous "Wang T, Matreyek KA, Yang X." citation +# was fabricated -- not the actual authors of either the preprint +# PMID 38617248 or the published paper). +# - 7 studies-table row counts corrected to match data (Tewhey, Griesemer, +# Abell, Mouri, McAfee, Cooper, Lu). +# - HTML mouseOver upgraded to bold/multi-line. +# - dataVersion "MPRAVarDB snapshot 2026-03-10" added to stanza. +# - urls rsid="https://www.ncbi.nlm.nih.gov/snp/$$" added so rsIDs are +# clickable linkouts. +# - Methods + Display Conventions paragraphs added: scoring methodology +# differs across studies, post-transcriptional vs transcriptional +# distinction (Griesemer/Schuster 3'UTR), Kircher saturation +# mutagenesis structure, log2FC interpretation. +# +# Punted to Redmine for Max / Tao Wang (potential next-rebuild items): +# - 5,092 rows (Mouri, Tewhey) have pvalue > 1 (impossible; max 8.96). +# FDR appears valid; pvalue field looks like a t-statistic mislabeled. +# mouseOver/details show misleading p-values for ~2% of significant +# rows. +# - 30,921 rows display literal "nan" / "None" in mouseOver and +# details fields where NA-coded values were preserved verbatim. Two +# sentinel conventions coexist ("None" in 53k eQTL rows, "NA" in 2k +# Kircher rows). +# - Upstream typos in 28,810 rows: "30 UTR" in 26,546 Schuster +# descriptions, "Familial hypercholesterol emia" in 2,176 Kircher +# diseases, "Alchol use disorder" in 88 Rao diseases. +# - 60,860 rows have description="GWAS" (no detail) -- upstream limit. +# - 1,069 rows have multi-allelic alt collapsed into one row (e.g. +# "T/A,G") with one log2FC/pvalue. +# - 2,088 rows preserve hg19-coord-style names (e.g. "1_1403972_CG") +# post-liftOver to hg38; coordinates and name no longer match. +# - 969 rows are colored red (FDR<0.05) but pvalue=nan -- mouseOver +# reads "FDR: 0.001 / p-value: nan" which looks contradictory. +# - 250-char truncation in mpravardbToBed.py cuts Griesemer +# descriptions mid-sentence; should raise/remove the cap.