888e7470c14eeecdca310ed36bb45c3c00ae8052 lrnassar Tue Apr 21 15:14:04 2026 -0700 QA fixes for MPRA superTrack. refs #37359 Fix broken mpraVarDb bigDataUrl — pointed at /gbdb/hg38/mpra/mpravardb.bb but the file is at /gbdb/hg38/mpra/mpravardb/mpravardb.bb, causing hgTrackDb -strict to silently drop the subtrack. Rebuild mpravardb.bb after two fixes in mpravardbToBed.py: sanitize UTF-8 in user-visible string fields (curly quotes, primes, NBSP mojibake) that the browser does not transcode, eliminating ~246k non-ASCII occurrences across 42% of rows; and change safe_float / pval_to_score to write NaN and return score 0 for NA / out-of-range p-values instead of 0.0 and score 1000 (previously inflated untested variants to the top of score-sorted views). trackDb stanza cleanup: shorten mpraVarDb longLabel, drop superfluous type bed 4 from superTrack, make bigBed 9+13 explicit, remove redundant mouseOverField, align parent mpra on, add filterValues for cell_line/assay/cellLine and filterByRange sliders for percentile_rank / fdr / log2FC, add labelFields and maxWindowToDraw. Description pages: add cross-species disclosure (mouse reporter cells used to assay human sequences), update mpraVarDb header to post-liftOver count 239,028 with Studies-table footnote, fix mpraVarDb.html download-server paths, soften imprecise "51 MPRA experiments" claim in mpra.html and mprabase.html. relatedTracks.ra: reciprocal mpra <-> wgEncodeReg4 and mpra <-> cCREs. Expand mpra.txt makedoc with upstream provenance and QA-rebuild log. diff --git src/hg/makeDb/trackDb/human/hg38/mprabase.html src/hg/makeDb/trackDb/human/hg38/mprabase.html index 837554a8c0c..c316baee431 100644 --- src/hg/makeDb/trackDb/human/hg38/mprabase.html +++ src/hg/makeDb/trackDb/human/hg38/mprabase.html @@ -1,34 +1,41 @@ <h2>Description</h2> <p> Massively Parallel Reporter Assays (MPRAs) and related methods such as STARR-seq enable quantitative testing of thousands of candidate regulatory DNA sequences in parallel by linking each sequence to a reporter gene and measuring transcriptional output using sequencing. </p> <p> The <b>MPRA Base</b> track shows 41,275 experimentally tested cis-regulatory elements -from the <a href="http://mprabase.ucsf.edu/app/mprabase" target="_blank">MPRA Base</a> +curated from the <a href="http://mprabase.ucsf.edu/app/mprabase" target="_blank">MPRA Base</a> database -(<a href="https://pubmed.ncbi.nlm.nih.gov/38045264/" target="_blank">Zhao et al., 2023</a>). +(<a href="https://pubmed.ncbi.nlm.nih.gov/38045264/" target="_blank">Zhao et al., 2023</a>), +drawn from MPRA, STARR-seq, and related reporter assay experiments. The database integrates data from multiple studies, assay platforms (lentiMPRA, plasmidMPRA, STARR-seq, CRE-seq, and others), and cell types while preserving experiment-level resolution. Only elements derived from genomic fragments that can be mapped to the reference genome are included; synthetic or designed oligonucleotide libraries without genomic coordinates are excluded. </p> +<p> +<b>Note on cell lines:</b> The cell line shown for each element is the reporter +cell line in which the genomic fragment was assayed. One study (Mattioli et al., +2020) used mouse embryonic stem cells (mESC) as one of its reporter systems; the +fragments retain their human (hg38) coordinates. +</p> <h2>Display Conventions</h2> <p> Each item represents a genomic fragment tested within a specific experiment, defined as a unique combination of cell line, assay type, and publication (PMID). The same genomic region may appear multiple times if tested in different experiments. </p> <p> Items are colored by percentile rank of the mean raw activity score within each experiment: </p> <ul> <li><span style="color:blue;"><b>Blue</b></span> — percentile < 50</li> <li><span style="color:orange;"><b>Orange</b></span> — percentile 50–74</li> <li><span style="color:red;"><b>Red</b></span> — percentile ≥ 75</li>