MSMB promoter saturation-mutagenesis MPRA in HEK293T
Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assayA saturation-mutagenized 591-bp human MSMB promoter library was assayed in HEK293T cells with three independent plasmid transfections. Variant reporter activity was estimated from matched RNA and DNA tag counts.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
Basal / Untreated
The episomal pGL4-derived promoter reporter carried the error-prone-PCR-mutagenized MSMB sequence and a random sequence tag in the reporter 3′ UTR. The library was transfected into HEK293T for 24 h; matched DNA/RNA tag counts from three independent transfections were fit with log2(RNA) ~ log2(DNA) + N + offset to estimate each variant coefficient.
Processed data
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 16 definitions
- element_id
- Paper Table 1 regulatory element name.
- source_element_id
- Element label in the authors' MPRA saturation-mutagenesis portal.
- variant_id
- Stable package identifier combining element, GRCh38 coordinate, reference allele, and alternate allele.
- chromosome
- GRCh38 chromosome with chr prefix.
- position_grch38
- 1-based GRCh38 position of the substituted nucleotide.
- position_in_element
- 1-based position within the paper's reported target interval.
- reference_allele
- Reference/template nucleotide in the tested library.
- alternate_allele
- Single-nucleotide substitution introduced by saturation mutagenesis.
- variant_class
- Variant class; all retained rows are SNV.
- barcode_count
- Number of unique random tags associated with the variant.
- dna_count
- Source count of DNA sequences carrying the variant.
- rna_count
- Source count of RNA sequences carrying the variant.
- log2_variant_effect
- Portal-fitted regression coefficient estimating the log2 RNA/DNA reporter effect of the variant.
- p_value
- P-value for the fitted variant coefficient.
- effect_direction
- Direction derived from the coefficient sign: up, down, or no_change.
- significant_p_lt_1e-5
- Boolean indicating whether p_value is below the paper's nominal 1e-5 threshold.
Quality control
The source saturation-mutagenesis analysis used a minimum of 10 associated tags per variant. Package QC retained 1,769 of 1,770 candidate SNVs in the paper's Table 1 interval: GRCh38 SNVs with barcode_count >= 10, positive DNA/RNA counts, and finite coefficient and p-value were retained; one low-tag row plus one-base deletions and out-of-interval records were excluded. The paper/CAGI analysis used p < 1e-5 as the nominal significance threshold, exposed as significant_p_lt_1e-5.
Curation notes
HEK293T is represented by Cellosaurus CVCL:0063. MSMB was one of the lower-performing prediction loci in the paper, but all finite, adequately tagged SNV effects are retained regardless of significance.