Experiment / E0AZJD69UEpisomal Plasmid MPRA

pMYC QUASARR-seq matched variant effects

Dual promoter–enhancer activities reflect a unified regulatory logic

This derived view isolates the main pMYC QUASARR-seq library's matched wild-type and mutant constructs and compares their promoter and enhancer activity in the same orientation. It covers the paper's disease, population, GWAS, and synthetic variant categories and reports mutant-minus-WT effects.

Download processed table (CSV)Raw source data API documentation

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.

Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0004
Reference genome: GRCh38
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

This is not a separate wet-lab run: it is a matched WT/mutant analysis derived from the pMYC QUASARR-seq dual-reporter MPRA. The source library contains 24 retained WT/mutant orientation pairs spanning Disease, Population, GWAS, and Synthetic categories. Promoter and enhancer deltas are calculated as mutant minus WT for the same orientation; boost indices use the pMYC orientation-specific negative-control-ORF means.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (35 of 35)

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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 · 35 definitions

element_id: Mutant source element identifier including strand orientation.
parent_element_id: Wild-type parent element identifier including the matched orientation.
base_element_id: Orientation-free wild-type parent element identifier.
orientation: Matched construct orientation (fwd or rev).
mutation: Allele or mutation notation for the mutant construct.
mutation_category: Source mutation category: Disease, Population, GWAS, SyntheticSingle, or SyntheticDouble.
chromosome: GRCh38 chromosome for the parent element.
start: GRCh38 start coordinate of the parent element.
end: GRCh38 end coordinate of the parent element.
reference_sequence: Wild-type parent/reference sequence; a separate mutant sequence is not supplied in the source workbook.
sequence_length: Wild-type reference sequence length in base pairs.
gc_content_percent: GC percentage calculated from the wild-type reference_sequence.
wt_promoter_log2_fold_change: WT promoter paBC limma log2 fold-change activity estimate.
mutant_promoter_log2_fold_change: Mutant promoter paBC limma log2 fold-change activity estimate.
promoter_delta_log2_fold_change: Mutant minus WT promoter log2 fold-change.
wt_promoter_boost_index: WT promoter log2 fold-change minus the pMYC negative-control-ORF mean for this orientation.
mutant_promoter_boost_index: Mutant promoter log2 fold-change minus the pMYC negative-control-ORF mean for this orientation.
promoter_delta_boost_index: Mutant minus WT promoter boost index.
promoter_effect_direction: Direction of the promoter delta: gain for positive, loss for negative, or no_change for zero.
wt_promoter_p_value: WT promoter raw limma P value.
mutant_promoter_p_value: Mutant promoter raw limma P value.
wt_promoter_fdr: WT promoter Benjamini-Hochberg adjusted limma P value.
mutant_promoter_fdr: Mutant promoter Benjamini-Hochberg adjusted limma P value.
wt_enhancer_log2_fold_change: WT enhancer eaBC limma log2 fold-change activity estimate.
mutant_enhancer_log2_fold_change: Mutant enhancer eaBC limma log2 fold-change activity estimate.
enhancer_delta_log2_fold_change: Mutant minus WT enhancer log2 fold-change.
wt_enhancer_boost_index: WT enhancer log2 fold-change minus the pMYC negative-control-ORF mean for this orientation.
mutant_enhancer_boost_index: Mutant enhancer log2 fold-change minus the pMYC negative-control-ORF mean for this orientation.
enhancer_delta_boost_index: Mutant minus WT enhancer boost index.
enhancer_effect_direction: Direction of the enhancer delta: gain for positive, loss for negative, or no_change for zero.
wt_enhancer_p_value: WT enhancer raw limma P value.
mutant_enhancer_p_value: Mutant enhancer raw limma P value.
wt_enhancer_fdr: WT enhancer Benjamini-Hochberg adjusted limma P value.
mutant_enhancer_fdr: Mutant enhancer Benjamini-Hochberg adjusted limma P value.
source_data: Provenance of the pMYC source tables, mutation categories, coordinates, and sequences used for the paired comparison.

Quality control

Source barcode processing and activity modeling followed the paper's fastp, Hamming-1 clustering, UMI correction, edgeR, negative-control/TMM, and limma-voom workflow. Package QC first applied the core pMYC finite/positive-count filters, then required a valid WT parent with the same orientation and valid promoter and enhancer measurements for both members of each pair. The resulting table contains 24 of 208 available variant element-orientation rows (9 Disease, 8 Population, 4 GWAS, and 3 Synthetic variant constructs); unmatched, incomplete, or invalid comparisons were excluded.

Curation notes

This is a useful derived variant-focused table rather than a separate experiment. It contains 24 orientation-level WT/mutant pairs and 16 unique mutant constructs. The reference_sequence column is the WT/parent sequence by design because the source workbook's Elements_Sequences sheet does not include a separate mutant sequence. Variant delta values are descriptive paired contrasts and are not new differential-test P values.