ZFAND3 enhancer saturation-mutagenesis MPRA in MIN6
Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assayA saturation-mutagenized 578-bp human ZFAND3 enhancer library was assayed in MIN6 mouse pancreatic beta 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 enhancer reporter carried the error-prone-PCR-mutagenized human ZFAND3 sequence upstream of a minimal promoter and a random sequence tag in the reporter 3′ UTR. The library was transfected into MIN6 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 human variant in MIN6 cells.
- 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 1,732 of 1,733 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
MIN6 is the mouse insulinoma/pancreatic beta-cell line Cellosaurus CVCL:0431, so target_organism follows the assay biosample (Mus musculus); the assayed ZFAND3 insert is human and its coordinates are GRCh38.