PASSPORT-seq 111-pharmacogene mirSNP library in HEK293
PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target SitesThe pharmacogene library contained reference and alternate 63-nt 3′-UTR inserts for 111 mirSNPs across 17 pharmacogenes. The pooled pIS-0 reporter was transiently assayed in HEK293, and variant effects are reported as percent change in reporter mRNA expression relative to the reference allele.
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 application used the pooled pIS-0 firefly-luciferase 3′-UTR reporter design with reference and alternate inserts for 111 pharmacogene mirSNPs. Barcode sequencing of reporter cDNA, normalized against plasmid input, measured allele-dependent mRNA expression in HEK293; protein translation was not measured.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 13 definitions
- variant_id
- Stable package identifier combining the source rsID and reference/alternate alleles.
- source_row
- Row number in the corresponding processed supplementary source table.
- rsid
- dbSNP reference SNP identifier.
- reference_allele
- Reference allele used in the reporter construct.
- alternate_allele
- Alternate/variant allele used in the reporter construct.
- gene
- Gene or genes whose 3′ UTR contains the tested site.
- predicted_mirna_binding_sites
- Predicted miRNA-binding-site annotation extracted from the source reference/variant columns; when PDF column boundaries were not recoverable, reference and variant annotations are concatenated in source order.
- variant_percent_change
- Source percent change in reporter mRNA expression for the alternate allele relative to the reference allele in this cell line.
- mpra_fdr_p_value
- BH-adjusted edgeR PASSPORT-seq p-value for alternate-versus-reference expression; blank where the source does not report a numeric value.
- mpra_significant_fdr_0_05
- Whether the reported MPRA BH-adjusted p-value is below 0.05; blank when no numeric p-value is available.
- effect_direction
- Derived direction from variant_percent_change: alternate_increases, alternate_decreases, or no_change.
- library
- Library/analysis arm represented by this experiment.
- source_table
- Supplementary table used as the primary source.
Quality control
Publication QC used mapping-quality >20, perfect barcodes at both ends, plasmid-input correction, edgeR negative-binomial modeling with replicate and genotype covariates, and Benjamini–Hochberg FDR correction. Package QC retained rows with a valid rsID, single-nucleotide A/C/G/T reference and alternate alleles, nonempty gene, and finite HEK293 percent change; 111/111 rows passed. Supplementary Table 4 provides color-coded significance but no numeric per-row MPRA FDR values, so p-value fields are blank rather than inferred.
Curation notes
The application tested 111 variants in 17 pharmacogenes and reports 6, 13, 12, and 27 significant variants in HeLa, HepG2, HEK293, and HepaRG, respectively, with 33 overall. Supplementary Table 4 encodes per-cell significance with PDF colors and does not provide numeric p-values. The predicted-miRNA field preserves concatenated source annotations when the PDF did not expose the reference/variant columns separately; the source does not specify a reference genome assembly, so reference_genome and region_of_interest are null.