Rare gnomAD/ExAC 3′-UTR variants in HeLa cells
Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genesThis library tested rare population 3′-UTR alleles from the gnomAD/ExAC collection across cancer-related and other host genes. Allele-specific mRNA abundance was measured with episomal MapUTR in HeLa cells.
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
Episomal pCAG-eGFP reporter assay using 200-nt reference/alternative oligos with a 164-nt tested 3′-UTR context. Plasmid DNA and poly(A)-selected reporter RNA were collected from three biological replicates approximately 24 h after electroporation; the author-provided MPRAnalyze statistics are retained alongside activity effects recomputed from deposited UMI counts.
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 · 48 definitions
- variant_id
- Stable identifier for the tested variant
- chromosome
- hg19 chromosome
- position_hg19
- 1-based hg19 genomic coordinate
- ref_allele
- Reference allele tested
- alt_allele
- Alternative allele tested
- gene
- Host gene containing the tested 3′-UTR variant
- gene_strand
- Strand of the host gene
- variant_group
- Source variant collection (rare gnomAD/ExAC or COSMIC)
- cell_line
- Assayed cell line
- chip_subpool
- Oligo synthesis subpool identifier (for example, C1Sp1)
- oligo_orientation
- Design/sequencing orientation (orig or rc) when a deposited raw construct matched
- published_result_qc_pass
- True for rows present in the authors' all-tested result sheet after their upstream read, mapping, and UMI processing
- author_functional_variant
- Author's functional/non-functional call
- effect_direction
- Direction of the author's alternative/reference effect
- author_lnfc_alt_vs_ref
- Author-provided natural-log alternative/reference fold change from MPRAnalyze
- author_activity_fold_change_alt_vs_ref
- Exponential of the author lnFC, representing alternative/reference activity
- author_activity_percent_change
- 100 times (author activity fold change minus 1)
- author_p_value
- Author-provided allelic test p-value
- author_fdr
- Author-provided multiple-testing-adjusted p-value
- raw_count_complete
- True when all 12 deposited DNA/RNA UMI count fields were available for both alleles
- raw_count_min_10_qc
- Diagnostic True when all 12 deposited DNA/RNA UMI counts were at least 10
- raw_dna_total_umis
- Sum of available deposited DNA UMI counts across both alleles and three replicates
- raw_rna_total_umis
- Sum of available deposited RNA UMI counts across both alleles and three replicates
- dna_ref_rep1
- Pre-transfection plasmid DNA UMI count for the reference allele, replicate 1
- dna_ref_rep2
- Pre-transfection plasmid DNA UMI count for the reference allele, replicate 2
- dna_ref_rep3
- Pre-transfection plasmid DNA UMI count for the reference allele, replicate 3
- dna_alt_rep1
- Pre-transfection plasmid DNA UMI count for the alternative allele, replicate 1
- dna_alt_rep2
- Pre-transfection plasmid DNA UMI count for the alternative allele, replicate 2
- dna_alt_rep3
- Pre-transfection plasmid DNA UMI count for the alternative allele, replicate 3
- rna_ref_rep1
- Poly(A)-selected reporter RNA UMI count for the reference allele, replicate 1
- rna_ref_rep2
- Poly(A)-selected reporter RNA UMI count for the reference allele, replicate 2
- rna_ref_rep3
- Poly(A)-selected reporter RNA UMI count for the reference allele, replicate 3
- rna_alt_rep1
- Poly(A)-selected reporter RNA UMI count for the alternative allele, replicate 1
- rna_alt_rep2
- Poly(A)-selected reporter RNA UMI count for the alternative allele, replicate 2
- rna_alt_rep3
- Poly(A)-selected reporter RNA UMI count for the alternative allele, replicate 3
- activity_ref_rep1
- Reference RNA/DNA UMI ratio, replicate 1
- activity_ref_rep2
- Reference RNA/DNA UMI ratio, replicate 2
- activity_ref_rep3
- Reference RNA/DNA UMI ratio, replicate 3
- activity_alt_rep1
- Alternative RNA/DNA UMI ratio, replicate 1
- activity_alt_rep2
- Alternative RNA/DNA UMI ratio, replicate 2
- activity_alt_rep3
- Alternative RNA/DNA UMI ratio, replicate 3
- raw_log2fc_rep1
- Raw log2 alternative/reference activity ratio, replicate 1
- raw_log2fc_rep2
- Raw log2 alternative/reference activity ratio, replicate 2
- raw_log2fc_rep3
- Raw log2 alternative/reference activity ratio, replicate 3
- raw_mean_log2fc_alt_vs_ref
- Mean raw log2 alternative/reference activity ratio across available replicates
- raw_activity_fold_change_alt_vs_ref
- 2 raised to the raw mean log2 activity ratio
- raw_activity_percent_change
- 100 times (raw activity fold change minus 1)
- source_result_sheet
- Source worksheet in the author's supplementary all-tested result workbook
Quality control
The authors retained perfectly mapped reads or reads with one mismatch outside the designed SNP, removed PCR duplicates using 15-mer UMIs, quantified DNA and poly(A) RNA UMI counts, quantile-normalized across three biological replicates, and tested allelic differences with a two-sided MPRAnalyze likelihood-ratio test. Functional calls use FDR ≤0.10 and an absolute relative-activity effect of at least 10%. This table retains all 17194 rows in the published all-tested Sheet 3 result sheet. Deposited UMI counts join completely for 14474 rows; 2720 author-reported result rows have blank raw-count fields because no matching construct is present in the compact GEO export. Of the matched rows, 14205 have all 12 UMI counts ≥10; this is reported diagnostically and does not override the authors' result/QC universe.
Curation notes
The supplementary workbook labels this result set as gnomAD, while the GEO compact UMI-count files use the label rare_3utr_exac. HeLa RNA replicate 3 is a combined subpool file and was keyed by construct identifier. A separate common-variant comparison is described in the paper but no distinct deposited common-variant result/count set was identified, so it is not represented as an additional experiment. Author result statistics are retained when no matching compact GEO UMI record exists; blank raw-count fields are not interpreted as zero.