Experiment / E5GA41UKR5' UTR / Translation Efficiency MPRA (MPTA)

Main PLUMAGE 30-bp randomer full-length 5′-UTR variant library in PC3 and HEK293T

Multiplexed functional genomic analysis of 5′ untranslated region mutations across the spectrum of prostate cancer

The main episomal PLUMAGE library assayed 914 synthesized full-length human 5′-UTR sequences covering 545 prostate-cancer somatic mutations using a 30-bp randomer barcode linked by PacBio long reads. PC3 and HEK293T cells were measured 24 h after transfection for DNA, total mRNA, and polysome-bound mRNA; the packaged table contains the published mutation-level transcript and translation-efficiency summaries joined to unambiguous WT/mutant constructs.

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: Not reported / not applicable
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated (24 h post-transfection)

Episomal pGL3-promoter luciferase reporter constructs contained full-length WT or mutant 5′-UTRs and a semi-random 30-bp barcode downstream of the luciferase coding sequence. PacBio CCS2 sequencing established barcode-to-UTR identities; Illumina PE100 sequencing quantified barcode counts in plasmid DNA, total mRNA, and polysome-bound mRNA. Transcript activity was summarized as log2(total mRNA/DNA) and translation efficiency as log2(polysome/total mRNA), with three biological replicates per cell line.

Processed data

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

Visible columns (28 of 28)

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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 · 28 definitions

variant_id: Stable variant identifier derived from the matched Supplementary Data 6a construct pair; for indels it records the sequence-catalog event.
published_effect_id: Mutant identifier from the published Supplementary Data 6d/6e effect summaries.
gene: Gene symbol for the assayed 5′-UTR.
assayed_cell_lines: Cell lines used for the main library assay; the published mutation-level summaries are aggregate and are not cell-line-stratified.
chromosome: Chromosome label from the published construct/effect annotation.
variant_position_hg19: SNV position or indel anchor position in hg19 as represented by the construct annotation.
reference_allele: Reference allele inferred from the WT/mutant construct relation and published variant label.
alternative_allele: Alternative allele inferred from the WT/mutant construct relation and published variant label.
variant_type: Sequence-level event type: SNV, deletion, or insertion.
utr_region_hg19: Broad 5′-UTR interval from the published effect annotation, in hg19 coordinates.
utr_length_bp: Length in base pairs of the matched WT full-length 5′-UTR construct.
wild_type_construct_id: Supplementary Data 6a identifier for the matched WT construct.
mutant_construct_id: Supplementary Data 6a identifier for the matched mutant construct.
wild_type_sequence: Full-length WT 5′-UTR sequence supplied in Supplementary Data 6a.
mutant_sequence: Full-length mutant 5′-UTR sequence supplied in Supplementary Data 6a.
sequence_relation: Relationship verified by direct sequence comparison between WT and mutant constructs.
sequence_difference: Number of single-base differences for SNVs, or the indel sequence-length difference for indels.
transcript_log2_fold_change: Published log2(total mRNA/DNA) mutant-versus-WT activity effect.
transcript_p_value: Published p-value for the transcript activity comparison.
transcript_fdr: Published FDR-adjusted p-value for the transcript activity comparison.
transcript_significant_fdr_lt_0_1: Whether the published transcript FDR is below 0.1.
translation_efficiency_log2_fold_change: Published log2(polysome/total mRNA) mutant-versus-WT translation-efficiency effect.
translation_efficiency_p_value: Published p-value for the translation-efficiency comparison.
translation_efficiency_fdr: Published FDR-adjusted p-value for the translation-efficiency comparison.
translation_efficiency_significant_fdr_lt_0_1: Whether the published translation-efficiency FDR is below 0.1.
functional_in_any_layer: Whether the published FDR is below 0.1 in either transcript activity or translation efficiency.
qc_pass: Package-level QC flag; only true rows are present in the processed table.
source_data: Supplementary Data 6a, 6d, and 6e and the deposited GEO series used to construct or audit the row.

Quality control

The paper required high-quality PacBio CCS2 reads (minimum three passes and predicted accuracy 0.9), exact matching of consensus 5′-UTRs to expected constructs, barcode extraction with matching 4-nt flanks, and at least 0.5 CPM for barcodes used in ratio calculations. It reports more than 96% of extracted barcodes matching the PacBio catalog and replicate correlations above 0.99 for DNA, 0.8 for total RNA, and 0.89 for polysome RNA. For this package, only published mutation-effect rows that could be joined unambiguously to one WT and one mutant sequence in Supplementary Data 6a were retained: 536 rows passed, while the duplicate CHRM2_C_G..._2 comparison and the DCAF6_T_G comparison with a non-clean sequence relation were excluded. Nonsignificant published rows remain in the table; FDR < 0.1 is represented by explicit Boolean columns.

Curation notes

This is one aggregate main-library experiment because the published Supplementary Data 6d/6e effect tables do not provide separate PC3 and HEK293T effect columns; biosample_id is therefore null rather than assigning aggregate statistics to one cell line. Raw GEO GSE149487 includes separate PC3 and HEK293T DNA, total-RNA, and polysome count files, but the deposited package does not provide a sufficiently direct cell-line-specific reanalysis table for these published mutation-level effects. The seven special 8-bp rows in Supplementary Data 6d/6e are represented in the separate pilot experiment where applicable. The MAT1A construct is retained as an insertion based on its actual sequence comparison despite the source identifier's deletion-like label; its source annotation is preserved in the variant_id and source fields.

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