Experiment / E7W5IPOFCOther

PC3 polysome-profiling 3′ UTR variant MPRA

Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3′ untranslated region mutations

An episomal luciferase library carrying paired 201-bp wild-type and mutant patient-derived human 3′ UTR fragments was transfected into PC3 prostate cancer cells. Six biological replicates were fractionated into total RNA, 80S, low-polysome, and high-polysome pools, with matched plasmid DNA to estimate allele-specific translation-efficiency 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:0035
Reference genome: GRCh38
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

The publication describes six biological replicates, average sequencing depth of 315 reads per insert, internal 3′ UTR MPRA controls, and xtail analysis of total-polysome/total-RNA and high-polysome/total-RNA ratios. The processed table derives normalized log2-CPM summaries from GEO and includes a total-polysome log2-CPM sum proxy; package-derived paired t-test p-values and Benjamini-Hochberg FDR values are not the authors’ xtail statistics.

Episomal pLuc2CP-noARE plasmid MPRA with paired WT/mutant 201-bp 3′ UTR inserts; PC3-cell polysome fractionation and sequencing of total RNA, 80S, low-polysome, high-polysome, and plasmid-DNA fractions were used to read out translation efficiency.

Processed data

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

Search table valuesFilter columnOperatorValue

Visible columns (39 of 39)

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 39 definitions

variant_id: Coordinate and REF-ALT identifier for the tested mutation.
chromosome: Chromosome parsed from variant_id.
position_grch38: 1-based GRCh38 coordinate parsed from variant_id.
reference_allele: Reference allele in the variant identifier.
alternate_allele: Alternate allele in the variant identifier.
wt_utr_sequence_201bp: 201-bp wild-type 3′ UTR insert sequence.
mutant_utr_sequence_201bp: 201-bp mutant 3′ UTR insert sequence.
replicate_count: Number of matched biological replicates summarized.
wt_mean_pdna_log2_cpm: Mean WT plasmid-DNA normalized log2 CPM across six replicates.
mutant_mean_pdna_log2_cpm: Mean mutant plasmid-DNA normalized log2 CPM across six replicates.
wt_mean_total_rna_log2_cpm: Mean WT total-RNA normalized log2 CPM.
mutant_mean_total_rna_log2_cpm: Mean mutant total-RNA normalized log2 CPM.
wt_mean_80s_rna_log2_cpm: Mean WT 80S/monosome RNA normalized log2 CPM.
mutant_mean_80s_rna_log2_cpm: Mean mutant 80S/monosome RNA normalized log2 CPM.
wt_mean_low_polysome_log2_cpm: Mean WT low-polysome RNA normalized log2 CPM.
mutant_mean_low_polysome_log2_cpm: Mean mutant low-polysome RNA normalized log2 CPM.
wt_mean_high_polysome_log2_cpm: Mean WT high-polysome RNA normalized log2 CPM.
mutant_mean_high_polysome_log2_cpm: Mean mutant high-polysome RNA normalized log2 CPM.
wt_mean_total_polysome_log2_cpm: WT mean of a derived log2-CPM total-polysome proxy, calculated as log2(2^high + 2^low) per replicate before averaging.
mutant_mean_total_polysome_log2_cpm: Mutant mean of the derived log2-CPM total-polysome proxy.
wt_total_polysome_te_proxy_log2: WT total-polysome translation-efficiency proxy: total-polysome log2-CPM proxy minus total-RNA log2 CPM.
mutant_total_polysome_te_proxy_log2: Mutant total-polysome translation-efficiency proxy.
total_polysome_te_variant_effect_log2: Mean paired mutant-minus-WT effect on the total-polysome translation-efficiency proxy.
total_polysome_te_effect_sd: Sample standard deviation of the six paired total-polysome effects.
total_polysome_te_effect_p_value: Package-derived two-sided paired t-test p-value across six replicate effects.
total_polysome_te_effect_fdr: Benjamini-Hochberg FDR across retained variants for the package-derived total-polysome p-values.
total_polysome_te_significant_fdr_0_10: Whether package-derived total-polysome FDR is below 0.10.
wt_high_polysome_te_proxy_log2: WT high-polysome translation-efficiency proxy: high-polysome log2 CPM minus total-RNA log2 CPM.
mutant_high_polysome_te_proxy_log2: Mutant high-polysome translation-efficiency proxy.
high_polysome_te_variant_effect_log2: Mean paired mutant-minus-WT effect on the high-polysome translation-efficiency proxy.
high_polysome_te_effect_sd: Sample standard deviation of the six paired high-polysome effects.
high_polysome_te_effect_p_value: Package-derived two-sided paired t-test p-value across six replicate effects.
high_polysome_te_effect_fdr: Benjamini-Hochberg FDR across retained variants for the package-derived high-polysome p-values.
high_polysome_te_significant_fdr_0_10: Whether package-derived high-polysome FDR is below 0.10.
total_rna_variant_effect_log2: Mean paired mutant-minus-WT total-RNA normalized log2-CPM effect.
wt_total_rna_activity_vs_pdna_log2: WT total-RNA activity proxy: total-RNA log2 CPM minus plasmid-DNA log2 CPM.
mutant_total_rna_activity_vs_pdna_log2: Mutant total-RNA activity proxy.
package_qc_pass: Always true because rows failing package QC were filtered out.
source_dataset: GEO source matrix and normalization used for this row.

Quality control

The authors used custom-reference alignment, removed reads with mismatches or duplicated UMIs (about 20%), checked replicate correlations and internal controls, and considered xtail FDR < 0.10 significant. Package QC retained only variant pairs with valid 201-bp WT/mutant oligos, complete finite values across all six WT and mutant replicates, and mean normalized plasmid-DNA and total-RNA log2 CPM ≥ 1 for both alleles; 6,154 rows passed. Non-significant but measured variants remain.

Curation notes

The GEO polysome matrix contains 6,772 variant rows versus 6,885 variant IDs in the oligo design; all matrix IDs joined to paired 201-bp oligos. Public GEO data expose normalized log2 CPM rather than raw UMI counts or the authors’ xtail result table, so p-value/FDR columns are explicitly package-derived. Gene symbols and dbSNP rs IDs were not provided in the public matrix; coordinate allele IDs are retained. Total-polysome values are a log-space sum proxy because the released matrix is already normalized log2 CPM.

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50