Random mutations introduced by error-prone PCR into conserved 160-nt 3′-UTR reporter inserts were analyzed in BEAS-2B cells to identify 6–20-nt intervals whose mutations altered reporter mRNA stability. The table contains the paper’s FDR-filtered element-level results and motif annotations.
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:0168
Reference genome
GRCh37/hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Doxycycline transcriptional shutoff (1 µg/ml; stability measured at 4 h)
The paper screened all 6-, 8-, 10-, 12-, 14-, 16-, 18-, and 20-nt intervals, comparing mutant and wild-type clones with two-sided Wilcoxon tests and selecting overlapping significant intervals by best FDR. Supplementary Table 2 summarizes 106 destabilizing and 44 stabilizing elements.
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 · 19 definitions
element_id
Stable identifier composed from gene, source segment, assembly coordinate, and strand-independent interval.
gene
Gene symbol of the source 3′-UTR segment.
chromosome
GRCh37/hg19 chromosome containing the element.
element_start_grch37_1based
1-based inclusive GRCh37/hg19 start coordinate from Supplementary Data 6.
element_end_grch37_1based
1-based inclusive GRCh37/hg19 end coordinate from Supplementary Data 6.
strand
Genomic strand of the source 3′-UTR.
segment_id
Source conserved-library segment identifier.
segment_start_1based_inclusive
1-based inclusive start of the element within the 160-nt segment, as reported.
segment_end_1based_inclusive
1-based inclusive end of the element within the 160-nt segment, as reported.
element_sequence_rna_5to3
Element sequence in reporter/RNA orientation.
n_mutant_clones
Number of mutant clones used for the element comparison.
n_wild_type_clones
Number of wild-type clones used for the element comparison.
delta_stability_percent
Published median mutant-minus-wild-type stability difference, in percent.
delta_stability_fraction
Same stability difference converted to a fraction (e.g. 0.60 = 60%).
p_value
Wilcoxon rank-sum p-value for mutant versus wild-type clone stability.
q_value
False-discovery-rate adjusted q-value.
protein_binding_motifs
Overlapping known RNA-binding-protein motif annotations from the source workbook.
predicted_mirna_targets
Overlapping TargetScan predicted miRNA target annotation from the source workbook.
figure_cross_reference
Supplementary figure cross-reference supplied by the source workbook.
Quality control
The authors required at least 20 mutant and 20 wild-type clones per interval and controlled the discovery list at FDR <5% using Wilcoxon tests and q-values. The package applies those requirements, finite-value checks, and q ≤0.05; all 150 published elements pass. No element-level rows are retained from intervals failing those criteria.
Curation notes
Positive delta stability means mutations increased reporter mRNA stability, consistent with a destabilizing element in the wild-type insert; negative values indicate a stabilizing element. Supplementary Data 6 uses GRCh37/hg19 element coordinates, while the associated Data2 segment design table is from the NCBI36/hg18-era assembly.