TRAF3IP2 exon 2 saturation-mutagenesis MPRA in mouse liver
Systematic Dissection of Coding Exons at Single Nucleotide Resolution Supports an Additional Role in Cell-Specific Transcriptional RegulationThe TRAF3IP2 exon 2 eExon library contained 10,029 distinct mutant haplotypes and 10,071 tagged constructs and covered all 1,962 possible single-nucleotide substitutions. The tagged pGL4.23 library was delivered to mouse liver by hydrodynamic tail-vein injection and RNA-derived tags were sequenced 24 hours later.
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
Hydrodynamic tail-vein delivery of 10 µg MPRA library plus 2 µg Renilla control; 24 h post-injection harvest
In vivo episomal MPRA using pGL4.23 luciferase reporter plasmids carrying approximately 97:1:1:1 doped eExon haplotypes and a 20-bp degenerate tag in the reporter 3′ UTR. The library was co-injected with pGL4.74[hRluc/TK] into CD1 mice by hydrodynamic tail vein; after 24 h, liver mRNA was selected, 16 RT-PCR aliquots per biological duplicate were indexed and sequenced on Illumina GAIIx. Tag–haplotype associations were established by tag-directed subassembly, and substitution effects were estimated by linear regression on the number of RNA aliquots in which each haplotype was observed.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (33 of 33)
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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 · 33 definitions
- variant_id
- Stable identifier combining the eExon, one-based position, reference allele, and alternate allele.
- element_id
- Identifier for the tested eExon library.
- gene
- Gene containing the tested eExon.
- position_in_element
- One-based position within the 654-bp TRAF3IP2 eExon test sequence.
- chromosome_hg19
- Chromosome reported for the tested sequence in hg19.
- coordinate_hg19
- One-based hg19 genomic coordinate of the tested position.
- reference_allele
- Wild-type nucleotide at the position.
- alternate_allele
- Specific alternate nucleotide substitution tested by the MPRA model.
- nucleotide_change
- RefSeq-style nucleotide change annotation when provided by the source; NA when unavailable.
- context
- Source sequence context annotation, such as exonic or intronic.
- effect_size_log2fc
- Published mouse-liver trivariate-model effect size, expressed as log2 predicted activity fold change relative to wild type.
- fold_change
- Linear predicted activity fold change calculated as 2 raised to effect_size_log2fc.
- p_value
- Published unadjusted p-value for the specific substitution effect.
- significant_p_0_05
- Boolean indicating whether the published p-value is at most 0.05; this flag was not used as a row filter.
- effect_direction
- Direction derived from the effect size: increased, decreased, or no_change.
- GERP
- GERP conservation score reported by the source.
- RefSeq
- RefSeq transcript identifier reported by the source.
- exon
- Exon annotation reported by the source.
- amino_acid_change
- Amino-acid consequence annotation reported by the source.
- amino_acid_context
- Synonymous, non-synonymous, stop-codon, or other coding context reported by the source.
- ENCODE_TF_ChIP_seq_peaks
- ENCODE transcription-factor ChIP-seq peak annotation at the position.
- TF_ChIP_seq_in_HEPG2
- HepG2 TF ChIP-seq annotation at the position.
- DNase_I_cluster
- DNase I hypersensitivity cluster indicator from the source.
- SNP135_database
- SNP135 database indicator from the source.
- SIFT_score
- SIFT score reported by the source.
- PolyPhen2_score
- PolyPhen-2 score reported by the source.
- TF_mark
- Transcription-factor motif whose reference-to-mutant mark score change was reported.
- WT_mark_score
- Reference-sequence motif mark score.
- mut_mark_score
- Mutant-sequence motif mark score.
- absolute_score_change
- Absolute difference between mutant and reference motif mark scores.
- relative_entropy
- Relative entropy threshold/score reported for the motif model.
- source_sheet
- Worksheet name in the publisher-supplied Table S5 workbook.
- source_table
- Publisher source table identifier.
Quality control
The authors quality-filtered the first 20 tag bases, counted tag observations, retained tags supported by at least 10 reads, established tag–haplotype links by subassembly, and assessed replicate reproducibility before combining biological duplicates (TRAF3IP2 tail-vein r=0.92). Package QC retained 1,961 of 1,962 source rows because each retained row had a valid integer hg19 coordinate, distinct A/C/G/T reference and alternate alleles, finite effect size, and p-value in [0,1]. One source row at position 558 encoded T>T and was excluded because it is not a nucleotide substitution. The paper's p≤0.05 criterion is represented by a boolean column and was not used to remove non-significant substitutions.
Curation notes
The tested sequence and hg19 coordinates are human-derived, while the biological assay sample is mouse liver. Table S5 includes one apparent self-substitution (T>T) at position 558; it was excluded from the processed table as a basic allele-integrity QC failure. Other non-significant substitutions are retained so the table remains a complete saturation map.