Upstream promoter-variant MPRA in Saccharomyces cerevisiae BY4741
Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast crossThe Upstream library tested natural BY/RM variants in 144-bp promoter fragments centered on variants located upstream of yeast genes. Six effective BY4741 replicate groups were assayed by matched plasmid-DNA and reporter-RNA barcode sequencing, with RM and BY allele oligos compared pairwise.
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
An episomal low-copy RCP83 reporter plasmid (Addgene 163466) carried synthetic 144-bp fragments centered on individual promoter variants and an invariant HIS3 minimal promoter between the fragment and codon-optimized yEGFP reporter. The library covered variants from approximately 72 bp upstream of the start codon toward the preceding gene, up to 1 kb. Reporter RNA and plasmid DNA barcode counts were measured in six effective replicate groups from BY4741 cultures; the two failed DNA samples were replaced with same-batch DNA as described by the authors. The published mpra R-package model produced the RM-versus-BY log2 fold changes and FDRs.
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 · 46 definitions
- variant_id
- Canonical sacCer3 BY-to-RM variant identifier (chromosome_position_reference_alternate).
- promoter_gene
- Systematic yeast gene whose promoter fragment was tested.
- library
- MPRA sub-library: TSS or Upstream.
- design_type
- Design class from the MPRA oligo design: firstTileUTR or singleVariantTiles.
- test_name
- Published limma test/construct label from Figure 2 source data 1.
- oligo_id
- Identifier of the designed oligo carrying the tested RM allele.
- orientation
- Genomic strand orientation used for the promoter fragment.
- chromosome
- sacCer3 chromosome.
- position_saccer3
- 1-based sacCer3 coordinate of the variant.
- reference_allele_by
- BY/S288C allele in the designed reference sequence.
- alternate_allele_rm
- RM allele substituted for the tested contrast.
- variant_type
- SNV when both alleles are one base; otherwise indel.
- variant_index_in_fragment
- 1-based index of this variant among variants in the TSS fragment (1 for Upstream).
- variant_position_in_fragment
- Variant position within the designed promoter fragment.
- fragment_variant_count
- Number of natural variants represented in the oligo fragment.
- fragment_anchor_position_saccer3
- TSS/anchor coordinate reported in the oligo design.
- fragment_allele_pattern
- Published oligo allele pattern; 1 denotes BY and 2 denotes RM.
- log2_fold_change_rm_vs_by
- Published log2 fold change for RM-allele versus BY-allele reporter activity.
- rm_vs_by_fold_change
- Linear fold change calculated as 2 raised to the published log2 fold change.
- mean_log_expression
- Published average normalized log expression for the tested oligo.
- t_statistic
- Published moderated t statistic.
- p_value
- Published nominal p-value for the allele-activity test.
- fdr
- Published multiple-testing-adjusted p-value.
- b_statistic
- Published limma B statistic.
- significant_fdr_0_05
- Whether the published FDR is at most 0.05.
- effect_direction
- Direction of the RM allele effect on reporter expression.
- n_barcodes_assigned_to_test_oligo
- Number of barcode rows assigned to the tested oligo in the GEO mapped-to-design matrix.
- dna_count_sum_effective_replicates
- Sum of plasmid-DNA barcode counts across the paper's effective replicate groups.
- rna_count_sum_effective_replicates
- Sum of reporter-RNA barcode counts across the paper's effective replicate groups.
- log2_rna_dna_ratio
- Descriptive log2 ratio of summed RNA barcode counts to summed DNA barcode counts; not the modeled allele effect.
- min_dna_count_across_effective_replicates
- Minimum aggregated DNA count across effective replicate groups; all retained rows are greater than zero.
- min_rna_count_across_effective_replicates
- Minimum aggregated RNA count across effective replicate groups; all retained rows are greater than zero.
- dna_replicate_count
- Number of effective DNA replicate groups summarized.
- rna_replicate_count
- Number of effective RNA replicate groups summarized.
- supplementary_annotation_available
- Whether a matching row was available in Supplementary file 3 annotations.
- population_frequency
- Population-frequency annotation supplied in Supplementary file 3.
- maf
- Minor-allele-frequency annotation supplied in Supplementary file 3.
- derived_allele_frequency
- Derived-allele-frequency annotation supplied in Supplementary file 3.
- rm_derived
- Indicator supplied by the paper for whether the RM allele is derived.
- distance_from_gene_bp
- Distance from the target gene reported in Supplementary file 3.
- in_a_nucleosome
- Indicator for overlap with a nucleosome annotation.
- nucleosome_score
- Nucleosome score supplied by the paper.
- has_human_homolog
- Indicator that the target gene has a human homolog.
- has_paralog
- Indicator that the target gene has a paralog.
- overlapping_gene_count
- Number of genes overlapped by the promoter annotation.
- source_table
- Source workbook and worksheet used for the published effect statistics.
Quality control
The authors retained barcode assignments whose primary oligo perfectly matched a designed oligo, excluded reads not matching known annotation barcodes, and replaced the two failed Upstream DNA samples with same-batch DNA measurements. They tested only oligos with summed barcode counts greater than zero in every DNA and RNA replicate. Package QC additionally required finite published statistics with p-values and FDRs in [0,1], removed the two Hunter control constructs, and retained 4,467 natural Upstream variant contrasts; every retained row has nonzero counts in all six effective DNA and six effective RNA replicate groups.
Curation notes
This table is one row per natural variant contrast, retaining separate promoter-gene/strand contexts when the same genomic variant was assayed in divergent promoters. The processed GEO count matrix was aggregated by oligo and summarized using the paper's six effective replicate groups, including the documented same-batch DNA replacements. Optional biological annotations are copied from Supplementary file 3 when a matching test row exists; blank annotation fields do not indicate failed MPRA QC.