Genome-wide HeLa-S3 ORI STARR-seq: inhibitor perturbation comparison
Resolving systematic errors in widely used enhancer activity assays in human cellsEpisomal whole-genome STARR-seq tested 1,000–1,500 bp human genomic fragments in HeLa-S3 cells using the plasmid origin of replication (ORI) as the core promoter. Duplicate inhibitor-treated and untreated genome-wide screens were compared; the table contains the authors' union of final peak calls with condition-specific activity and differential statistics.
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
1 µM BX-795 (TBK1/IKKε inhibitor) + 1 µM C16 (PKR inhibitor), compared with no-drug control
Unbiased genomic DNA fragments were cloned into an episomal STARR-seq reporter with the ORI used as the core promoter. Reporter RNA was collected 6 h after electroporation and sequenced on an Illumina HiSeq 2500 as paired-end 50-cycle reads; inhibitor-treated and untreated screens were analyzed as a genome-wide comparison.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 27 definitions
- element_id
- Stable region identifier formatted as chrom:start-end using the source interval coordinates.
- chrom
- Chromosome of the tested genomic fragment.
- start
- Start coordinate of the source genomic interval.
- end
- End coordinate of the source genomic interval.
- length_bp
- Interval length in base pairs (end minus start).
- inhibitor_peak_rank
- Identifier/rank of the final peak in the inhibitor-treated screen (peak_N); blank when absent.
- inhibitor_corrected_enrichment
- Corrected STARR-seq enrichment over input for the inhibitor-treated screen.
- inhibitor_pval
- Peak-calling P value for the inhibitor-treated screen.
- inhibitor_chromHMM
- ChromHMM state at the inhibitor-treated peak summit.
- inhibitor_genomic_annotation
- Genomic feature annotation at the inhibitor-treated peak summit.
- inhibitor_HeLaS3_DHS_sig
- Study flag indicating significant HeLa-S3 DHS support for the inhibitor-treated peak (1/0).
- inhibitor_Other_DHS_sig
- Study flag indicating significant DHS support in other cell lines for the inhibitor-treated peak (1/0).
- inhibitor_enriched_TE
- Study flag for an enriched transposable-element family in the inhibitor-treated peak (1/0).
- no_inhibitor_peak_rank
- Identifier/rank of the final peak in the untreated screen (peak_N); blank when absent.
- no_inhibitor_corrected_enrichment
- Corrected STARR-seq enrichment over input for the untreated screen.
- no_inhibitor_pval
- Peak-calling P value for the untreated screen.
- no_inhibitor_chromHMM
- ChromHMM state at the untreated peak summit.
- no_inhibitor_genomic_annotation
- Genomic feature annotation at the untreated peak summit.
- log2fc_inhibitor_vs_no_inhibitor
- Differential activity log2 fold change calculated as inhibitor-treated over untreated.
- p_over_adj
- FDR-adjusted P value for enrichment/higher activity with inhibitor treatment.
- p_under_adj
- FDR-adjusted P value for depletion/lower activity with inhibitor treatment.
- differential_fdr05
- TRUE when either adjusted differential P value is < 0.05; otherwise FALSE.
- differential_direction
- Direction implied by the differential log2 fold change.
- nearest_tss_ensembl75
- Nearest transcript TSS Ensembl identifier from the source Ensembl 75 annotation.
- nearest_tss_gene
- Common gene name associated with the nearest transcript TSS.
- is_inhibitor_peak
- TRUE when the region is present in the final inhibitor-treated peak set.
- is_no_inhibitor_peak
- TRUE when the region is present in the final untreated peak set.
Quality control
Study QC was retained from the authors' pipeline: uniquely mapped reads with up to 3 mismatches and a maximum paired-end insert size of 2 kb; combined biological replicates; initial shortlisted regions required P < 1e-5 and enrichment >= 3; final peaks required corrected enrichment >= 4 (z = 3); peaks dominated by a single fragment (>50% of overlapping fragments) or overlapping ENCODE blacklisted regions were removed. The processed table additionally required a chr1–chr22/X coordinate, a 1,000–2,000 bp interval, finite differential statistics, and at least one condition-specific peak rank. All 12,424 source union-peak rows passed these packaging checks; 0 rows were excluded.
Curation notes
This is a region-focused enhancer screen, not an allele/variant MPRA. The table is the authors' merged final-peak comparison and therefore contains blank condition-specific fields for regions called only in the other condition. Some overlapping union rows share a source condition-specific peak rank; these rows were retained as distinct source intervals rather than silently collapsed. corrected_enrichment is an enrichment-over-input measure, whereas log2fc_inhibitor_vs_no_inhibitor is the paired differential activity statistic. Source files call the assembly hg19 (equivalent GRCh37-era coordinates). Focused BAC screens, luciferase validation, and STAP-seq samples were not included because the compact genome-wide peak comparison is the most directly useful activity table for this package.