A customized promoter Capture Hi-C library from HepG2 cells was cloned directly into an integrated lentiMPRA reporter so captured promoters and their interacting genomic sequences were assayed together. The processed CMPRA5 table reports BCalm MPRA activity statistics for paired bins and isolated promoter/singleton records.
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:0027
Reference genome
GRCh38
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The main ccMPRA construct contains a captured promoter-cCRE pair and a unique 15 bp barcode upstream of an EGFP reporter; it does not use a minimal promoter. Long-read association sequencing linked constructs to bins and short-read barcode sequencing measured DNA and RNA three days after lentiviral transduction. The experiment used two biological replicates with three technical replicates each; activity was quantified as the log RNA/DNA ratio and normalized against promoter-only activity where available. The paper also reports a separate standard minimal-promoter lentiMPRA comparison of 6,231 200-270 bp cCREs, but no corresponding processed table was present in the public Zenodo deposit, so this package represents the primary ccMPRA experiment only.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (21 of 21)
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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 · 21 definitions
interaction_id
Stable package identifier derived from the source-table row order.
source_row
One-based data-row number in CMPRA5_0.tsv.gz, excluding the source header.
record_type
Record class: promoter_CRE_pair, promoter_only, unlabeled_pair, or unlabeled_singleton.
promoter_bin
Promoter bin from the author annotation; for annotated promoter-only baselines with a null right bin, the left bin is made explicit here.
other_element_bin
Other-end/cCRE bin from the author annotation (OE column in the source table).
promoter_chrom
Chromosome parsed from promoter_bin.
promoter_start
Start coordinate parsed from promoter_bin as encoded in the source bin string.
promoter_end
End coordinate parsed from promoter_bin as encoded in the source bin string.
promoter_strand
Strand parsed from promoter_bin.
other_chrom
Chromosome parsed from other_element_bin.
other_start
Start coordinate parsed from other_element_bin as encoded in the source bin string.
other_end
End coordinate parsed from other_element_bin as encoded in the source bin string.
other_strand
Strand parsed from other_element_bin.
target_genes
Target promoter gene label(s) supplied by the authors; unlabeled denotes no resolved target gene.
effect_class
Author activity classification: upregulating, downregulating, or no effect; blank source classifications are normalized to unlabeled.
Benjamini-Hochberg adjusted p-value supplied by the authors for the MPRA activity result.
z_score
Author promoter-normalized activity z-score; values greater than 2 identify enhancers and values less than -2 identify silencers.
left_bin
Left genomic bin in the source paired-bin record.
right_bin
Right genomic bin in the source paired-bin record; null-null-null-null is the source sentinel for an isolated/singleton record.
qc_pass
TRUE for every row retained after the author processing and package-level validation filters.
Quality control
The author workflow removed association barcodes with fewer than 50 reads, quality-trimmed association reads, filtered invalid Hi-C interactions with HiCUP, and called significant promoter Capture Hi-C loops at 5 kb resolution with CHiCAGO score >5. For MPRA quantification, a barcode required an RNA count of at least 1 in at least 3 of the 6 total replicates and each bin required at least 5 representative barcodes. For this package, all 83,501 rows in the author-processed CMPRA5 result passed additional validation for finite logFC, BH-adjusted p-values in [0,1], a valid left coordinate, and either a valid right coordinate or the documented null singleton sentinel; 0 rows failed these checks.
Curation notes
The processed table contains 83,501 retained rows: 56,847 annotated promoter-cCRE pairs, 1,267 annotated promoter-only baseline records, 22,774 unlabeled paired records, and 2,613 unlabeled singleton records. Effect classes are 886 upregulating, 1,251 downregulating, 54,710 no effect, and 26,654 unlabeled. The public table contains no allele identifiers or variant contrasts; it is a promoter-context regulatory activity dataset derived from captured genomic intervals. The region_of_interest is null because the assay uses a genome-wide targeted promoter panel rather than one continuous locus or an unbiased whole-genome library.