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:0019
Reference genome
GRCh37
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / proliferating SH-SY5Y culture
Lentiviral integrated MPRA using 145-bp hg19/GRCh37 reference/alternate inserts, a 10-bp filler/linker between restriction sites, 20-bp barcodes (10 barcodes per genomic instance), plasmid DNA baseline and barcode RNA readout analyzed with MPRAnalyze v1.4.0.
Processed data
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Column dictionary · 30 definitions
variant_id
Variant coordinate in hg19/GRCh37, formatted chromosome:1-based-position.
rs_id
Linked dbSNP identifier from Supplementary Data 3; blank where unavailable.
reference_allele
Reference allele for the tested reference/alternate sequence pair.
alternate_allele
Alternate allele for the tested reference/alternate sequence pair.
lead_snp
Index/lead SNP(s) linked to the tested variant in Supplementary Data 3.
diseases
Abbreviated neuropsychiatric disease association(s) linked to the variant.
gene_annotation
Gene annotation associated with the variant in Supplementary Data 3.
eGenes
Genes nominated by eQTL/eGene sources in Supplementary Data 3.
nearest_gene
Nearest or primary annotated gene from Supplementary Data 3.
annotated_mpra_significant_conditions
MPRA conditions listed as significant for this daSNV in Supplementary Data 3.
atac_context
ATAC-seq tissue/cell context annotations from Supplementary Data 3.
hichip_context
HiChIP tissue/cell context annotations from Supplementary Data 3.
annotation_mpra_pval_mean_across_sig_conditions
Mean MPRA p-value across significant conditions as reported in Supplementary Data 3; not condition-specific.
Mean MPRA log2 fold change across significant conditions as reported in Supplementary Data 3; not condition-specific.
barcode_count_ref
Number of reference-allele barcode rows in the GEO count matrix.
barcode_count_alt
Number of alternate-allele barcode rows in the GEO count matrix.
plasmid_dna_count_ref
Aggregate plasmid DNA count for reference-allele barcode rows in the GEO matrix.
plasmid_dna_count_alt
Aggregate plasmid DNA count for alternate-allele barcode rows in the GEO matrix.
rna_count_ref
Aggregate RNA count across the condition's GEO replicate columns for reference barcode rows.
rna_count_alt
Aggregate RNA count across the condition's GEO replicate columns for alternate barcode rows.
rna_detected_replicates_ref
Number of condition replicates with nonzero aggregate reference RNA count.
rna_detected_replicates_alt
Number of condition replicates with nonzero aggregate alternate RNA count.
raw_mean_log2_activity_ref
Mean pseudocount-smoothed log2 RNA/DNA activity from GEO counts for the reference allele; sample-depth normalized.
raw_mean_log2_activity_alt
Mean pseudocount-smoothed log2 RNA/DNA activity from GEO counts for the alternate allele; sample-depth normalized.
raw_log2_fc_alt_vs_ref
Mean raw count-derived alternate-minus-reference log2 activity across GEO replicates; independent of the published MPRAnalyze estimate.
published_statistic
MPRAnalyze likelihood-ratio statistic from Supplementary Data 5 for this condition.
published_p_value
MPRAnalyze p-value from Supplementary Data 5 for this condition.
published_fdr
FDR-adjusted MPRAnalyze p-value from Supplementary Data 5 for this condition.
published_log2_fc_alt_vs_ref
Published MPRAnalyze alternate/reference log2 fold change from Supplementary Data 5 for this condition.
raw_qc_pass
Package-level QC flag; all retained rows have both allele groups and finite count-derived metrics in GEO.
Quality control
The paper used barcode concordance across biological replicates, RNA/plasmid model diagnostics, replicate reproducibility and exclusion of poorly replicating or poor-quality cultures; MPRAnalyze v1.4.0 likelihood-ratio p-values were FDR-adjusted. Published daSNVs were required to have FDR < 0.05 and absolute log2 fold change > 0.05. Package-level QC additionally required both Ref and all_alt groups to be present in the GEO matrix and all count-derived metrics to be finite. No arbitrary depth cutoff was added because the released GEO aggregation does not reproduce the S5 MPRAnalyze summaries exactly.
Curation notes
GEO sample columns: SH-SY5Y.prog_1=GSM6862281; SH-SY5Y.prog_2=GSM6862282; SH-SY5Y.prog_3=GSM6862283. The paper's nomenclature calls the genome assembly hg19/hg37; this package represents it as GRCh37. S5 SHSY5Y.prog provides 1814 finite coordinate-labelled model results, of which 114 meet the published daSNV threshold; 1806 remained after requiring both allele groups and finite GEO-derived metrics. Raw GEO scores are provided as independently calculated, sample-depth-normalized log2 RNA/DNA activities and should not be interpreted as replacements for the published MPRAnalyze estimates.