SuRE raQTLs (Dataset 2), SORT1 luciferase saturation (Dataset 3) and eQTL-LD MPRA (Dataset 5)
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Release 2026-10-10-7fcc3e48a123 · Evidence verified: Not verified
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24 evaluations · 24 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Borzoi (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.125 pearson-correlation unitless · higher Uncertainty: SE 0.025. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBorzoi on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Borzoi', column 'HepG2 (16,255 SNPs)' |
| Configuration: Caduceus (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.108 pearson-correlation unitless · higher Uncertainty: SE 0.021. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCaduceus on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Caduceus', column 'HepG2 (16,255 SNPs)' |
| Configuration: ChromBPNet (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.295 pearson-correlation unitless · higher Uncertainty: SE 0.021. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceChromBPNet on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'ChromBPNet', column 'HepG2 (16,255 SNPs)' |
| Configuration: DNABERT-2 (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.096 pearson-correlation unitless · higher Uncertainty: SE 0.191. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDNABERT-2 on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'DNABERT-2', column 'HepG2 (16,255 SNPs)' |
| Configuration: Enformer (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.141 pearson-correlation unitless · higher Uncertainty: SE 0.110. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEnformer on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Enformer', column 'HepG2 (16,255 SNPs)' |
| Configuration: Gena LM b-multi (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.062 pearson-correlation unitless · higher Uncertainty: SE 0.024. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGena LM b-multi on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM b-multi', column 'HepG2 (16,255 SNPs)' |
| Configuration: Gena LM-base (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.05 pearson-correlation unitless · higher Uncertainty: SE 0.033. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGena LM-base on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM-base', column 'HepG2 (16,255 SNPs)' |
| Configuration: Gena LM bigbird (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.099 pearson-correlation unitless · higher Uncertainty: SE 0.029. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGena LM bigbird on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM bigbird', column 'HepG2 (16,255 SNPs)' |
| Configuration: Gena LM large (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.088 pearson-correlation unitless · higher Uncertainty: SE 0.036. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGena LM large on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM large', column 'HepG2 (16,255 SNPs)' |
| Configuration: Geneformer (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.027 pearson-correlation unitless · higher Uncertainty: SE 0.160. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceGeneformer on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Geneformer', column 'HepG2 (16,255 SNPs)' |
| Configuration: Hyenadna 1 mf (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.136 pearson-correlation unitless · higher Uncertainty: SE 0.059. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenadna 1 mf on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 1 mf', column 'HepG2 (16,255 SNPs)' |
| Configuration: Hyenadna 160 k (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.142 pearson-correlation unitless · higher Uncertainty: SE 0.040. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenadna 160 k on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 160 k', column 'HepG2 (16,255 SNPs)' |
| Configuration: Hyenadna 32 k (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.098 pearson-correlation unitless · higher Uncertainty: SE 0.061. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenadna 32 k on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 32 k', column 'HepG2 (16,255 SNPs)' |
| Configuration: Hyenadna 450 k (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.134 pearson-correlation unitless · higher Uncertainty: SE 0.050. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceHyenadna 450 k on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 450 k', column 'HepG2 (16,255 SNPs)' |
| Configuration: NT 2.5b-1000g (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.112 pearson-correlation unitless · higher Uncertainty: SE 0.021. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT 2.5b-1000g on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 2.5b-1000g', column 'HepG2 (16,255 SNPs)' |
| Configuration: NT 2.5b-m-s (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.139 pearson-correlation unitless · higher Uncertainty: SE 0.027. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT 2.5b-m-s on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 2.5b-m-s', column 'HepG2 (16,255 SNPs)' |
| Configuration: NT 500m-h-ref (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.119 pearson-correlation unitless · higher Uncertainty: SE 0.038. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT 500m-h-ref on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 500m-h-ref', column 'HepG2 (16,255 SNPs)' |
| Configuration: NT 500m1000g (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.116 pearson-correlation unitless · higher Uncertainty: SE 0.023. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT 500m1000g on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 500m1000g', column 'HepG2 (16,255 SNPs)' |
| Configuration: NT v2-100m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.127 pearson-correlation unitless · higher Uncertainty: SE 0.050. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT v2-100m-ms on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2-100m-ms', column 'HepG2 (16,255 SNPs)' |
| Configuration: NT v2-250m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.11 pearson-correlation unitless · higher Uncertainty: SE 0.020. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT v2-250m-ms on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2-250m-ms', column 'HepG2 (16,255 SNPs)' |
| Configuration: NT v2 500m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.114 pearson-correlation unitless · higher Uncertainty: SE 0.007. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT v2 500m-ms on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2 500m-ms', column 'HepG2 (16,255 SNPs)' |
| Configuration: NT v2-50m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.103 pearson-correlation unitless · higher Uncertainty: SE 0.036. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceNT v2-50m-ms on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2-50m-ms', column 'HepG2 (16,255 SNPs)' |
| Configuration: SEI (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.298 pearson-correlation unitless · higher Uncertainty: SE 0.029. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSEI on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'SEI', column 'HepG2 (16,255 SNPs)' |
| Configuration: TREDNet (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HepG2 (Manzo et al. 2025 Table 1) Dataset: HepG2 regulatory variant reporter data (Manzo et al. 2025) | 0.314 pearson-correlation unitless · higher Uncertainty: SE 0.018. Standard error as printed in brackets; its basis is not defined in the caption Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceTREDNet on HepG2 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'TREDNet', column 'HepG2 (16,255 SNPs)' |
Source checking is not independent reproduction. Release 2026-10-10-7fcc3e48a123.
A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
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7 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.population 16255 SNPs in HepG2 per the Table 1 header; SuRE raQTLs (Dataset 2), SORT1 luciferase saturation (Dataset 3) and eQTL-LD MPRA (Dataset 5) Context-only references | Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants Table 1 header; Table 4 Version: Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator Table 1 header; Table 4 Context-only references | Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants Table 1 header; Table 4 Version: Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.split Evaluation of variant effects; no variant-level training for CNNs Context-only references | Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants Table 1 header; Table 4 Version: Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.variants 16255 Context-only references | Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants Table 1 header; Table 4 Version: Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.version Manzo et al. Table 4 (as published) Context-only references | Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants Table 1 header; Table 4 Version: Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| description SuRE raQTLs (Dataset 2), SORT1 luciferase saturation (Dataset 3) and eQTL-LD MPRA (Dataset 5) Context-only references | Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants Table 1 header; Table 4 Version: Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| name HepG2 regulatory variant reporter data (Manzo et al. 2025) Context-only references | Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants Table 1 header; Table 4 Version: Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-10-7fcc3e48a123 · Record review: source checked
Stable ID: regulatory-variant-20261009-data-manzo2025-hepg2