SuRE raQTLs (Dataset 1) and MPRA variants (Dataset 4)
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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 K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.033 pearson-correlation unitless · higher Uncertainty: SE 0.016. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Borzoi', column 'K562 (19,321 SNPs)' |
| Configuration: Caduceus (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.133 pearson-correlation unitless · higher Uncertainty: SE 0.030. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Caduceus', column 'K562 (19,321 SNPs)' |
| Configuration: ChromBPNet (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.287 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 sourceChromBPNet on K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'ChromBPNet', column 'K562 (19,321 SNPs)' |
| Configuration: DNABERT-2 (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.086 pearson-correlation unitless · higher Uncertainty: SE 0.039. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'DNABERT-2', column 'K562 (19,321 SNPs)' |
| Configuration: Enformer (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.059 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 sourceEnformer on K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Enformer', column 'K562 (19,321 SNPs)' |
| Configuration: Gena LM b-multi (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.077 pearson-correlation unitless · higher Uncertainty: SE 0.051. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM b-multi', column 'K562 (19,321 SNPs)' |
| Configuration: Gena LM-base (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.077 pearson-correlation unitless · higher Uncertainty: SE 0.042. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM-base', column 'K562 (19,321 SNPs)' |
| Configuration: Gena LM bigbird (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.136 pearson-correlation unitless · higher Uncertainty: SE 0.055. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM bigbird', column 'K562 (19,321 SNPs)' |
| Configuration: Gena LM large (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.117 pearson-correlation unitless · higher Uncertainty: SE 0.044. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM large', column 'K562 (19,321 SNPs)' |
| Configuration: Geneformer (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.005 pearson-correlation unitless · higher Uncertainty: SE 0.198. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Geneformer', column 'K562 (19,321 SNPs)' |
| Configuration: Hyenadna 1 mf (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.118 pearson-correlation unitless · higher Uncertainty: SE 0.056. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 1 mf', column 'K562 (19,321 SNPs)' |
| Configuration: Hyenadna 160 k (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.148 pearson-correlation unitless · higher Uncertainty: SE 0.053. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 160 k', column 'K562 (19,321 SNPs)' |
| Configuration: Hyenadna 32 k (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.084 pearson-correlation unitless · higher Uncertainty: SE 0.071. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 32 k', column 'K562 (19,321 SNPs)' |
| Configuration: Hyenadna 450 k (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.077 pearson-correlation unitless · higher Uncertainty: SE 0.074. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 450 k', column 'K562 (19,321 SNPs)' |
| Configuration: NT 2.5b-1000g (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.147 pearson-correlation unitless · higher Uncertainty: SE 0.052. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 2.5b-1000g', column 'K562 (19,321 SNPs)' |
| Configuration: NT 2.5b-m-s (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.153 pearson-correlation unitless · higher Uncertainty: SE 0.055. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 2.5b-m-s', column 'K562 (19,321 SNPs)' |
| Configuration: NT 500m-h-ref (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.149 pearson-correlation unitless · higher Uncertainty: SE 0.139. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 500m-h-ref', column 'K562 (19,321 SNPs)' |
| Configuration: NT 500m1000g (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.123 pearson-correlation unitless · higher Uncertainty: SE 0.084. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 500m1000g', column 'K562 (19,321 SNPs)' |
| Configuration: NT v2-100m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.152 pearson-correlation unitless · higher Uncertainty: SE 0.065. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2-100m-ms', column 'K562 (19,321 SNPs)' |
| Configuration: NT v2-250m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.166 pearson-correlation unitless · higher Uncertainty: SE 0.064. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2-250m-ms', column 'K562 (19,321 SNPs)' |
| Configuration: NT v2 500m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.199 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 500m-ms on K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2 500m-ms', column 'K562 (19,321 SNPs)' |
| Configuration: NT v2-50m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.147 pearson-correlation unitless · higher Uncertainty: SE 0.058. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2-50m-ms', column 'K562 (19,321 SNPs)' |
| Configuration: SEI (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.297 pearson-correlation unitless · higher Uncertainty: SE 0.022. 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 K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'SEI', column 'K562 (19,321 SNPs)' |
| Configuration: TREDNet (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1) Dataset: K562 regulatory variant reporter data (Manzo et al. 2025) | 0.315 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceTREDNet on K562 reporter variant effects regulatory-variant-20261009-protocol-manzo2025-k562-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'TREDNet', column 'K562 (19,321 SNPs)' |
Source checking is not independent reproduction. Release 2026-10-10-7fcc3e48a123.
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7 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.population 19321 SNPs in K562 per the Table 1 header; SuRE raQTLs (Dataset 1) and MPRA variants (Dataset 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.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 19321 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 1) and MPRA variants (Dataset 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 |
| name K562 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-k562