Coding-exon MPRA of SORL1, TRAF3IP2 and PPARG exons (Datasets 7-9)
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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 HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | −0.066 pearson-correlation unitless · higher Uncertainty: SE 0.005. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Borzoi', column 'Hela (5241 SNPs)' |
| Configuration: Caduceus (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.02 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 sourceCaduceus on HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Caduceus', column 'Hela (5241 SNPs)' |
| Configuration: ChromBPNet (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.289 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 sourceChromBPNet on HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'ChromBPNet', column 'Hela (5241 SNPs)' |
| Configuration: DNABERT-2 (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.12 pearson-correlation unitless · higher Uncertainty: SE 0.140. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'DNABERT-2', column 'Hela (5241 SNPs)' |
| Configuration: Enformer (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.245 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 sourceEnformer on HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Enformer', column 'Hela (5241 SNPs)' |
| Configuration: Gena LM b-multi (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.026 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 sourceGena LM b-multi on HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM b-multi', column 'Hela (5241 SNPs)' |
| Configuration: Gena LM-base (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.029 pearson-correlation unitless · higher Uncertainty: SE 0.227. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM-base', column 'Hela (5241 SNPs)' |
| Configuration: Gena LM bigbird (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.045 pearson-correlation unitless · higher Uncertainty: SE 0.015. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM bigbird', column 'Hela (5241 SNPs)' |
| Configuration: Gena LM large (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.069 pearson-correlation unitless · higher Uncertainty: SE 0.216. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Gena LM large', column 'Hela (5241 SNPs)' |
| Configuration: Geneformer (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | −0.007 pearson-correlation unitless · higher Uncertainty: SE 0.057. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Geneformer', column 'Hela (5241 SNPs)' |
| Configuration: Hyenadna 1 mf (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.046 pearson-correlation unitless · higher Uncertainty: SE 0.013. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 1 mf', column 'Hela (5241 SNPs)' |
| Configuration: Hyenadna 160 k (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.046 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 | Independent external evaluation · Source checkedMethods, coverage and sourceHyenadna 160 k on HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 160 k', column 'Hela (5241 SNPs)' |
| Configuration: Hyenadna 32 k (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.031 pearson-correlation unitless · higher Uncertainty: SE 0.013. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 32 k', column 'Hela (5241 SNPs)' |
| Configuration: Hyenadna 450 k (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.055 pearson-correlation unitless · higher Uncertainty: SE 0.015. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'Hyenadna 450 k', column 'Hela (5241 SNPs)' |
| Configuration: NT 2.5b-1000g (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.087 pearson-correlation unitless · higher Uncertainty: SE 0.105. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 2.5b-1000g', column 'Hela (5241 SNPs)' |
| Configuration: NT 2.5b-m-s (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.066 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 2.5b-m-s', column 'Hela (5241 SNPs)' |
| Configuration: NT 500m-h-ref (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.067 pearson-correlation unitless · higher Uncertainty: SE 0.043. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 500m-h-ref', column 'Hela (5241 SNPs)' |
| Configuration: NT 500m1000g (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.022 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 | Independent external evaluation · Source checkedMethods, coverage and sourceNT 500m1000g on HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 500m1000g', column 'Hela (5241 SNPs)' |
| Configuration: NT v2-100m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.042 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 v2-100m-ms on HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2-100m-ms', column 'Hela (5241 SNPs)' |
| Configuration: NT v2-250m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.03 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 | Independent external evaluation · Source checkedMethods, coverage and sourceNT v2-250m-ms on HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2-250m-ms', column 'Hela (5241 SNPs)' |
| Configuration: NT v2 500m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.036 pearson-correlation unitless · higher Uncertainty: SE 0.011. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2 500m-ms', column 'Hela (5241 SNPs)' |
| Configuration: NT v2-50m-ms (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.074 pearson-correlation unitless · higher Uncertainty: SE 0.047. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT v2-50m-ms', column 'Hela (5241 SNPs)' |
| Configuration: SEI (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.28 pearson-correlation unitless · higher Uncertainty: SE 0.008. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'SEI', column 'Hela (5241 SNPs)' |
| Configuration: TREDNet (Manzo et al. 2025) | Protocol: Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1) Dataset: HeLa regulatory variant reporter data (Manzo et al. 2025) | 0.076 pearson-correlation unitless · higher Uncertainty: SE 0.063. 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 HeLa reporter variant effects regulatory-variant-20261009-protocol-manzo2025-hela-pearson Aggregation: Not reported Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'TREDNet', column 'Hela (5241 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 5241 SNPs in HeLa per the Table 1 header; Coding-exon MPRA of SORL1, TRAF3IP2 and PPARG exons (Datasets 7-9) 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 5241 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 Coding-exon MPRA of SORL1, TRAF3IP2 and PPARG exons (Datasets 7-9) 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 HeLa 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-hela