Protocol

Allelic reporter effect correlation in HeLa (Manzo et al. 2025 Table 1)

Pearson correlation between predicted and measured log2 fold-change of variant effects in reporter assays.

Overview

Pearson correlation between predicted and measured log2 fold-change of variant effects in reporter assays.

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24 recorded evaluations, 24 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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24 evaluations · 24 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
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 checked Methods, coverage and source Borzoi 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 checked Methods, coverage and source Caduceus 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 checked Methods, coverage and source ChromBPNet 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 checked Methods, coverage and source DNABERT-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 checked Methods, coverage and source Enformer 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 checked Methods, coverage and source Gena 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 checked Methods, coverage and source Gena 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 checked Methods, coverage and source Gena 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 checked Methods, coverage and source Gena 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 checked Methods, coverage and source Geneformer 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 checked Methods, coverage and source Hyenadna 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 checked Methods, coverage and source Hyenadna 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 checked Methods, coverage and source Hyenadna 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 checked Methods, coverage and source Hyenadna 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 checked Methods, coverage and source NT 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 checked Methods, coverage and source NT 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 checked Methods, coverage and source NT 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 checked Methods, coverage and source NT 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 checked Methods, coverage and source NT 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 checked Methods, coverage and source NT 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 checked Methods, coverage and source NT 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 checked Methods, coverage and source NT 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 checked Methods, coverage and source SEI 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 checked Methods, coverage and source TREDNet 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)'

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Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Original source · Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML

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Technical metadata and extraction receipts

Stable ID: regulatory-variant-20261009-protocol-manzo2025-hela-pearson

areas: dna-genomes
contexts: research
protocol: Score 1 kb reference and alternative sequences centred on each SNP; correlate the predicted log2 ratio with the experimental log2 fold-change; standard error in brackets.
version: Table 1
source locator: Table 1 column 'Hela (5241 SNPs)'; Results 2.1; Methods 4.1
limitations: Reporter (SuRE, MPRA, luciferase) activity on episomal constructs, not endogenous regulation.; TREDNet was developed by the senior author's group (reference 18) and is author_reported; the other 23 models were run by the authors.; Models were not adapted equally: Transformers were fine-tuned for enhancer classification per cell line; CNNs and long-context models were used for inference. The source describes the adaptation of Enformer, Borzoi and HyenaDNA inconsistently (Table 2 versus Section 4.2); Enformer and Borzoi are excluded from this judgement for that reason.; Geneformer, a single-cell transcriptome model, was applied to DNA tokens; it is excluded from this judgement.; The bracketed values are labelled standard errors; how they were computed is not stated.; Results 2.1 and 2.3 give dataset-averaged values that differ from Table 1, and the HeLa ranking in the text differs from the table; table values are recorded.; HeLa is three coding-exon MPRA sets (SORL1, TRAF3IP2, PPARG; 5,241 SNPs in total).

Related records

uses data: HeLa regulatory variant reporter data (Manzo et al. 2025)
assessment: Borzoi on HeLa reporter variant effects
assessment: Caduceus on HeLa reporter variant effects
assessment: ChromBPNet on HeLa reporter variant effects
assessment: DNABERT-2 on HeLa reporter variant effects
assessment: Enformer on HeLa reporter variant effects
assessment: Gena LM b-multi on HeLa reporter variant effects
assessment: Gena LM-base on HeLa reporter variant effects
assessment: Gena LM bigbird on HeLa reporter variant effects
assessment: Gena LM large on HeLa reporter variant effects
assessment: Geneformer on HeLa reporter variant effects
assessment: Hyenadna 1 mf on HeLa reporter variant effects
assessment: Hyenadna 160 k on HeLa reporter variant effects
assessment: Hyenadna 32 k on HeLa reporter variant effects
assessment: Hyenadna 450 k on HeLa reporter variant effects
assessment: NT 2.5b-1000g on HeLa reporter variant effects
assessment: NT 2.5b-m-s on HeLa reporter variant effects
assessment: NT 500m-h-ref on HeLa reporter variant effects
assessment: NT 500m1000g on HeLa reporter variant effects
assessment: NT v2-100m-ms on HeLa reporter variant effects
assessment: NT v2-250m-ms on HeLa reporter variant effects
assessment: NT v2 500m-ms on HeLa reporter variant effects
assessment: NT v2-50m-ms on HeLa reporter variant effects
assessment: SEI on HeLa reporter variant effects
assessment: TREDNet on HeLa reporter variant effects
assessed by: Select regulatory variants and genes for functional follow-up

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