rewirebio.iobenchmarks
Protocol

Allelic reporter effect correlation in K562 (Manzo et al. 2025 Table 1)

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

24 evaluations · 24 results

Overview

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

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

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.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

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

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence 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 checked
Methods, coverage and source

Borzoi 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 checked
Methods, coverage and source

Caduceus 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 checked
Methods, coverage and source

ChromBPNet 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 checked
Methods, coverage and source

DNABERT-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 checked
Methods, coverage and source

Enformer 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 checked
Methods, coverage and source

Gena 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 checked
Methods, coverage and source

Gena 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 checked
Methods, coverage and source

Gena 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 checked
Methods, coverage and source

Gena 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 checked
Methods, coverage and source

Geneformer 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 checked
Methods, coverage and source

Hyenadna 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 checked
Methods, coverage and source

Hyenadna 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 checked
Methods, coverage and source

Hyenadna 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 checked
Methods, coverage and source

Hyenadna 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 checked
Methods, coverage and source

NT 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 checked
Methods, coverage and source

NT 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 checked
Methods, coverage and source

NT 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 checked
Methods, coverage and source

NT 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 checked
Methods, coverage and source

NT 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 checked
Methods, coverage and source

NT 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 checked
Methods, coverage and source

NT 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 checked
Methods, coverage and source

NT 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 checked
Methods, coverage and source

SEI 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 checked
Methods, coverage and source

TREDNet 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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Author-reported evaluations
1
External evaluations
23

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Evidence

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Evidence table

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Release 2026-10-10-7fcc3e48a123 · Record review: source checked

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Technical metadata and extraction receipts

Stable ID: regulatory-variant-20261009-protocol-manzo2025-k562-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 'K562 (19,321 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.; K562 combines SuRE raQTLs (19,237) and an MPRA set (2,756), which sum to 21,993, not the 19,321 in the Table 1 header; no filtering step is stated.
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