Result

0.139 pearson-correlation

manzo2025-hepg2-nt-2-5b-m-s-pearson pearson-correlation

Tested 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)
Procedure: regulatory-variant-20261009-protocol-manzo2025-hepg2-pearson
Evaluation: NT 2.5b-m-s on HepG2 reporter variant effects
Coverage: Not reported scored / Not reported eligible
Uncertainty: SE 0.027. Standard error as printed in brackets; its basis is not defined in the caption
Evidence: Independent external evaluation · source checkedComparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants · Table 1 row 'NT 2.5b-m-s', column 'HepG2 (16,255 SNPs)'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Per cell line
Adaptation: Fine-tuned per cell line for enhancer versus control classification on 1 kb sequences (Table 2); variant effect is the log2 ratio of alternative to reference scores
Scoring implementation: Pearson correlation of predicted and measured log2 fold-change

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

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.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-7fcc3e48a123
Property and statement	Original source and location	Review and provenance
Reported result 0.139 Individual claims	Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants Original source ↗ Table 1 row 'NT 2.5b-m-s', column 'HepG2 (16,255 SNPs)' Version: Genes 16(10):1223, published 2025-10-15; PMC12562713 full-text XML Retrieved: 2026-10-09T21:04:27Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 independent paper Audit details Deterministic parse of the pinned article XML table (extract/extract_regulatory_variant.py) with caption, column headers and row labels asserted. Pending independent review. Independent review 2026-10-09: value, interval or standard error, and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `c49e7cef821d7c1a7966db9922b58c2f51d852df13f5cdc3969bf54818e5ed9e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `c49e7cef821d7c1a7966db9922b58c2f51d852df13f5cdc3969bf54818e5ed9e` Extraction artifact

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Sources and history

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

1 source records and release history

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-result-manzo2025-hepg2-nt-2-5b-m-s-pearson

metric: pearson-correlation
metric direction: higher
unit: unitless
printed value: 0.139
numeric value: 0.139
source locator: Table 1 row 'NT 2.5b-m-s', column 'HepG2 (16,255 SNPs)'
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the article XML and matched its SHA-256. Read Table 1 with the reviewer's own table-wrap reader; checked printed value (including the Unicode minus), numeric value, the bracketed standard error, column, model label and linked configuration and protocol.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: c49e7cef821d7c1a7966db9922b58c2f51d852df13f5cdc3969bf54818e5ed9e; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12562713/fullTextXML; note: Deterministic parse of the pinned article XML table (extract/extract_regulatory_variant.py) with caption, column headers and row labels asserted. Pending independent review. Independent review 2026-10-09: value, interval or standard error, and identity match the source.
uncertainty: type: standard_error; value: 0.027; printed: (0.027); note: Standard error as printed in brackets; its basis is not defined in the caption
metric qualifier: predicted versus measured log2 fold-change of variant effect

Related records

evaluation: NT 2.5b-m-s on HepG2 reporter variant effects

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