Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Can sequence capture gene-expression differences within a tissue?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-trainingExplanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Dataset and biological context | Borzoi-matched RNA-seq coverage aggregated over GENCODE v46 exons with strand matching; retain genes with at least half their exons in a test interval.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training |
| Split | Held-out human genomic intervals under the relevant fold. General training follows Borzoi folds, extending intervals to the AlphaGenome context and removing validation/test windows overlapping training after extension; use the comparison-specific split below rather than the variant chromosome split. Borzoi fold-1 RNA comparison.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training |
| Allowed inputs and adaptation | Predicted and observed log-transformed mean exon coverage; normalized endpoints additionally use quantile normalization across genes and subtract each gene’s mean across tracks.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training |
| Metrics as reported | Gene TPM (cross-gene pearsonr); Gene TPM normalized (cross-gene pearsonr)AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training |
| Aggregation | Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training |
| Uncertainty | Not reported for these summary-table scores. · Not reported in inspected sourcesAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training |
| Entity type | protocol |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
Conceptual summary of the cited procedure; model-specific conditions are given below.
Can sequence capture gene-expression differences within a tissue?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-trainingCompute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-trainingRelease 2026-09-17-a757f4af4277 · 2 evaluations · 4 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Borzoi (paper Table 3): RNA expression correlation across genes Model: Borzoi (paper Table 3) · Benchmark: RNA expression correlation across genes (AlphaGenome paper) · Dataset: RNA expression correlation across genes: evaluated data subset Compute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.765 Gene TPM
(cross-gene pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J13 Source checking is not independent reproduction. |
| 0.449 Gene TPM normalized
(cross-gene pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!J15 Source checking is not independent reproduction. |
| AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head: RNA expression correlation across genes Model: AlphaGenome Borzoi-fold-1 model fine-tuned with base-resolution Borzoi RNA-seq head · Benchmark: RNA expression correlation across genes (AlphaGenome paper) · Dataset: RNA expression correlation across genes: evaluated data subset Compute per-track cross-gene correlation on raw log-expression and, separately, normalized/mean-centred expression. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.52 Gene TPM normalized
(cross-gene pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K15 Source checking is not independent reproduction. |
| 0.80 Gene TPM
(cross-gene pearsonr) Unit: correlation · Direction: higher Aggregation: Pearson correlation across genes. Preserve raw versus normalized Table3 rows; the inspected task paragraph does not specify the weighting used to reduce all correlations to the table scalar. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 3 Track performance'!K13 Source checking is not independent reproduction. |
No source-reviewed explanatory claims are recorded here yet.
Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.
Stable record: alphagenome-2026-t3-protocol-7Trace 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.
42 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Diagram steps ["Aggregate exon coverage","Apply endpoint-specific normalization","Correlate across genes","Retain raw/normalized endpoint identity"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram steps ["Aggregate exon coverage","Apply endpoint-specific normalization","Correlate across genes","Retain raw/normalized endpoint identity"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Diagram steps ["Aggregate exon coverage","Apply endpoint-specific normalization","Correlate across genes","Retain raw/normalized endpoint identity"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Diagram title RNA expression correlation across genes: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title RNA expression correlation across genes: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Diagram title RNA expression correlation across genes: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Dataset and biological context Borzoi-matched RNA-seq coverage aggregated over GENCODE v46 exons with strand matching; retain genes with at least half their exons in a test interval. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 3 Track performance'!A13:N13; 'Suppl Table 3 Track performance'!A15:N15; Supplementary Methods pp.22,24, Gene Expression Correlation and Benchmarking Against Borzoi Track Predictions; methods: pp.21–22, Genome Track Evaluation / Gene Expression Correlation; methods: p.24, Benchmarking Against Borzoi Track Predictions; paper: Extended Data Fig.3c,d; tables: Suppl Table 3 Track performance; evaluation index 7; sheet rows 13, 15; methods: p.19, Training / Pre-training Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Release 2026-09-17-a757f4af4277 · Record review: needs review
Stable ID: alphagenome-2026-t3-protocol-7