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Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025

Nature Methods · 2025 · Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article · Peer-reviewed

DOI: 10.1038/s41592-025-02772-6 Original source

586193 bytes. Each row of sheet "Panel A" is one held-out perturbation in one test-training split (column seed), labelled test or val in column train.

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21 results
3 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Value	Metric	Model or configuration	Dataset	Evaluation
0.726 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	GEARS (Ahlmann-Eltze et al. 2025)	Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS distribution, Ahlmann-Eltze et al. 2025)	GEARS on Adamson (Ahlmann-Eltze et al. 2025)
0.388 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	GEARS (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, K562 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	GEARS on Replogle K562 (Ahlmann-Eltze et al. 2025)
0.636 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	GEARS (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, RPE1 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	GEARS on Replogle RPE1 (Ahlmann-Eltze et al. 2025)
0.726 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	Geneformer (Ahlmann-Eltze et al. 2025)	Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS distribution, Ahlmann-Eltze et al. 2025)	Geneformer on Adamson (Ahlmann-Eltze et al. 2025)
0.404 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	Geneformer (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, K562 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	Geneformer on Replogle K562 (Ahlmann-Eltze et al. 2025)
0.678 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	Geneformer (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, RPE1 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	Geneformer on Replogle RPE1 (Ahlmann-Eltze et al. 2025)
0.717 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	Linear model (G and P from training data) (Ahlmann-Eltze et al. 2025)	Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS distribution, Ahlmann-Eltze et al. 2025)	Linear model (G and P from training data) on Adamson (Ahlmann-Eltze et al. 2025)
0.436 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	Linear model (G and P from training data) (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, K562 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	Linear model (G and P from training data) on Replogle K562 (Ahlmann-Eltze et al. 2025)
0.680 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	Linear model (G and P from training data) (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, RPE1 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	Linear model (G and P from training data) on Replogle RPE1 (Ahlmann-Eltze et al. 2025)
0.724 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	Mean (Ahlmann-Eltze et al. 2025)	Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS distribution, Ahlmann-Eltze et al. 2025)	Mean on Adamson (Ahlmann-Eltze et al. 2025)
0.408 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	Mean (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, K562 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	Mean on Replogle K562 (Ahlmann-Eltze et al. 2025)
0.678 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	Mean (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, RPE1 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	Mean on Replogle RPE1 (Ahlmann-Eltze et al. 2025)
0.728 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	scBERT (Ahlmann-Eltze et al. 2025)	Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS distribution, Ahlmann-Eltze et al. 2025)	scBERT on Adamson (Ahlmann-Eltze et al. 2025)
0.408 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	scBERT (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, K562 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	scBERT on Replogle K562 (Ahlmann-Eltze et al. 2025)
0.678 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	scBERT (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, RPE1 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	scBERT on Replogle RPE1 (Ahlmann-Eltze et al. 2025)
0.595 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	scGPT (Ahlmann-Eltze et al. 2025)	Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS distribution, Ahlmann-Eltze et al. 2025)	scGPT on Adamson (Ahlmann-Eltze et al. 2025)
0.316 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	scGPT (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, K562 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	scGPT on Replogle K562 (Ahlmann-Eltze et al. 2025)
0.588 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	scGPT (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, RPE1 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	scGPT on Replogle RPE1 (Ahlmann-Eltze et al. 2025)
0.724 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	UCE (Ahlmann-Eltze et al. 2025)	Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS distribution, Ahlmann-Eltze et al. 2025)	UCE on Adamson (Ahlmann-Eltze et al. 2025)
0.409 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	UCE (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, K562 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	UCE on Replogle K562 (Ahlmann-Eltze et al. 2025)
0.680 unitless	Pearson delta (1,000 most highly expressed control genes; mean over held-out perturbations and splits)	UCE (Ahlmann-Eltze et al. 2025)	Replogle et al. 2022 Perturb-seq essential-gene screen, RPE1 CRISPRi (GEARS distribution, Ahlmann-Eltze et al. 2025)	UCE on Replogle RPE1 (Ahlmann-Eltze et al. 2025)

Claims

Statements this source supports, each with where in the source it was checked.

Relevance of Adamson: expression prediction for unseen single perturbations (Ahlmann-Eltze et al. 2025 Fig. 2a and Extended Data Fig. 8a) to "Assess models for genetic perturbation experiments": Assessed by Adamson: expression prediction for unseen single perturbations (Ahlmann-Eltze et al. 2025 Fig. 2a and Extended Data Fig. 8a) (perturbation-ahlmann-20261011-source-article: Fig. 2 and Extended Data Fig. 8 legends and Methods; perturbation-ahlmann-20261011-source-data-fig2: sheet "Panel A"; perturbation-ahlmann-20261011-source-data-ed-fig8: sheet "Panel A")
Relevance of Replogle K562: expression prediction for unseen single perturbations (Ahlmann-Eltze et al. 2025 Fig. 2a and Extended Data Fig. 8a) to "Assess models for genetic perturbation experiments": Assessed by Replogle K562: expression prediction for unseen single perturbations (Ahlmann-Eltze et al. 2025 Fig. 2a and Extended Data Fig. 8a) (perturbation-ahlmann-20261011-source-article: Fig. 2 and Extended Data Fig. 8 legends and Methods; perturbation-ahlmann-20261011-source-data-fig2: sheet "Panel A"; perturbation-ahlmann-20261011-source-data-ed-fig8: sheet "Panel A")
Relevance of Replogle RPE1: expression prediction for unseen single perturbations (Ahlmann-Eltze et al. 2025 Fig. 2a and Extended Data Fig. 8a) to "Assess models for genetic perturbation experiments": Assessed by Replogle RPE1: expression prediction for unseen single perturbations (Ahlmann-Eltze et al. 2025 Fig. 2a and Extended Data Fig. 8a) (perturbation-ahlmann-20261011-source-article: Fig. 2 and Extended Data Fig. 8 legends and Methods; perturbation-ahlmann-20261011-source-data-fig2: sheet "Panel A"; perturbation-ahlmann-20261011-source-data-ed-fig8: sheet "Panel A")

Evidence

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Evidence table

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21 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
attributes.artifact_sha256 040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3 Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record
Doi 10.1038/s41592-025-02772-6 Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.doi` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record
Evidence concerns 1 values source id perturbation-ahlmann-20261011-source-data-ed-fig8 message Panel A repeats Source Data Fig. 2 Panel A row for row (48, 262 and 413 rows per method over two splits). Methods restricts the analysis to 73, 398 and 629 perturbations predicted by all models; the sheet does not have these counts. source locator Methods 'Single perturbation benchmark setup' paragraph 4 versus Source Data Extended Data Fig. 8, sheet "Panel A" artifact sha256 040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3 reviewed at 2026-10-11T00:00:00Z review method ai-assisted-source-review Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.evidence_concerns` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record
Licence CC-BY-4.0 Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.licence` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record
Media type application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.media_type` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record
Publication status peer_reviewed Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.publication_status` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record
Retrieved at 2026-10-11T00:48:13Z Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record
Scope note 586193 bytes. Each row of sheet "Panel A" is one held-out perturbation in one test-training split (column seed), labelled test or val in column train. Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.scope_note` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record
Source location Article 'Data availability' and the 'Source Data Extended Data Fig. 8' link under the figure; the article licence covers its supplementary material Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record
Url https://static-content.springer.com/esm/art%3A10.1038%2Fs41592-025-02772-6/MediaObjects/41592_2025_2772_MOESM10_ESM.xlsx Source metadata	Source Data Extended Data Fig. 8, Ahlmann-Eltze et al. 2025 Original source ↗ No field-specific location recorded Version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article Retrieved: 2026-10-11T00:48:13Z	catalogued No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.url` Source artifact SHA-256: `040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3` Hash scope: Hash scope not separately documented; inspect source record

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

Authors' Source Data workbook for Extended Data Fig. 8, published by the journal with the article.

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Technical metadata and extraction receipts

Stable ID: perturbation-ahlmann-20261011-source-data-ed-fig8

areas: cells-tissues; single-cell
contexts: research
url: https://static-content.springer.com/esm/art%3A10.1038%2Fs41592-025-02772-6/MediaObjects/41592_2025_2772_MOESM10_ESM.xlsx
version: Source Data Extended Data Fig. 8 (41592_2025_2772_MOESM10_ESM.xlsx) as published with the article
retrieved at: 2026-10-11T00:48:13Z
artifact sha256: 040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3
doi: 10.1038/s41592-025-02772-6
publication status: peer_reviewed
licence: CC-BY-4.0
media type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
venue: Nature Methods
year: 2025
source locator: Article 'Data availability' and the 'Source Data Extended Data Fig. 8' link under the figure; the article licence covers its supplementary material
scope note: 586193 bytes. Each row of sheet "Panel A" is one held-out perturbation in one test-training split (column seed), labelled test or val in column train.
evidence concerns: source id: perturbation-ahlmann-20261011-source-data-ed-fig8; message: Panel A repeats Source Data Fig. 2 Panel A row for row (48, 262 and 413 rows per method over two splits). Methods restricts the analysis to 73, 398 and 629 perturbations predicted by all models; the sheet does not have these counts.; source locator: Methods 'Single perturbation benchmark setup' paragraph 4 versus Source Data Extended Data Fig. 8, sheet "Panel A"; artifact sha256: 040dae4985b4461817b96eb807390c8fe3f2c115523f4dfcb7692485aa0734e3; reviewed at: 2026-10-11T00:00:00Z; review method: ai-assisted-source-review

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