Dataset

Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)

Perturb-seq dataset processed with cell-gears v0.0.1 and split by perturbation as in the GEARS publication.

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Release 2026-10-10-7fcc3e48a123 · Evidence verified: Not verified

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Evaluation results

15 evaluations · 88 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: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.988 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_go on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C36, row 'Replogle_K562 / EN_go', column 'Pearson'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.96 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_go on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D36, row 'Replogle_K562 / EN_go', column 'Pearson DE'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.43 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_go on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E36, row 'Replogle_K562 / EN_go', column 'Pearson Delta'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.533 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_go on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F36, row 'Replogle_K562 / EN_go', column 'Pearson Delta DE'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.558 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_go on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H36, row 'Replogle_K562 / EN_go', column 'Pearson Delta DE without KOd gene'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.553 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_go on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G36, row 'Replogle_K562 / EN_go', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: EN_scElmo (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.987 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scElmo on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C37, row 'Replogle_K562 / EN_scElmo', column 'Pearson'
Configuration: EN_scElmo (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.955 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scElmo on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D37, row 'Replogle_K562 / EN_scElmo', column 'Pearson DE'
Configuration: EN_scElmo (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.375 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scElmo on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E37, row 'Replogle_K562 / EN_scElmo', column 'Pearson Delta'
Configuration: EN_scElmo (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.469 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scElmo on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F37, row 'Replogle_K562 / EN_scElmo', column 'Pearson Delta DE'
Configuration: EN_scElmo (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.493 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scElmo on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H37, row 'Replogle_K562 / EN_scElmo', column 'Pearson Delta DE without KOd gene'
Configuration: EN_scElmo (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.49 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scElmo on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G37, row 'Replogle_K562 / EN_scElmo', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: EN_scFoundation (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.987 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scFoundation on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C38, row 'Replogle_K562 / EN_scFoundation', column 'Pearson'
Configuration: EN_scFoundation (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.954 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scFoundation on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D38, row 'Replogle_K562 / EN_scFoundation', column 'Pearson DE'
Configuration: EN_scFoundation (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.373 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scFoundation on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E38, row 'Replogle_K562 / EN_scFoundation', column 'Pearson Delta'
Configuration: EN_scFoundation (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.461 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scFoundation on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F38, row 'Replogle_K562 / EN_scFoundation', column 'Pearson Delta DE'
Configuration: EN_scFoundation (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.484 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scFoundation on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H38, row 'Replogle_K562 / EN_scFoundation', column 'Pearson Delta DE without KOd gene'
Configuration: EN_scFoundation (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.482 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scFoundation on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G38, row 'Replogle_K562 / EN_scFoundation', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: EN_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.987 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C39, row 'Replogle_K562 / EN_scGPT', column 'Pearson'
Configuration: EN_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.955 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D39, row 'Replogle_K562 / EN_scGPT', column 'Pearson DE'
Configuration: EN_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.376 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E39, row 'Replogle_K562 / EN_scGPT', column 'Pearson Delta'
Configuration: EN_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.472 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F39, row 'Replogle_K562 / EN_scGPT', column 'Pearson Delta DE'
Configuration: EN_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.498 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H39, row 'Replogle_K562 / EN_scGPT', column 'Pearson Delta DE without KOd gene'
Configuration: EN_scGPT (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.489 pearson-delta unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EN_scGPT on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G39, row 'Replogle_K562 / EN_scGPT', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: KNN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, K562 CRISPRi (GEARS processing, Csendes et al. 2025)	0.988 pearson-correlation unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source KNN_go on Replogle_K562 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-k562-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C40, row 'Replogle_K562 / KNN_go', column 'Pearson'

Source checking is not independent reproduction. Release 2026-10-10-7fcc3e48a123.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

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.

14 evidence rows 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
attributes.denominator 272 Context-only references	Benchmarking foundation cell models for post-perturbation RNA-seq prediction Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: BMC Genomics 26:393, published 2025-04-23; PMC12016270 full-text XML Retrieved: 2026-10-09T20:58:48Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.denominator` Source artifact SHA-256: `b59088e4169385c602d0b7a51253d7c1131688666e64e95c06fb54950a514c19` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.denominator 272 Context-only references	Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 12864_2025_11600_MOESM4_ESM.xlsx from the Europe PMC supplementary bundle (hash is of the workbook; the bundle zip is rebuilt per request) Retrieved: 2026-10-09T20:58:56Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.denominator` Source artifact SHA-256: `b5bfcb633921a642de077a39fcb015c6d36bc36a52d9c5e9ceca33be483d3261` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.population 162,751 single cells, single-gene CRISPRi; 734 train, 82 validation and 272 test perturbations (Supplementary Table 1) Context-only references	Benchmarking foundation cell models for post-perturbation RNA-seq prediction Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: BMC Genomics 26:393, published 2025-04-23; PMC12016270 full-text XML Retrieved: 2026-10-09T20:58:48Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `b59088e4169385c602d0b7a51253d7c1131688666e64e95c06fb54950a514c19` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.population 162,751 single cells, single-gene CRISPRi; 734 train, 82 validation and 272 test perturbations (Supplementary Table 1) Context-only references	Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 12864_2025_11600_MOESM4_ESM.xlsx from the Europe PMC supplementary bundle (hash is of the workbook; the bundle zip is rebuilt per request) Retrieved: 2026-10-09T20:58:56Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `b5bfcb633921a642de077a39fcb015c6d36bc36a52d9c5e9ceca33be483d3261` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Context-only references	Benchmarking foundation cell models for post-perturbation RNA-seq prediction Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: BMC Genomics 26:393, published 2025-04-23; PMC12016270 full-text XML Retrieved: 2026-10-09T20:58:48Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `b59088e4169385c602d0b7a51253d7c1131688666e64e95c06fb54950a514c19` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Context-only references	Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 12864_2025_11600_MOESM4_ESM.xlsx from the Europe PMC supplementary bundle (hash is of the workbook; the bundle zip is rebuilt per request) Retrieved: 2026-10-09T20:58:56Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `b5bfcb633921a642de077a39fcb015c6d36bc36a52d9c5e9ceca33be483d3261` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.split Perturbation exclusive: unseen perturbations (or, for Norman, unseen combinations) in the test set Context-only references	Benchmarking foundation cell models for post-perturbation RNA-seq prediction Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: BMC Genomics 26:393, published 2025-04-23; PMC12016270 full-text XML Retrieved: 2026-10-09T20:58:48Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `b59088e4169385c602d0b7a51253d7c1131688666e64e95c06fb54950a514c19` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.split Perturbation exclusive: unseen perturbations (or, for Norman, unseen combinations) in the test set Context-only references	Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 12864_2025_11600_MOESM4_ESM.xlsx from the Europe PMC supplementary bundle (hash is of the workbook; the bundle zip is rebuilt per request) Retrieved: 2026-10-09T20:58:56Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `b5bfcb633921a642de077a39fcb015c6d36bc36a52d9c5e9ceca33be483d3261` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.version cell-gears v0.0.1 processing; GEARS perturbation-exclusive split Context-only references	Benchmarking foundation cell models for post-perturbation RNA-seq prediction Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: BMC Genomics 26:393, published 2025-04-23; PMC12016270 full-text XML Retrieved: 2026-10-09T20:58:48Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `b59088e4169385c602d0b7a51253d7c1131688666e64e95c06fb54950a514c19` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.version cell-gears v0.0.1 processing; GEARS perturbation-exclusive split Context-only references	Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) Original source ↗ Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 12864_2025_11600_MOESM4_ESM.xlsx from the Europe PMC supplementary bundle (hash is of the workbook; the bundle zip is rebuilt per request) Retrieved: 2026-10-09T20:58:56Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `b5bfcb633921a642de077a39fcb015c6d36bc36a52d9c5e9ceca33be483d3261` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Benchmarking foundation cell models for post-perturbation RNA-seq prediction · Original source · BMC Genomics 26:393, published 2025-04-23; PMC12016270 full-text XML
Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Original source · 12864_2025_11600_MOESM4_ESM.xlsx from the Europe PMC supplementary bundle (hash is of the workbook; the bundle zip is rebuilt per request)

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Stable ID: perturbation-response-20261009-data-csendes2025-replogle-k562

areas: cells-tissues
contexts: research
version: cell-gears v0.0.1 processing; GEARS perturbation-exclusive split
population: 162,751 single cells, single-gene CRISPRi; 734 train, 82 validation and 272 test perturbations (Supplementary Table 1)
split: Perturbation exclusive: unseen perturbations (or, for Norman, unseen combinations) in the test set
denominator: 272
source locator: Results 'Benchmarking of post-perturbation RNA-seq prediction methods' paragraph 2; Methods 'Benchmark datasets'; Supplementary Table 1 row 'replogle_k562'

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