Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CPA	Protocol: GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE Dataset subset: Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)	0.354 ± 0.049 mse squared_expression_units_unreported · lower Uncertainty: type: unreported; reported spread: 0.049; note: Printed ± spread; SD/SE/CI type not established by inspected table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source CPA on GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted. Aggregation: Not reported GEARS primary supplement, Table6 · Supplementary Table6, printed p34 / PDF p35, row CPA, column MSE
Configuration: CPA	Protocol: GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE Dataset subset: Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)	0.440 ± 0.036 pearson_delta_expression correlation · higher Uncertainty: type: unreported; reported spread: 0.036; note: Printed ± spread; SD/SE/CI type not established by inspected table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source CPA on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted. Aggregation: Not reported GEARS primary supplement, Table6 · Supplementary Table6, printed p34 / PDF p35, row CPA, column Pearson DE
Configuration: CPA + KG	Protocol: GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE Dataset subset: Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)	0.333 ± 0.046 mse squared_expression_units_unreported · lower Uncertainty: type: unreported; reported spread: 0.046; note: Printed ± spread; SD/SE/CI type not established by inspected table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source CPA + KG on GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted. Aggregation: Not reported GEARS primary supplement, Table6 · Supplementary Table6, printed p34 / PDF p35, row CPA + KG, column MSE
Configuration: CPA + KG	Protocol: GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE Dataset subset: Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)	0.504 ± 0.029 pearson_delta_expression correlation · higher Uncertainty: type: unreported; reported spread: 0.029; note: Printed ± spread; SD/SE/CI type not established by inspected table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source CPA + KG on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted. Aggregation: Not reported GEARS primary supplement, Table6 · Supplementary Table6, printed p34 / PDF p35, row CPA + KG, column Pearson DE
Configuration: GEARS	Protocol: GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE Dataset subset: Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)	0.216 ± 0.053 mse squared_expression_units_unreported · lower Uncertainty: type: unreported; reported spread: 0.053; note: Printed ± spread; SD/SE/CI type not established by inspected table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source GEARS on GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted. Aggregation: Not reported GEARS primary supplement, Table6 · Supplementary Table6, printed p34 / PDF p35, row GEARS, column MSE
Configuration: GEARS	Protocol: GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE Dataset subset: Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)	0.556 ± 0.030 pearson_delta_expression correlation · higher Uncertainty: type: unreported; reported spread: 0.030; note: Printed ± spread; SD/SE/CI type not established by inspected table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source GEARS on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted. Aggregation: Not reported GEARS primary supplement, Table6 · Supplementary Table6, printed p34 / PDF p35, row GEARS, column Pearson DE
Configuration: No Perturb	Protocol: GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE Dataset subset: Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)	0.551 ± 0.029 mse squared_expression_units_unreported · lower Uncertainty: type: unreported; reported spread: 0.029; note: Printed ± spread; SD/SE/CI type not established by inspected table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source No Perturb on GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted. Aggregation: Not reported GEARS primary supplement, Table6 · Supplementary Table6, printed p34 / PDF p35, row No Perturb, column MSE
Configuration: No Perturb	Protocol: GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE Dataset subset: Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)	0.004 ± 0.006 pearson_delta_expression correlation · higher Uncertainty: type: unreported; reported spread: 0.006; note: Printed ± spread; SD/SE/CI type not established by inspected table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source No Perturb on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted. Aggregation: Not reported GEARS primary supplement, Table6 · Supplementary Table6, printed p34 / PDF p35, row No Perturb, column Pearson DE

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Property and statement	Original source and location	Review and provenance
description Dataset subset reported in GEARS primary supplement, Table6. Exact split manifest remains unextracted; source-table identity is retained. Context-only references	GEARS primary supplement, Table6 Original source ↗ No field-specific location recorded Version: 10.1038/s41587-023-01905-6 publisher supplement Retrieved: 2026-09-23T11:36:52.243763+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `1daaeb10f072577a3e420a796cd7e29e88ea9462639de7332ae91b2fe86b3b24` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
name Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split) Context-only references	GEARS primary supplement, Table6 Original source ↗ No field-specific location recorded Version: 10.1038/s41587-023-01905-6 publisher supplement Retrieved: 2026-09-23T11:36:52.243763+00:00	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `1daaeb10f072577a3e420a796cd7e29e88ea9462639de7332ae91b2fe86b3b24` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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GEARS primary supplement, Table6 · Original source · 10.1038/s41587-023-01905-6 publisher supplement

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Stable ID: gears-2023-supp-table6-dataset-norman-et-al-2019-perturbation-data-used-in-gears-supplementary-table6

areas: cells-spatial-multiomics
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