Configuration

EN_go (Csendes et al. 2025)

EN regression with go features of the perturbed gene.

Overview

EN regression with go features of the perturbed gene.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

4 evaluations · 24 results. Different protocols are not a single leaderboard.

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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: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.992 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 Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C6, row 'Adamson / EN_go', column 'Pearson'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.972 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 Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D6, row 'Adamson / EN_go', column 'Pearson DE'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.711 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 Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E6, row 'Adamson / EN_go', column 'Pearson Delta'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.751 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 Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F6, row 'Adamson / EN_go', column 'Pearson Delta DE'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.805 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 Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H6, row 'Adamson / EN_go', column 'Pearson Delta DE without KOd gene'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Adamson et al. 2016 Perturb-seq, K562 CRISPRi single perturbations (GEARS processing, Csendes et al. 2025)	0.753 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 Adamson (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-adamson-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G6, row 'Adamson / EN_go', column 'Pearson Delta DE (based on Wilcoxon)'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.986 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 Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C21, row 'Norman / EN_go', column 'Pearson'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.917 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 Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D21, row 'Norman / EN_go', column 'Pearson DE'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.535 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 Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E21, row 'Norman / EN_go', column 'Pearson Delta'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.62 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 Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F21, row 'Norman / EN_go', column 'Pearson Delta DE'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.636 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 Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H21, row 'Norman / EN_go', column 'Pearson Delta DE without KOd gene'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Norman et al. 2019 Perturb-seq, K562 CRISPRa single and double perturbations (GEARS processing, Csendes et al. 2025)	0.619 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 Norman (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-norman-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G21, row 'Norman / EN_go', column 'Pearson Delta DE (based on Wilcoxon)'
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_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi (GEARS processing, Csendes et al. 2025)	0.978 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_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell C51, row 'Replogle_RPE1 / EN_go', column 'Pearson'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi (GEARS processing, Csendes et al. 2025)	0.919 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_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell D51, row 'Replogle_RPE1 / EN_go', column 'Pearson DE'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi (GEARS processing, Csendes et al. 2025)	0.638 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_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell E51, row 'Replogle_RPE1 / EN_go', column 'Pearson Delta'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi (GEARS processing, Csendes et al. 2025)	0.669 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_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell F51, row 'Replogle_RPE1 / EN_go', column 'Pearson Delta DE'
Configuration: EN_go (Csendes et al. 2025)	Protocol: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi (GEARS processing, Csendes et al. 2025)	0.673 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_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell H51, row 'Replogle_RPE1 / 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, RPE1 CRISPRi: unseen-perturbation expression prediction (Csendes et al. 2025 Supplementary Table 2) Dataset: Replogle et al. 2022 genome-wide Perturb-seq subset, RPE1 CRISPRi (GEARS processing, Csendes et al. 2025)	0.74 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_RPE1 (Csendes et al. 2025) perturbation-response-20261009-protocol-csendes2025-replogle-rpe1-pex Aggregation: Not reported Csendes et al. 2025, Supplementary Material 4 (Supplementary Tables 1-3) · Supplementary Table 2, cell G51, row 'Replogle_RPE1 / EN_go', column 'Pearson Delta DE (based on Wilcoxon)'

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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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Technical metadata and extraction receipts

Stable ID: perturbation-response-20261009-config-csendes2025-en-go

areas: cells-tissues
contexts: research
method types: conventional_pipeline
reported name: EN_go
source locator: Supplementary Table 2 column 'model'; Methods 'Foundation models' and 'Baseline models'
foundation model eligible: false
parameters: Features: Gene Ontology term matrix (decoupler) reduced to 256 principal components of the perturbed gene (summed for combinations); target: pseudo-bulk expression; l1_ratio tuned on the validation set
version: scikit-learn 1.5.2

Related records

configuration of: Elastic net regression on perturbed-gene features
system: EN_go on Adamson (Csendes et al. 2025)
system: EN_go on Norman (Csendes et al. 2025)
system: EN_go on Replogle_K562 (Csendes et al. 2025)
system: EN_go on Replogle_RPE1 (Csendes et al. 2025)

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