Which drug-response programs are visible after accounting for the dataset’s technical structure?
The analysis examined a public HepG2 DIA-MS perturbation dataset to compare each compound with DMSO, cluster continuous proteomic signatures, and prioritize response programs. The report treats mechanism-of-action interpretations as hypotheses rather than confirmed targets.
- Source dataset
- jgmeyer/mississippi on Hugging Face
- Assay
- HepG2 drug-perturbation DIA-MS proteomics
- Controls
- 23 DMSO, 24 DFO, and 155 pooled QC samples
- DE matrix
- 1,052 drug and control samples after one placeholder exclusion
Workflow and methodology-review corrections
The session preserved the distinction between statistical modeling and visualization-only correction, then regenerated downstream rankings after review.
The strongest conclusions concern shared response programs and confounding—not individual drug mechanisms
E2F and G2M programs were repeatedly downregulated across multiple drug-signature clusters.
Eight non-RedMix drugs showed broad, replicate-consistent loss of detected proteins consistent with cytotoxicity or global stress.
Twelve compounds lacked in-batch DMSO controls, preventing their apparent drug effects from being separated from batch or series.
The strongest candidates were predominantly pan-drug stress signals, not validated drug-specific biomarkers.
Limitations materially change what can be claimed
- Batch explained R² = 0.59 of PC1 variance and was the dominant global technical axis.
- The 12 RedMix compounds have no in-batch control, so their differential-abundance, ranking, and mechanism claims are lower-confidence.
- Overall missingness was 10.6%; 758 of 8,630 proteins were missing in more than half of samples, and no alternative-imputation sensitivity analysis was performed.
- Eight drugs showed broad proteome collapse, making targeted pathway interpretations unsafe without viability data.
- Pathway enrichment, biomarkers, and mechanism hypotheses are exploratory and lack external validation by targeted MS, transcriptomics, or viability assays.
Moderate for the QC/batch characterization and recurring cell-cycle-suppression pattern; low-to-moderate for specific mechanisms; low for conclusions involving RedMix-only compounds.
Reproducibility artifacts recorded in the session
The report inventories the result tables, model objects, QC flags, corrected rankings, figures, and scripts used across the analysis and review cycle.
drug_vs_control_DE_results.csvPer-drug limma resultsdrug_perturbation_ranking.csvCorrected FDR-only perturbation rankingdrug_signature_matrix_tstat.csvContinuous response signaturespathway_enrichment_per_cluster.csvExploratory Hallmark enrichmentanalysis_flags.jsonMachine-readable interpretation caveatslimma_fit_objects.rdsFitted statistical model objects