Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

  PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

  epithelial-based tcga gdsc muscle-invasive differential co-expression signature

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Radiogenomics predicts immune microenvironment heterogeneity and response to combination immunotherapy in hepatocellular carcinoma.

  PMID 41555384 · PMC12895822 · Journal of translational medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  A parsimonious 2-gene immune-related signature (IRS = 0.425×KPNA2 + 0.302×SMG5) is significantly associated with immune heterogeneity and response to ICI plus anti-angiogenic combination therapy in HCC

  hcc gse202642 paired hcc-derived bulk single-cell immunohistochemistry

• Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

  PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

  Full-text index only

  Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

  luad demtdmrgs gse131907 wgcna kegg univariate

• Comprehensive analysis of the causal risk factor from hypertension associated with prognosis and therapeutic response in renal cell carcinoma by multi-omics analysis and validation.

  PMID 41680825 · PMC12998095 · Biology direct · 2026 · 8 claims · 8 setups

  Full-text index only

  A 48-gene cross-species hypertension (HTN) gene module identified from human and SHR rat scRNA-seq can classify ccRCC patients into two molecular subgroups with distinct survival and targeted therapy response

  aortic spontaneously tcga icgc single-cell bulk summary-data-based

• Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

  PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

  Has reproduction · 71

  AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

  aml hovon cancer tcga bulk consensus machine

• Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

  PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.

  fresh tcga gbm bulk rna-seq consensus

• Acquired resistance to KRAS G12C small-molecule inhibitors via genetic/nongenetic mechanisms in lung cancer.

  PMID 37831779 · PMC10575592 · Science advances · 2023 · 8 claims · 8 setups

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  Acquired resistance to sotorasib in isogenic cells correlates with increased ITGB4 expression

  h358 h23 sw1573 proliferation spheroid immunoblot

• Small molecule inhibition rescues the skeletal dysplasia phenotype of Trpv4 mutant mice.

  PMID 41574606 · PMC12892883 · JCI insight · 2026 · 8 claims · 8 setups

  Full-text index only

  Chondrocyte-specific (Col2a1-Cre-driven) expression of the p.R594H Trpv4 mutation reproduces the human TRPV4 skeletal dysplasia phenotype in mice, including short stature, long bone and craniofacial abnormalities, and vertebral defects.

  col2a1-cre proximal growth cervical radiography histology rnascope

• Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

  PMID 41772327 · PMC12979290 · Clinical and experimental medicine · 2026 · 7 claims · 8 setups

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  A 6-LYMRG risk model (ANGPT1, HGF, MAPK8, PCNA, TBL1XR1, TLR4) is the optimal prognostic signature for AML

  gse142698 tcga-laml tcga-laml1 gse116256 differential univariate kaplan-meier

• Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity.

  PMID 41842971 · PMC13132380 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  PRC2i/EZH2i alone or combined with AR inhibitors induce diverse cell state programs (CSPs) that increase tumor cell invasion, metastasis, and drug resistance despite only modest suppression of tumor growth.

  lncap pca pdx clinical viability tumor ic50

• Identification of a prognostic signature based on ammonia metabolism-related genes in clear cell renal cell carcinoma: an integrated analysis of bulk and single-cell transcriptomics.

  PMID 42112332 · PMC13149443 · Frontiers in immunology · 2026 · 7 claims · 8 setups

  Full-text index only

  A 6-gene (RGS20, ADA, AICDA, SLC12A5, RUFY4, CDK5RAP3) prognostic risk model was constructed for ccRCC from ammonia death-related genes

  tcga-kirc gse159115 clinical bulk univariate gsea

• A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

  PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups

  Has reproduction · 85

  Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution

  tcga-hnscc gse41613 gse103322 prjeb23709 bulk single-cell immunohistochemistry

• FOXM1 inhibitor, RCM‑1, enhances venetoclax mediated apoptosis through downregulation of ATP2B4 in rhabdomyosarcoma.

  PMID 41789627 · PMC12987556 · International journal of oncology · 2026 · 8 claims · 8 setups

  Has reproduction · 10

  Combination therapy of RCM-1 and venetoclax inhibits RMS tumor growth more efficiently than venetoclax alone in an animal model by decreasing proliferation and inducing apoptosis

  rms injected muscle cck-8 caspase subcutaneous

• Pharmacogenomics of gemcitabine: can genetic studies lead to tailor-made therapy?

  PMID 17595663 · PMC2360307 · British journal of cancer · 2007 · 8 claims · 14 setups

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  A SNP in the cytidine deaminase (CDA) gene (208G>A, haplotype *3) decreases gemcitabine clearance, increases Cmax/AUC, and increases neutropenia risk when gemcitabine is combined with platinum drugs or 5-FU

  japanese paraffin-embedded tumour recombinant prospective immunohistochemistry pcr

• Midostaurin response in AML is shaped by a progenitor-like cell state selectively targeted by SMAC mimetics.

  PMID 41813823 · PMC12996285 · NPJ precision oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  A progenitor-like CD38+CD45RA+ leukemic cell population is associated with midostaurin resistance

  bm-mncs flt3mut drug ms-based rna-sequencing

• Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

  PMID 41681864 · PMC12897147 · Cancers · 2026 · 8 claims · 8 setups

  Full-text index only

  A 4-ARG prognostic model (NBEA, CLOCK, NLRX1, MAGEA3) built via stepwise multivariate Cox regression stratifies ESCC patients into high- and low-risk groups with significantly different survival.

  escc gse53625 gse160269 imvigor210 microarray univariate single-cell

• RUVBL1 and RUVBL2 are druggable MYC effector regulators in neuroblastoma cells.

  PMID 41940329 · PMC13049659 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  RUVBL1 and RUVBL2 target gene sets are significantly depleted in MYCN-driven NB mouse tumors treated with ATR inhibitors (elimusertib, ceralasertib)

  th-mycn neuroblastoma clb-bar clb-ga rna-seq gene western

• Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.

  PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments

  tcga-blca famc1-3 differentially gse32894 bulk consensus gene

• Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

  PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups

  Has reproduction · 59

  NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering

  tcga-nsclc geo bulk microarray unsupervised