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).

• Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.

  PMID 39682743 · PMC11640164 · Cells · 2024 · 8 claims · 5 setups

  Has reproduction

  Estimated T-cell infiltration differs significantly across melanoma, bladder, ovarian, and pancreatic cancers, tracking known immunogenic potential.

  tumor melanoma orien bulk gene kaplan-meier

• Machine learning developed an intratumor heterogeneity signature for predicting clinical outcome and immunotherapy benefit in bladder cancer.

  PMID 39100839 · PMC11291408 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 40

  An integrative machine learning procedure (10 methods, 101 algorithm combinations) identified an Enet (alpha=0.2)-based intratumor heterogeneity-related signature (IRS) with the highest average C-index (0.69) across TCGA and GEO cohorts

  bladder skin bulk integrative immune

• Nested co-expression network analysis identifies compact gene clusters in a black box.

  PMID 41934621 · PMC13163169 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

  Full-text index only

  Nested-WGCNA is a two-stage algorithm that identifies coarse-grained modules (CGMs) and then, via core decomposition and renormalization, derives fine-grained modules (FGMs) representing subprocesses within each CGM

  tcga-blca tcga-kirc tcga-luad imvigor210 bulk scrna-seq

• 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

• Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.

  PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 71

  IRG expression pattern clusters LUAD patients into groups with significantly different survival outcomes and immune cell infiltration

  luad normal bulk wgcna tumor

• Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

  PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 8 claims · 8 setups

  Has reproduction

  A three-class WSI cluster (C0/C1/C2) derived via mini batch K-means clustering on Inception V3-extracted image features is significantly associated with overall survival and is an independent prognostic predictor in BLCA.

  tcga-blca gse32894 deep transfer machine

• Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

  PMID 41488744 · PMC12764181 · International journal of genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  Epithelial and endothelial cells show the highest anoikis-enriched scores among LUAD TME cell types, with AT2-like Epi being the most anoikis-related epithelial subpopulation.

  luad pan-cancer tumor scrna-seq spatial bulk

• 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

• PRDM1+ Malignant Cells Mediate an Immunosuppressive Landscape and Resistance to Neoadjuvant Chemoradiotherapy and Immunotherapy in Esophageal Squamous Cell Carcinoma.

  PMID 41556358 · PMC13042517 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  A PRDM1+ malignant epithelial cell subcluster (Epi_C4) is enriched in NMPR patients and is associated with nICRT treatment resistance

  locally escc pd-1 kyse-30 single-arm scrna-seq bulk

• Single-cell mitophagy signature-based artificial intelligence model enhances prediction of prognosis and immunotherapy response in non-small-cell lung cancer.

  PMID 41851738 · PMC13112628 · Respiratory research · 2026 · 8 claims · 8 setups

  Full-text index only

  A six-gene MRG panel (FOS, CANX, EIF4G1, CALCOCO2, HSP90AB1, PRKAR1A) was selected via LASSO regression as prognostic markers in NSCLC.

  nsclc tcga external immunotherapy single-cell bulk transcriptomic

• Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.

  PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 51

  A higher immune infiltration-related risk score (IRS) indicates worse prognosis and lower sensitivity to immunotherapy in breast cancer patients

  tcga candidate cancer univariate weighted lasso

• Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

  PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

  Full-text index only

  RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

  tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic

• Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

  PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

  Full-text index only

  HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

  tcga-luad best brain advanced bulk kaplan-meier pearson

• 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

• Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

  PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Full-text index only

  25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

  kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide

• Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

  PMID 41613532 · PMC12847018 · Frontiers in oncology · 2025 · 7 claims · 8 setups

  Full-text index only

  Tumor cells show significantly upregulated nucleotide metabolic activity, allowing stratification into NUhighepi and NUlowepi subgroups

  tcga-brca breast scrna-seq epithelial ssgsea single-cell cell-cell

• Computational analysis of multi-omics data reveals CXCL10(+) DC-Treg interaction drives immunosuppressive microenvironment in AFP-positive hepatocellular carcinoma.

  PMID 41854876 · PMC13038760 · Cellular and molecular life sciences : CMLS · 2026 · 8 claims · 8 setups

  Full-text index only

  STMN1+ and AFP+ malignant cell subsets are enriched in AFP-positive HCC, while CYP3A4+ malignant cells are enriched in AFP-negative HCC

  hcc tcga-lihc scrna-seq immunotherapy single-cell bulk spatial

• 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

• Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

  PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

  Has reproduction · 50

  Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

  hnscc tcga-hnscc caf fibroblast single-cell bulk spatial

• Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

  PMID 41971443 · PMC13061668 · Frontiers in oncology · 2026 · 7 claims · 8 setups

  Full-text index only

  HERV expression differs between primary and metastatic cutaneous melanoma

  tcga-skcm metastatic normal selected bulk consensus orf