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).

• Mining novel biomarkers for prognosis of gastric cancer with serum proteomics.

  PMID 19740432 · PMC2753349 · Journal of experimental & clinical cancer research : CR · 2009 · 7 claims · 4 setups

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  A 5-peak prognosis pattern (4474, 4542, 6443/6643, 4988, 6685 Da) predicts poor vs good prognosis in GC with higher sensitivity/specificity than CEA and TNM stage

  serum seldi seldi-tof-ms chemiluminescence bioinformatic

• 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

• Research and experimental verification on the mechanisms of cellular senescence in triple-negative breast cancer.

  PMID 38435998 · PMC10909353 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 67

  TNBC can be classified into three molecular subtypes (clusters 1, 2, 3) based on cellular senescence-related pathway scores

  tnbc tcga tcga-tnbc mda-mb-468 scrna-seq ssgsea unsupervised

• 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

• Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.

  PMID 41501725 · PMC12870398 · Cancer cell international · 2026 · 7 claims · 8 setups

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  MEST is a key oncogenic GLD-related gene and a novel therapeutic target in glioma, identified via a machine learning feature selection framework

  bulk single-cell tcga glioma gsva aucell machine

• Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.

  PMID 41792569 · PMC13079247 · Discover oncology · 2026 · 8 claims · 8 setups

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  SEMA3 family expression defines two molecular subtypes (A and B) of PDAC with significantly different overall survival

  pdac bulk ssgsea differential

• Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

  PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups

  Has reproduction · 77

  457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis

  tcga-oc tcga-oc-gse26193 ov_gse154600 iose-80 bulk univariate copy

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.

  PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups

  Has reproduction · 48

  Breast cancer samples can be classified into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on Z-score median of Set1 (writer+reader) and Set2 (eraser) gene expression

  breast tcga-brca gse25066 bioinformatics survival alternative

• Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.

  PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 69

  66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs

  melanoma tcga-skcm prjeb23709 microarray wgcna differential consensus

• Application of proteomics in the study of tumor metastasis.

  PMID 15862116 · PMC5172469 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 8 setups

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  Cell function is directly regulated through proteins, not genes or mRNA, so metastasis-related gene findings need protein-level validation via proteomics.

  young metastatic hepatocellular lines microarray 2de cdna

• Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

  PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups

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  SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.

  serum seldi dlbcl pooled seldi-tof-ms proteinchip decision

• Divide and conquer: progress in the molecular stratification of cancer.

  PMID 19718393 · PMC2730607 · Yonsei medical journal · 2009 · 8 claims · 8 setups

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  Cancers exhibit significant clinical, histopathologic, and molecular heterogeneity between individual patients

  breast nsclc colon early-stage immunohistochemistry gene comparative

• 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

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  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

• Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.

  PMID 41566530 · PMC12906006 · Genome biology · 2026 · 7 claims · 6 setups

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  Pseudobulk and real bulk RNA-seq deconvolution performance differ significantly, and method ranking consistency is lower between pseudobulk and real bulk than within either data type alone

  breast real colon tcga paired pseudobulk bulk

• Integrative single-cell analysis uncovers distinct tumour microenvironment ecotypes and immune evasion across skin cancers.

  PMID 41636115 · PMC12869349 · Clinical and translational medicine · 2026 · 7 claims · 8 setups

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  A malignant NARS2+NDUFC2+ melanoma cell subpopulation with reduced MHC-I expression is enriched in advanced-stage tumours and associated with worse survival and immunotherapy response.

  skin prognosis melanoma macrophage single-cell bulk immunofluorescence

• UBE2M as a bridge spanning neddylation and cell cycle regulation in colorectal adenocarcinoma.

  PMID 41680469 · PMC12993059 · Experimental & molecular medicine · 2026 · 8 claims · 8 setups

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  Neddylation is associated with G2M phase progression in CRC

  crc paired hek293t cell-free single-cell bulk immunohistochemistry

• scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

  PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

  Has reproduction · 62

  scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

  panglaodb cancer geo gse137829 single-cell bulk

• Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

  PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 71

  Mitophagy-related genes associated with immune infiltration have diagnostic/prognostic significance in ALS

  blood als microarray spearman univariate

• 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