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).

• 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

• Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

  PMID 35143511 · PMC8830616 · PloS one · 2022 · 8 claims · 6 setups

  Has reproduction · 48

  A Hybrid signature combining the NPI with 14 SIS-selected genes was constructed from METABRIC training data

  metabric gse96058 test gene sure cox

• YAP1 Dysfunction Promotes Molecular Properties Linked to Breast Cancer Susceptibility.

  PMID 41431390 · PMC13040214 · Cancer prevention research (Philadelphia, Pa.) · 2026 · 7 claims · 8 setups

  Full-text index only

  YAP1 nuclear localization and mRNA expression significantly increase in luminal epithelial cells (LEp) with increased age and with genetic risk for breast cancer (e.g., BRCA1/2 mutation carriers)

  breast hmec post-stasis 184d-p16sh ihc bulk odds

• A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.

  PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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  A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease

  duke nci-60 mayo spanish gene cdna igvh

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups

  Has reproduction · 66

  Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level

  prostate bulk weighted reverse

• Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

  PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups

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  DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)

  breast sars serum tumour microarray custom mass

• A taxonomy of epithelial human cancer and their metastases.

  PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

  epithelial tumor metastatic breast microarray gene fisher

• Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

  PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 88

  APOBEC family genes are differentially expressed across cancer types and tissues, with APOBEC3B being the most aberrantly upregulated gene in most cancers including LUAD

  tcga tcga-luad beas-2b rna-seq somatic gene

• AGPAT3 reshapes tumor cell vulnerability to IFNγ-mediated ferroptosis and enhances immunotherapy efficacy through lipid remodeling.

  PMID 41807033 · PMC12983827 · Journal for immunotherapy of cancer · 2026 · 8 claims · 8 setups

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  A ferroptosis-driver gene signature (FD.sig) and machine learning model (FD.model) can predict ICI response

  pan-cancer tcga a375 machine single-cell bulk

• 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

• Comparison of prognostic gene expression signatures for breast cancer.

  PMID 18717985 · PMC2533026 · BMC genomics · 2008 · 8 claims · 5 setups

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  The three prognostic signatures (70-gene, 76-gene, GGI) show similar prognostic performance for predicting DMFS despite differing gene identity and development approach

  tbagd tbvdx gene clinical survival

• Human CRAMP1 specifically promotes the expression of histone H1 genes.

  PMID 41663757 · PMC12979687 · EMBO reports · 2026 · 8 claims · 8 setups

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  CRAMP1 is a selective regulator of histone H1 gene expression that does not significantly affect core histone gene expression

  cancer hek293t rpe1 genome-wide immunoprecipitation-mass western

• Microarray analysis: genome-scale hypothesis scanning.

  PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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  Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

  drosophila yeast diffuse breast microarray integrated gene

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

  Full-text index only

  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental

• Helicobacter pylori-linked gene CFAP73 rewires epithelial programs and shapes the gastric cancer microenvironment.

  PMID 41934579 · PMC13199538 · Discover oncology · 2026 · 8 claims · 8 setups

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  CFAP73 is progressively downregulated during HP infection and is the top-ranked predictor among nine HP-suppressed genes associated with favorable gastric cancer survival

  gastric tcga-stad tcga t-cell–tumor jonckheere-terpstra survival random

• Advances in breast cancer: pathways to personalized medicine.

  PMID 19088015 · PMC4535810 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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  Germline BRCA1/BRCA2 mutations are strong predictors of breast and ovarian cancer, conferring a 40-80% lifetime risk of breast cancer

  population-based women breast high-risk germline genome-wide microarray

• A Plastic EMP1+ to LGR5+ Cell State Conversion as a Bypass to KRASG12D Pharmacologic Inhibition in Metastatic Colorectal Cancer.

  PMID 41128661 · PMC12877754 · Cancer discovery · 2026 · 8 claims · 8 setups

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  RMC-9945 exerts durable antitumor activity in early-stage liver metastasis but has diminished therapeutic effect in advanced metastatic disease

  aktp colorectal drug single-cell rnascope

• Discovery and Evaluation of Biomarkers for Triple-Negative Breast Cancer Subtypes Uncovers Patient Stratification and Targeted Therapeutic Strategies.

  PMID 41671401 · PMC13176827 · Cancer research · 2026 · 7 claims · 8 setups

  Full-text index only

  A set of basal identity genes (SMA/ACTA2, TAGLN, TPM2) defined by scRNA-seq analysis enables subclassification of TNBC into a subgroup termed true basal TNBC (tB-TNBC)

  healthy ffpe tcga i-spy2 scrna-seq immunohistochemistry bulk

• CCL3+ Neutrophil Signature Predicts Response to Neoadjuvant Toripalimab plus Chemotherapy in Patients with Hypopharyngeal Squamous Cell Carcinoma: A Phase II Trial.

  PMID 41817286 · PMC13223550 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2026 · 7 claims · 8 setups

  Full-text index only

  A proinflammatory, CCL3-high neutrophil subset (Neu_CCL3) is significantly enriched in the pretreatment tumor microenvironment of patients who respond to nCIT.

  pretreatment microarray cohorts moc1 single-cell bulk immunohistochemistry

• HCCaging: a liver physiological aging-related biomarker for hepatocellular carcinoma diagnosis based on transcriptome data.

  PMID 41942446 · PMC13230847 · npj aging · 2026 · 8 claims · 8 setups

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  A 16-gene HCCaging signature was derived via GSVA from genes overlapping age-associated upregulated genes in TCGA, scRNA-seq, and ICGC datasets

  tcga-lihc hcc icgc six bulk single-cell gsva-based