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).

• CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.

  PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 81

  Higher stromal and ESTIMATE scores are associated with favorable prognosis in DLBCL

  dlbcl ici-related degs ffpe estimate consensus differential

• Stromal androgen signaling acts as tumor niches to drive prostatic basal epithelial progenitor-initiated oncogenesis.

  PMID 36323713 · PMC9630272 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  Loss of AR in stromal Gli1-lineage cells diminishes prostate epithelial oncogenesis and tumor development in vivo

  ugm hi-myc prostate hmyctg+ genetically single-cell immunohistochemistry

• High incidence of p53 gene mutation in human ovarian cancer and its association with nuclear accumulation of p53 protein and tumor DNA aneuploidy.

  PMID 1429209 · PMC5918982 · Japanese journal of cancer research : Gann · 1992 · 7 claims · 4 setups

  Full-text index only

  p53 gene mutations occur at high incidence in human ovarian carcinoma, especially common epithelial type

  ovarian pcr-single direct immunohistochemistry

• Community assessment of methods to deconvolve cellular composition from bulk gene expression.

  PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups

  Has reproduction · 63

  Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.

  admixtures cancer tumor bulk bulk admixture crowdsourced

• Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities.

  PMID 32695266 · PMC7352056 · Computational and structural biotechnology journal · 2020 · 8 claims · 8 setups

  Has reproduction · 78

  Meta-analysis of gene expression profiles reveals differentially regulated pathways and comorbidity risk differences between lean and obese PCOS phenotypes

  lutein subcutaneous cumulus skeletal microarray

• Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.

  PMID 35425715 · PMC9004628 · Frontiers in oncology · 2022 · 8 claims · 7 setups

  Has reproduction · 53

  Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)

  crc colorectal crcos crco organoid drug bulk

• A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

  PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity

  coad consensus cibersort mcp-counter

• Identification of a novel 10 immune-related genes signature as a prognostic biomarker panel for gastric cancer.

  PMID 34382341 · PMC8446556 · Cancer medicine · 2021 · 8 claims · 8 setups

  Has reproduction

  A 10-IRG prognostic signature (BMPR1B, GHR, IL11RA, INHBB, NPR3, OBP2A, PTN, R3HDML, TAC1, TPM2) predicts overall survival in gastric cancer.

  gastric tcga-stad overlapping candidate microarray gene rna-seq

• Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.

  PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts

  tcga-brca triple-negative ffpe bulk univariate kaplan-meier

• Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

  PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 80

  WGCNA identified 214 key genes in the blue module most correlated with LUAD

  tcga-luad merged tedc2-associated a549 wgcna differential machine

• Irisin ameliorates obesity and insulin resistance via adipose tissue IL-33 and regulatory T cells.

  PMID 41933175 · PMC13052164 · Nature metabolism · 2026 · 8 claims · 8 setups

  Has reproduction · 48

  Irisin modulates adipose tissue inflammation by increasing IL-33 production and preserving ST2+ regulatory T cells in white adipose tissues, thereby improving obesity and glucose intolerance.

  4-week-old hfd-fed bat iwat aav8-mediated body intraperitoneal

• Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.

  PMID 39775580 · PMC11684664 · PloS one · 2024 · 7 claims · 8 setups

  Full-text index only

  MitoDEGs in MI are mainly involved in mitochondrial function and ATP synthesis pathways

  left mus combined heart microarray weighted bulk

• Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.

  PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 91

  CP and PDAC share a co-expression gene network identifiable via WGCNA on independent GEO datasets

  pancreatic pdac shared overlapping wgcna geo2r cluego

• 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

• 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

• LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

  PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 49

  LRP1 is a hub gene with the highest diagnostic performance among 30 candidate hub genes identified by machine learning

  ectopic geo gse5108 training microarray wgcna machine

• Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

  PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 66

  At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

  subcutaneous sat rhesus bulk gsea xcell

• 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

• comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.

  PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups

  Has reproduction · 65

  comBO is a single iPSC-derived organoid differentiation that generates osteolineage, vascular, lymphoid, and myeloid compartments together

  hipsc-derived combo combo-derived healthy-donor flow single-cell confocal