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).

• Comparison of multidimensional shotgun technologies targeting tissue proteomics.

  PMID 19960471 · PMC3465977 · Electrophoresis · 2009 · 6 claims · 4 setups

  Full-text index only

  CITP-based multidimensional separation achieves superior overall proteome performance (more total peptide, distinct peptide, and distinct protein identifications) than SCX/MuDPIT under matched conditions

  glioblastoma peptide shotgun spectral database

• 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

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

  PMID 39074091 · PMC11285958 · PloS one · 2024 · 7 claims · 8 setups

  Full-text index only

  JAG, DLL, and NOTCH family gene/protein expression varies diversely across 15 cancer types relative to normal tissue, sometimes discordant between mRNA and protein levels.

  tumor degs cancer jag bulk proteomics gene

• An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

  PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 88

  SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

  kidney tubuloids immunodeficient tub rt-qpcr western histology

• Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

  PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 83

  CHCT, a two-tier hierarchical classification tool built from methylation data, accurately classifies primary cancer type across 30 cancer types.

  tumor clinical methylation clustered methylation unsupervised anova

• Evaluation of BRCA1 and BRCA2 mutations and risk-prediction models in a typical Asian country (Malaysia) with a relatively low incidence of breast cancer.

  PMID 18627636 · PMC2575532 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

  Full-text index only

  27 deleterious BRCA1/BRCA2 mutations were detected in 28 breast cancer patients (14 in BRCA1, 13 in BRCA2) among 187 tested

  blood-derived family brca1 direct multiplex boadicea

• Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.

  PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 7 claims · 6 setups

  Has reproduction · 65

  UC patient-derived organoids histologically phenocopy primary UC tissue, showing disorganized stratified epithelium, reduced mucin/goblet cells, and non-uniform proliferation compared to non-IBD organoids

  patient-derived h3k27ac rna-seq chip-seq histology

• Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma.

  PMID 33634984 · PMC7882098 · Clinical and translational medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  JMJD6 is identified as a potent epigenetic vulnerability/fitness gene in RCC by integrating GeCK CRISPR screening data with TCGA-KIRC epigenetic regulator survival analysis

  pan-cancer tcga-kirc rcc balb crispr rna-seq mtt

• The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

  PMID 15743497 · PMC1064126 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

  Full-text index only

  The AR CAG repeat polymorphism does not modify breast cancer risk in BRCA1 mutation carriers

  peripheral brca1 same simulated fluorescent cox weighted

• ATM variants 7271T>G and IVS10-6T>G among women with unilateral and bilateral breast cancer.

  PMID 14562025 · PMC2394328 · British journal of cancer · 2003 · 8 claims · 4 setups

  Full-text index only

  Women with bilateral breast cancer show greater genetic predisposition (higher family history prevalence) than women with unilateral breast cancer

  blood-derived blood random dhplc microsatellite duplicate

• Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

  PMID 18701470 · PMC2562548 · Cancer research · 2008 · 7 claims · 4 setups

  Full-text index only

  Carriers of common ATM variants (>=1% frequency) have a statistically significant reduction in risk of contralateral breast cancer (CBC)

  peripheral wecare atm mutation case-control variant

• Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

  PMID 41963303 · PMC13181133 · Cell death & disease · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  The integrated stress response (ISR) induces CRC cell plasticity, subclonal diversity, and tumor progression in stress-surviving cells

  ht29-derived ht29 nod rna-seq faire-qpcr chip-seq

• Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

  PMID 36232369 · PMC9569723 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 87

  Common genes shared across five cancer types differ from those found in nonmalignant tissue-resident T-cells for each subset (CD4-T, CD8-T, Treg)

  breast lung colorectal melanoma single-cell gene reactome

• BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

  PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

  Full-text index only

  BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

  french-canadian families brca1-positive same targeted full-length multiplex

• CHEK2 variants associate with hereditary prostate cancer.

  PMID 14612911 · PMC2394451 · British journal of cancer · 2003 · 8 claims · 6 setups

  Full-text index only

  CHEK2 1100delC frameshift mutation is significantly more frequent in Finnish HPC patients than in population controls

  index hpc unselected affected sscp sequencing minisequencing

• 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

• A common missense variant in BRCA2 predisposes to early onset breast cancer.

  PMID 16280055 · PMC1410744 · Breast cancer research : BCR · 2005 · 7 claims · 4 setups

  Full-text index only

  BRCA2 C5972T homozygosity (TT genotype) is rare but confers a roughly five-fold increased risk of breast cancer.

  peripheral blood-derived blood case-control genotyping sequencing mutation

• Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

  PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

  lncap lncap-derived r1881-treated massively blast blat

• Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

  PMID 18560578 · PMC2409963 · PloS one · 2008 · 8 claims · 6 setups

  Full-text index only

  Ovarian cancer cells exhibit extensive shedding of extra-cellular domains from cell surface proteins into the extracellular milieu.

  ovcar3 analysis lc-ms cell-surface silac