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).
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Getting knit-PI3Ky: PIK3CA mutation status to direct multimodality therapy?
PMID 19903790 · PMC3400141 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 1 setups
PIK3CA mutations are associated with local disease recurrence in rectal cancer patients
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WAF1/CIP1 structural abnormalities do not contribute to cell cycle deregulation in ovarian cancer.
PMID 8645586 · PMC2074480 · British journal of cancer · 1996 · 7 claims · 5 setups
No WAF1/CIP1 coding mutations were found in any of 36 ovarian carcinomas sequenced, including tumors with LOH on 6p and those lacking p53 mutations
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Ovarian cancer has frequent loss of heterozygosity at chromosome 12p12.3-13.1 (region of TEL and Kip1 loci) and chromosome 12q23-ter: evidence for two new tumour-suppressor genes.
PMID 9155043 · PMC2228239 · British journal of cancer · 1997 · 8 claims · 4 setups
Two commonly deleted regions on chromosome 12 were identified in ovarian cancer: 12p12.3-13.1 (6/23 samples) and 12q23-ter (7/23 samples)
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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
A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease
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Has reproduction · 88
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
APOBEC family genes are differentially expressed across cancer types and tissues, with APOBEC3B being the most aberrantly upregulated gene in most cancers including LUAD
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Has reproduction · 71
Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.
PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups
Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.
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Dicer, Drosha, and outcomes in patients with ovarian cancer.
PMID 19092150 · PMC2710981 · The New England journal of medicine · 2008 · 8 claims · 6 setups
Dicer and Drosha mRNA levels correlate with corresponding protein levels and are decreased in 60% and 51% of ovarian-cancer specimens, respectively
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Next-generation sequencing.
PMID 20030863 · PMC2797692 · Breast cancer research : BCR · 2009 · 8 claims · 7 setups
Massively parallel sequencing can simultaneously capture base-pair mutations, copy number aberrations and somatic rearrangements of a cancer genome in a single experiment
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Has reproduction · 35
Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.
PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 8 setups
ZBTB38 mRNA expression is significantly lower in prostate cancer than in normal/benign prostate tissue, and further reduced in metastatic versus localised tumours
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A critical reassessment of the role of mitochondria in tumorigenesis.
PMID 16187796 · PMC1240051 · PLoS medicine · 2005 · 8 claims · 8 setups
A significant number of published medical mtDNA cancer studies are based on obviously flawed sequencing results.
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Prioritization of candidate cancer genes--an aid to oncogenomic studies.
PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups
Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes
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Sequence and structure signatures of cancer mutation hotspots in protein kinases.
PMID 19834613 · PMC2759519 · PloS one · 2009 · 8 claims · 6 setups
Developed CKMD (Composite Kinase Mutation Database), an integrated bioinformatics resource mapping genetic variation in protein kinase genes to sequence, structural, and functional data
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Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.
PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups
Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database
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Has reproduction · 78
Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.
PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups
KCTD16, CD3D, and GSDMB were identified as prognostic succinylation-related genes in BLCA
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Has reproduction · 53
Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.
PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 7 claims · 5 setups
A computational framework integrating independently measured CNV (DNA sequencing) and single-cell RNA-seq from the same patients identifies recurrent concordant copy number gain and gene upregulation (CNG-UP) events and functional modules at the single-cell level.