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).

• Performance of mitochondrial DNA mutations detecting early stage cancer.

  PMID 18834532 · PMC2572633 · BMC cancer · 2008 · 8 claims · 6 setups

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  The Affymetrix MitoChip resequencing array is a high-throughput, higher-resolution alternative to capillary sequencing for detecting mtDNA point mutations and heteroplasmy in clinical specimens.

  matched blood mtdna low-quantity mitochondrial capillary str

• Complex landscapes of somatic rearrangement in human breast cancer genomes.

  PMID 20033038 · PMC3398135 · Nature · 2009 · 8 claims · 6 setups

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  There are more somatic rearrangements in some breast cancers than previously appreciated by cytogenetic methods.

  breast subset confirmed paired-end fish exon-exon

• Lack of mutation at codon 531 of SRC in advanced colorectal cancers from Italian patients.

  PMID 11161376 · PMC2363715 · British journal of cancer · 2001 · 6 claims · 4 setups

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  No SRC codon 531 mutation was detected in any of 155 Italian colorectal cancer cases (171 tissue specimens, primary tumours and liver metastases)

  colorectal liver scalar subset pcr-rflp direct

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

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

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  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

• A novel approach for rapid screening of mitochondrial D310 polymorphism.

  PMID 16433919 · PMC1388229 · BMC cancer · 2006 · 7 claims · 4 setups

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  A single-step BsaXI RFLP assay can rapidly determine 7-C carriers at the D310 first polyC stretch of mtDNA without sequencing

  colorectal breast peripheral subset pcr-rflp sanger

• An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.

  PMID 18676830 · PMC2680495 · Cancer research · 2008 · 8 claims · 5 setups

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  PIK3CA mutations are more common in hormone receptor-positive and HER2-positive tumors than in basal-like breast cancers

  breast hormone early-stage mass sanger reverse-phase

• iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

  PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

  nsclc coad brca tcga scrna-seq bulk rna-seq

• 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

  Has reproduction · 71

  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.

  breast colorectal brca representative gene comparative multi-omic

• Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

  PMID 17054774 · PMC1636663 · Molecular cancer · 2006 · 7 claims · 7 setups

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  The alternative splice isoform Δp53 mRNA is co-expressed with full-length p53 mRNA in breast tumors and cell lines

  breast universal p53 subset qrt-pcr bioinformatic structure

• Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

  PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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  MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

  prostate subset lncap 22rv1 microrna quantitative western

• Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.

  PMID 38253993 · PMC10810249 · BMC bioinformatics · 2024 · 8 claims · 8 setups

  Has reproduction · 59

  The BGWO_SA_Ens algorithm (hybrid BGWO + simulated annealing with an ensemble classifier objective function) selects predictive breast cancer biomarker genes with high classification performance

  merged gse45827 superior differential feature comparative

• Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

  PMID 10027313 · PMC2362434 · British journal of cancer · 1999 · 7 claims · 5 setups

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  Allelic distribution of the Cyp19 intron 4 STRP differs significantly between breast cancer cases and controls

  peripheral ceph individuals cases strp genotyping fluorescent

• BRCA1 and BRCA2 mutations in Turkish breast/ovarian families and young breast cancer patients.

  PMID 10952777 · PMC2363542 · British journal of cancer · 2000 · 7 claims · 4 setups

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  11 mutations (9 BRCA1, 2 BRCA2) were identified across 105 Turkish patients using combined PTT, sequencing, and heteroduplex analysis.

  peripheral genomic truncation direct heteroduplex

• 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

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  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

• Towards precise classification of cancers based on robust gene functional expression profiles.

  PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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  Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

  nci60 lymphoma fep go-annotated cdna recursive hypergeometric

• Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

  PMID 36450752 · PMC9712620 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 70

  AR enhancer/chromatin binding usage is highly heterogeneous between primary prostate tumors, with <5% of all AR binding sites shared by half of tumors analyzed.

  prostate normal ar+ pca chip-seq rna-seq massively

• High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

  PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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  A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

  breast computational array-cgh gene bac

• Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.

  PMID 17317684 · PMC1874629 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  Gene-Collector is a method for multiplex nucleic acid amplification that specifically circularizes only correctly paired (cognate) PCR primer products on a Collector probe, degrading non-cognate artifacts by exonuclease treatment.

  genomic multiplex circularized circular multiplex probe-guided exonuclease

• Analysis of variants in DNA damage signalling genes in bladder cancer.

  PMID 18638378 · PMC2488326 · BMC medical genetics · 2008 · 7 claims · 5 setups

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  SNPs in DSB signalling genes may modulate predisposition to bladder cancer and influence effects of environmental exposures

  peripheral case-control unphased extracted snp confirmatory logistic

• Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

  PMID 19936259 · PMC2775948 · PloS one · 2009 · 8 claims · 8 setups

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  Integrated proteomic analysis of a cancer mouse model and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

  k-ras ovarian lists tumor quantitative pathway immunoblot