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).

• A sequence-based survey of the complex structural organization of tumor genomes.

  PMID 18364049 · PMC2397511 · Genome biology · 2008 · 8 claims · 6 setups

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  End sequencing profiling (ESP) can identify all classes of genome rearrangements in tumor genomes by paired-end sequencing of BAC clones

  tumors breast bac bt474 bac low-coverage fluorescence

• High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

  PMID 18344524 · PMC2367728 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  A protocol combining PCR-based whole genome amplification with arrays of highly purified BAC clones enables detection of DNA copy number changes in single cells

  single bac amplified pi-scei array quantitative dot

• DNA methylation of cancer genome.

  PMID 19960550 · PMC2940836 · Birth defects research. Part C, Embryo today : reviews · 2009 · 8 claims · 7 setups

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  Cancer epigenome alterations fall into two main categories: hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin.

  embryonic germ heterozygous cancer gene hypomorphic methyltransferase

• 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

• Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth.

  PMID 19920251 · PMC2812789 · Science signaling · 2009 · 7 claims · 8 setups

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  Oncogenic FGFR1 directly phosphorylates PKM2 at tyrosine 105 (Y105), inhibiting its enzymatic activity

  293t kg-1a recombinant h1299 ms-based co-transfection enzymatic

• MALDI profiling of human lung cancer subtypes.

  PMID 19890392 · PMC2767501 · PloS one · 2009 · 8 claims · 8 setups

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  PIMAC/MALDI-TOF peptide profiles combined with classification models can distinguish normal lung from tumor and differentiate NSCLC histological subtypes

  lung tryptic peak ffpe maldi-tof parallel stepwise

• Methods for genome-wide analysis of DNA methylation in intestinal tumors.

  PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

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  Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

  cd19+ lung gpx1 tumor mira medip goldengate

• 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

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  Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

  tumors cancer tumor lung direct database quantitative

• Ectopic expression of BEX genes in T-cell acute lymphoblastic leukemia.

  PMID 40811813 · PMC12830129 · Blood advances · 2026 · 6 claims · 8 setups

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  Bex1 (and to a lesser extent Bex4) is ectopically expressed in Pten-deficient mouse T-ALL blasts

  thymocytes thymocyte t-all normal scrna-seq rt-qpcr bulk

• Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.

  PMID 41159380 · PMC12979040 · Neuro-oncology · 2026 · 8 claims · 8 setups

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  A unified UMAP-based transcriptomic landscape built from 888 medulloblastoma and 370 ependymoma tumors reveals distinct clusters corresponding to known and novel molecular subtypes.

  medulloblastoma ependymoma healthy shh bulk fusion copy

• scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

  PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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  scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

  single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type

• DHODH links mitochondrial bioenergetics, one-carbon metabolism, and DNA repair to sustain aggressive prostate adenocarcinoma.

  PMID 41612476 · PMC12930642 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

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  DHODH is markedly overexpressed in malignant prostate epithelial cells and abundant in tumors

  tcga-prad gse141445 22rv1 bulk single-cell lentiviral

• POSTN(+) fibroblast‑secreted small extracellular vesicles drive macrophage M2 polarization through BMP4/BMPR2/Smad signaling.

  PMID 41645751 · PMC12891935 · Oncology reports · 2026 · 8 claims · 8 setups

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  Integration of two HNSCC scRNA-seq datasets reveals two distinct fibroblast subtypes: POSTN- and POSTN+ fibroblasts

  hnscc tcga-hnscc oscc oscc-derived single-cell bulk immunohistochemistry

• The Presence of CD11c+ B Cells with Potent Effector Memory Phenotype in Lung Adenocarcinoma Correlates with Overall Patient Survival.

  PMID 41686183 · PMC12988592 · Cancer immunology research · 2026 · 7 claims · 7 setups

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  CD79A is a reliable transcriptomic/protein quantifier of B lymphocytes across differentiation stages, unlike CD19/CD20 whose expression changes upon activation

  healthy tcga luad til-b flow bulk single-cell

• HIF sustain a transcriptional regulatory circuit of EPAS1 expression in renal clear cell carcinoma.

  PMID 41714613 · PMC12921326 · Nature communications · 2026 · 8 claims · 8 setups

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  HIF-2α mRNA is specifically overexpressed in ccRCC tumor tissue/cells compared to normal kidney, while it is reduced in papillary and chromophobe RCC

  erlangen tcga ccrcc tubule qpcr rna-seq rnascope

• The complement system contributes to the immunosuppressive microenvironment of uveal melanoma.

  PMID 41803879 · PMC13130498 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  Primary UM (pUM) preferentially expresses early complement pathway components over terminal membrane attack complex elements, with early factors showing prognostic significance.

  short-term metastatic normal pum bulk label-free single-cell

• Molecular genetic diagnosis of von Hippel-Lindau disease: analysis of five Japanese families.

  PMID 8641976 · PMC5921130 · Japanese journal of cancer research : Gann · 1996 · 5 claims · 3 setups

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  Four of five Japanese VHL disease families showed germ line VHL gene mutations, comprising 2 missense mutations, 1 deletion, and 1 splice-site mutation

  blood-derived hemangioblastoma single-strand direct sscp

• Social and ethical implications of genomics, race, ethnicity, and health inequities.

  PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

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  Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

  population prostate non-small-cell breast genome-wide gene somatic

• Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

  PMID 15854232 · PMC1142514 · BMC genomics · 2005 · 8 claims · 2 setups

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  Correlations between qRT-PCR and microarray data are generally strong, especially when identical transcripts are targeted by both methods (r = 0.89 for fold-change).

  pediatric same oligonucleotide quantitative

• Wx: a neural network-based feature selection algorithm for transcriptomic data.

  PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.

  tcga gse72056 gse40419 gse103322 bulk single-cell rna-seq