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).

Publications 1.3k Datasets 392.5k Experiments 18

System / cell line: tumor ✕ Assay: unsupervised ✕ Clear

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

Full-text index only

Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

lms independent soft gene array immunohistochemistry
Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 7 setups

Has reproduction · 45

Eight distinct T cell populations are identifiable in CRC tumor tissue and seven in peripheral blood by unsupervised clustering of scRNA-seq data.

tumor peripheral cd4+ eight single-cell unsupervised ligand-receptor
Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 63

Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes

hnscc combined gse164690 tcga-hnsc ssgsea unsupervised immune
A taxonomy of epithelial human cancer and their metastases.

PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

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Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

epithelial tumor metastatic breast microarray gene fisher
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.

PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups

Has reproduction · 71

LUAD samples cluster into IRG-high and IRG-low groups, with the IRG-high group showing significantly better survival and greater immune cell infiltration.

luad geo degs immunotherapy-treated bulk weighted ppi
Tissue microarrays characterise the clinical significance of a VEGF-A protein expression signature in gastrointestinal stromal tumours.

PMID 17299397 · PMC2360083 · British journal of cancer · 2007 · 8 claims · 5 setups

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A combined VEGF-A ligand and flt-1 receptor protein expression signature discriminates malignant from benign GIST

archival tma genomic pcr immunohistochemistry unsupervised pcr-dhplc
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
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
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

aml tumor novo additional genome snp comparative
2D-DIGE proteomic characterization of head and neck squamous cell carcinoma.

PMID 19861202 · PMC2847880 · Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery · 2009 · 8 claims · 4 setups

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Cornulin is downregulated in HNSCC relative to normal adjacent tissue and represents a novel biomarker in HNSCC.

hnscc excised independent identified 2d-dige lc-ms immunohistochemistry
Oncogenic mutations in GNAQ occur early in uveal melanoma.

PMID 18719078 · PMC2634606 · Investigative ophthalmology & visual science · 2008 · 8 claims · 7 setups

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Activating GNAQ mutations at codon 209 occur in 33/67 (49%) of primary uveal melanomas, making it the most common known oncogenic mutation in UM

uveal peripheral normal well-characterized pcr sequencing array-based
Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 5 setups

Has reproduction · 83

CHCT, a hierarchical classification tool, splits classification of 30 cancer types into ten smaller subproblems using a two-tier architecture to classify primary cancer by methylation profile

cancer clinical training independent methylation upgma random
MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

PMID 19798417 · PMC2749450 · PloS one · 2009 · 7 claims · 7 setups

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High grade serous carcinomas with and without BRCA1/2 abnormalities show very similar miRNA expression profiles, with no clear clustering separation by BRCA1/2 status

high ovarian mir-29a mirna unsupervised significance
Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

serous same lmp braf-mutant gene hotspot erbb2
DNA demethylation is associated with malignant progression of lower-grade gliomas.

PMID 30760837 · PMC6374451 · Scientific reports · 2019 · 8 claims · 8 setups

Has reproduction

Nearly half of IDH-mutant glioblastomas that progressed from lower-grade gliomas show characteristic partial DNA demethylation in previously methylated (G-CIMP) genomic regions of their initial tumor.

gliomas neural analysis tcga methylation whole-exome sequencing
Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

PMID 19915670 · PMC2771920 · PloS one · 2009 · 8 claims · 6 setups

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Proteomic analysis of glioma samples reveals three signaling subclasses of GBM associated with predominant EGFR activation, PDGFR activation, or loss of NF1

surgical standardized glioma gbm western principal k-means
Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

PMID 19861435 · PMC2783876 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 7 claims · 7 setups

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Comprehensive genomic analysis shows thymic carcinomas are molecularly distinct from thymomas

resected thymic previously mass dideoxynucleotide array
iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.

PMID 19674965 · PMC2773724 · Molecular & cellular proteomics : MCP · 2009 · 6 claims · 5 setups

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Serial transplantation of human GBM xenografts in nude rats converts an initially highly infiltrative, non-angiogenic phenotype into a highly angiogenic phenotype over 4-6 generations.

membrane-enriched xenograft homogenate quantified itraq western bradford

Experiments

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

A taxonomy of epithelial human cancer and their metastases.

Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.

Tissue microarrays characterise the clinical significance of a VEGF-A protein expression signature in gastrointestinal stromal tumours.

Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

2D-DIGE proteomic characterization of head and neck squamous cell carcinoma.

Oncogenic mutations in GNAQ occur early in uveal melanoma.

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

MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

DNA demethylation is associated with malignant progression of lower-grade gliomas.

Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.