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 taxonomy of epithelial human cancer and their metastases.

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

  Full-text index only

  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

• Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

  PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 5 setups

  Has reproduction · 83

  A multigene peripheral-blood gene-expression biomarker accurately classifies which women from high-risk families develop familial breast cancer.

  peripheral pbmcs blood normal gene-expression lymphocyte gene

• Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

  PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

  immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime

• Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.

  PMID 35901050 · PMC9333241 · PloS one · 2022 · 7 claims · 7 setups

  Has reproduction · 55

  Several WGCNA gene co-expression modules are significantly associated with both LVEF and the DCM phenotype in heart failure patients.

  heart degs gene genes bulk gene kegg

• A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

  PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups

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  A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS

  pooled sickle centenarian snp pooled gene

• pmid-40857330

  PMID 40857330 · PMC12380325 · 6 claims · 8 setups

  Full-text index only

  90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes

  abdominal gingival overlapping interacting microarray weighted kegg

• GeneTrail--advanced gene set enrichment analysis.

  PMID 17526521 · PMC1933132 · Nucleic acids research · 2007 · 8 claims · 2 setups

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  GeneTrail is a comprehensive, easy-to-use web-based tool for gene set enrichment analysis supporting both Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA)

  example sorted over-representation gene

• 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