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

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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

• CLEAN: CLustering Enrichment ANalysis.

  PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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  The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

  four breast combined hierarchical cluster csimm-based

• Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues.

  PMID 12865921 · PMC2394238 · British journal of cancer · 2003 · 6 claims · 3 setups

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  Hierarchical cluster analysis of 2-DE proteome data can distinguish normal breast, benign breast, and breast cancer tissues based on protein expression profiles

  breast two-dimensional hierarchical mann-whitney

• Protein expression patterns in primary carcinoma of the vagina.

  PMID 15199389 · PMC2409807 · British journal of cancer · 2004 · 5 claims · 4 setups

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  Cluster analysis of 2-DE proteomic data allows accurate discrimination between normal vaginal mucosa, primary vaginal carcinoma and primary cervical carcinoma

  fresh-frozen excised normal same two-dimensional matrix-assisted hierarchical

• 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

• Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

  PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 6 claims · 8 setups

  Has reproduction

  A deep learning WSI cluster (three-class mini batch K-means on Inception V3 features) is associated with overall survival (P<0.001) and is an independent prognostic predictor (P=0.031) in BLCA.

  tcga-blca blca tcga deep transfer-learning neural-network

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• 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

• Iterative class discovery and feature selection using Minimal Spanning Trees.

  PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups

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  Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering

  simulated breast acute diffuse synthetic cdna microarray

• 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

• Comparative genomic analysis of Campylobacter jejuni associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity.

  PMID 17919333 · PMC2174954 · BMC genomics · 2007 · 8 claims · 4 setups

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  GBS/MFS strains are genomically heterogeneous, falling into about six major lineages rather than a single clonal group

  jejuni subset matched comparative fisher's hierarchical

• Integromics: challenges in data integration.

  PMID 12186644 · PMC139396 · Genome biology · 2002 · 8 claims · 7 setups

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  There is no simple solution to database integration in genomics/bioinformatics

  lines molecular gene monsanto high-throughput cluster-correlation microarray

• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

  PMID 36088548 · PMC9487593 · Briefings in bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  Well-established, hierarchically organized pathway annotation systems (e.g. GO, Reactome, KEGG) yield the best overall enrichment performance despite covering much of the human genome only in general terms.

  user-submitted string pubmed protein-coding gene hierarchical text-mining

• PulmonDB: a curated lung disease gene expression database.

  PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 6 claims · 6 setups

  Has reproduction · 53

  PulmonDB is a curated, web-based gene expression database and R package integrating microarray and RNA-seq data for COPD and IPF with manually curated controlled-vocabulary annotation.

  lung ipf copd curated hierarchical differential

• Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

  PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

  Has reproduction · 86

  CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

  tissues predicted tss-enhancer cattle cage extraction coexpression

• Independent component analysis reveals new and biologically significant structures in micro array data.

  PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups

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  ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone

  acute serum-stimulated head aml microarray clust term

• Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni.

  PMID 17535437 · PMC1892558 · BMC microbiology · 2007 · 8 claims · 6 setups

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  Cjd strains are phylogenetically distinct from Cjj strains based on MLST and CGI analysis

  geographically cjd novel jejuni multilocus comparative phenotypic

• Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

  PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups

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  RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix

  yeast liver eight-node microarray k-means hybrid

• Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

  PMID 18205922 · PMC2374452 · Arthritis research & therapy · 2008 · 7 claims · 4 setups

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  A standardized 3D in vitro alginate bead model of chondrocytes stimulated with synovial fibroblast supernatants can be used to profile RA-related cartilage destruction genes

  sv40 articular differentially antibody-based oligonucleotide real-time

• Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

  PMID 19924232 · PMC2773120 · PloS one · 2009 · 8 claims · 5 setups

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  37 miRNAs are significantly differentially expressed between MYCN-amplified (MNA) and non-MNA neuroblastoma tumors, suggesting direct or indirect regulation by MYCN

  neuroblastoma shep-tet21 stem-loop array tlda