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).

• Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

  PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

  postmortem genes gene proteins microarray protein-protein hierarchical

• Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6.

  PMID 19738201 · PMC2857963 · Science signaling · 2009 · 8 claims · 8 setups

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  A novel ligand-affinity/cross-linking proteomic methodology enables isolation of labile integrin-associated signaling complexes

  α5+ computational k562 embryonic ligand tandem hierarchical

• Non-linear mapping for exploratory data analysis in functional genomics.

  PMID 15661072 · PMC548129 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A relaxation method for non-linear mapping adapts one pair of points per step rather than all points at once, and was originally shown by Chang and Lee to outperform Sammon's mapping in cluster detection effectiveness and computational efficiency.

  leukaemia small srbct brain relaxation self-organising sammon's

• FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

  PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

  user-supplied gene predicted interactome gene kegg transcription

• 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

• The dystrobrevin-binding protein 1 gene: features and networks.

  PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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  DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

  vertebrate dtnbp1 comparative cross-species molecular

• Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

  PMID 19906700 · PMC2808873 · Nucleic acids research · 2010 · 7 claims · 4 setups

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  NCG is a web database integrating duplicability, orthology, evolutionary appearance, and network topology data for 736 human cancer genes

  cancer proteome pten genome orthology protein-protein

• Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

  PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

  Has reproduction · 70

  AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

  head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr