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: interactome ✕ Assay: interaction ✕ Clear

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
Organization of physical interactomes as uncovered by network schemas.

PMID 18949022 · PMC2561054 · PLoS computational biology · 2008 · 7 claims · 5 setups

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A computational procedure can systematically identify 'emergent' network schemas that are both recurrent and over-represented relative to randomized networks preserving lower-order subschema distributions

cerevisiae sapiens uncharacterized network cross-species functional
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
Seeded Bayesian Networks: constructing genetic networks from microarray data.

PMID 18601736 · PMC2474592 · BMC systems biology · 2008 · 8 claims · 4 setups

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Seeding Bayesian Network analysis with prior networks derived from literature and/or PPI data improves recovery of known gene-gene interactions compared to BN analysis without a seed

leukemia interactome pubmed-indexed computational microarray yeast literature
Network properties of complex human disease genes identified through genome-wide association studies.

PMID 19956617 · PMC2779513 · PloS one · 2009 · 7 claims · 6 setups

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Complex disease genes are significantly less central (lower degree/closeness, higher eccentricity) in the human interactome than essential and monogenic disease genes, occupying an intermediate niche between monogenic disease genes and non-disease genes

complex interactome gene disease-sharing gene protein-protein
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
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

Has reproduction · 88

COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

peripheral leukocytes plasma degs bulk single-cell plasma
The post-genomic era for a select few.

PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

takifugu physcomitrella coli vibrio comparative genetic dna-microarray
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
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
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

PMID 18053250 · PMC2246260 · Genome biology · 2007 · 8 claims · 4 setups

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Loss-of-function phenotypes in yeast are predictable from a gene's connections in a functional gene network via guilt-by-association.

saccharomyces guilt-by-association comparison network-guided
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
SMAC, a computational system to link literature, biomedical and expression data.

PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 7 claims · 6 setups

Has reproduction · 50

SMAC is a tool that extracts, prioritises, integrates and analyses biomedical literature and molecular data according to user-defined terms, linking PubMed and GEO.

pubmed invasive geo cancer semantic computational gene
Systems biology and the host response to viral infection.

PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

lung cd4 rhesus kshv microarray quantitative genomic
Prioritization of candidate cancer genes--an aid to oncogenomic studies.

PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

genes cancer interpro interactome averaged cross-validation domain
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
Of mice and men: comparative proteomics of bronchoalveolar fluid.

PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

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Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

pooled oxidative unpooled balf shotgun functional 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

Experiments

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

Organization of physical interactomes as uncovered by network schemas.

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

Seeded Bayesian Networks: constructing genetic networks from microarray data.

Network properties of complex human disease genes identified through genome-wide association studies.

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

Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

The post-genomic era for a select few.

Using random walks to identify cancer-associated modules in expression data.

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

Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes.

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

SMAC, a computational system to link literature, biomedical and expression data.

Systems biology and the host response to viral infection.

Prioritization of candidate cancer genes--an aid to oncogenomic studies.

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

Of mice and men: comparative proteomics of bronchoalveolar fluid.

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