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 46

System / cell line: interacting ✕ Clear

Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

PMID 40857330 · PMC12380325 · PloS one · 2025 · 6 claims · 8 setups

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

abdominal gingival overlapping interacting microarray weighted kegg
Protein function assignment through mining cross-species protein-protein interactions.

PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

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CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

sapiens cross-species majority simple
Filtering high-throughput protein-protein interaction data using a combination of genomic features.

PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

saccharomyces bank caenorhabditis homo yeast mass naive
Proteomic screen defines the hepatocyte nuclear factor 1alpha-binding partners and identifies HMGB1 as a new cofactor of HNF1alpha.

PMID 18160415 · PMC2275099 · Nucleic acids research · 2008 · 8 claims · 8 setups

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HMGB1 is a novel HNF1α-interacting protein identified via a co-IP-MS screening strategy

hepg2 recombinant co-immunoprecipitation immunofluorescence gst
Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

PMID 19912651 · PMC2784748 · BMC cell biology · 2009 · 7 claims · 7 setups

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hnRNP L is a novel Sam68-interacting protein partner identified by proteomics and confirmed by co-immunoprecipitation

lncap hek293 nih3t3 co-immunoprecipitation sucrose indirect
Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

PMID 18922787 · PMC3523710 · Science signaling · 2008 · 8 claims · 8 setups

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VILIP1 was identified via a proteomic (GST pull-down) approach as a protein interacting with the P2X2 receptor C-terminal tail

brain hek gst co-immunoprecipitation immunocytochemistry
Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities.

PMID 18617507 · PMC2577208 · Molecular & cellular proteomics : MCP · 2008 · 8 claims · 8 setups

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Nuclear Ran GTPase was identified by mass spectrometry as a novel interacting partner of VRK1 and VRK2B

hek293t recombinant hela gst western co-immunoprecipitation
Protein co-evolution, co-adaptation and interactions.

PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

nuoe intra-protein coli interacting phylogenetic correlated domain-restricted
Threshold-dominated regulation hides genetic variation in gene expression networks.

PMID 18062810 · PMC2238762 · BMC systems biology · 2007 · 8 claims · 2 setups

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Threshold robustness (insensitivity of a singular/regulating variable's equilibrium value to parameter perturbations, except threshold changes) increases with increasing response function steepness and is present even under Michaelis-Menten conditions, not just in the step-function limit.

three-gene illustrative numerical analytical
Ontological visualization of protein-protein interactions.

PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks

gene interacting interaction annotation yeast co-immunoprecipitation
Computational verification of protein-protein interactions by orthologous co-expression.

PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous
The nuclear pore complex.

PMID 11574060 · PMC138961 · Genome biology · 2001 · 8 claims · 8 setups

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NPC structure is broadly conserved across eukaryotes but differs substantially in size and architecture between yeast and vertebrates

xenopus saccharomyces yeast caenorhabditis cryo-electron proteomic protein-a
Proteomics: characterizing the cogs in the machinery of life.

PMID 14630521 · PMC1241753 · Environmental health perspectives · 2003 · 8 claims · 5 setups

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Protein expression patterns in blood serum, detected via SELDI-TOF mass spectrometry and analyzed with a genetic algorithm, can distinguish ovarian cancer patients from healthy individuals with very high sensitivity and specificity.

blood lung hemoglobin proteins seldi-tof proteome tandem
The secrets of a functional synapse--from a computational and experimental viewpoint.

PMID 16723009 · PMC1810317 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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Kinesin motor proteins move cargo along axonal microtubules to the synapse, with cargo specificity determined by adaptor/linker proteins rather than lipid recognition

mammalian kinesin cholinergic dendrites kinesin sequence-based comparative
Screening large-scale association study data: exploiting interactions using random forests.

PMID 15588316 · PMC545646 · BMC genetics · 2004 · 7 claims · 3 setups

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Random forest importance measure significantly outperforms the Fisher Exact test as a screening tool when risk SNPs interact.

simulated same simulation random fisher
Back to basics.

PMID 12186643 · PMC139395 · Genome biology · 2002 · 8 claims · 8 setups

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Human PDS (Pendrin) gene mutations damage ear structures and are linked to hereditary deafness and goiter

chromosome pendrin yeast carbonic genome gene mudpit
Improvements to cardiovascular gene ontology.

PMID 19046747 · PMC2706316 · Atherosclerosis · 2009 · 8 claims · 8 setups

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Gene Ontology (GO) provides a controlled vocabulary that links current functional knowledge of genes to high-throughput genomic and proteomic datasets, aiding data interpretation.

coronary phospholamban mammalian lines gene expression large-scale
Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

PMID 36450752 · PMC9712620 · Nature communications · 2022 · 8 claims · 8 setups

Has reproduction · 70

AR chromatin binding is highly heterogeneous between primary prostate tumors, with <5% of all AR binding sites (ARBS) shared by half of the 88 tumors analyzed

prostate normal pca lncap chip-seq starr-seq luciferase
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

Has reproduction · 76

GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

user-assembled archs4 generif-derived aggregated gene gene-gene literature
Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

Has reproduction · 64

Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

heart degs dgat2 mitodegs microarray kegg protein-protein

Experiments

Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

Protein function assignment through mining cross-species protein-protein interactions.

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

Proteomic screen defines the hepatocyte nuclear factor 1alpha-binding partners and identifies HMGB1 as a new cofactor of HNF1alpha.

Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities.

Protein co-evolution, co-adaptation and interactions.

Threshold-dominated regulation hides genetic variation in gene expression networks.

Ontological visualization of protein-protein interactions.

Computational verification of protein-protein interactions by orthologous co-expression.

The nuclear pore complex.

Proteomics: characterizing the cogs in the machinery of life.

The secrets of a functional synapse--from a computational and experimental viewpoint.

Screening large-scale association study data: exploiting interactions using random forests.

Back to basics.

Improvements to cardiovascular gene ontology.

Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.