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 20

System / cell line: protein-protein ✕ Assay: size ✕ Clear

Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer.

PMID 33777753 · PMC7991912 · Frontiers in oncology · 2021 · 7 claims · 8 setups

Has reproduction · 81

Cisplatin exposure induces significant deregulation of protein expression networks in NSCLC cells

h460 nsclc swath-ms western machine
Next-generation high-density self-assembling functional protein arrays.

PMID 18469824 · PMC3070491 · Nature methods · 2008 · 8 claims · 7 setups

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A next-generation NAPPA method produces high-density protein microarrays displaying over 1500 unique proteins with >90% expression success

test high-density amine-coated array picogreen anti-gst fluorescently
From single cells to whole organisms.

PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups

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The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods

saccharomyces caenorhabditis mammalian cylindromatosis automated interference rnai
Proteomics in alcohol research.

PMID 12875051 · PMC6683837 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2002 · 7 claims · 8 setups

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The proteome is larger and more complex than the genome due to differential splicing, post-translational modifications (PTMs), and protein-protein interactions.

mixtures tryptic liver plasma two-dimensional liquid maldi-tof
Oligomeric protein structure networks: insights into protein-protein interactions.

PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

non-redundant same known complexes structure hub comparison
Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.

PMID 19779549 · PMC2739292 · PLoS computational biology · 2009 · 8 claims · 8 setups

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Human disease genes are much closer to aging genes in the PPI network than expected by chance

protein-protein randomized dan aging network degree-conserved closeness
The role of positive selection in determining the molecular cause of species differences in disease.

PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

orthologous omim meta-database panther comparative disease protein-protein
Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

PMID 18598366 · PMC2474618 · BMC bioinformatics · 2008 · 7 claims · 6 setups

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Experimentally measured protein-protein interaction sub-networks are not random samples of their parent networks.

yeast drosophila networks dppi reanalysis computer repeated
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
Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups

Has reproduction · 83

scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach

liver hepatocyte detected adipose single-cell differential protein-protein
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
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
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
Genetical genomics: spotlight on QTL hotspots.

PMID 18949031 · PMC2563687 · PLoS genetics · 2008 · 8 claims · 4 setups

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Distant eQTL hotspots are rare and difficult to reliably verify across published genetical genomics studies

adipose saccharomyces genome-wide permutation gene
The Proteomic Code: a molecular recognition code for proteins.

PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide
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
Research Spotlight: New multiparameter bioanalytical technologies for applications in personalized medicine, drug discovery and fundamental biology.

PMID 21083072 · PMC3106349 · Bioanalysis · 2009 · 8 claims · 8 setups

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High-density arrays of silicon photonic microring resonators enable label-free, multiplexed detection of DNA, miRNA, and protein biomarkers from a single small-volume sample

silicon undiluted model label-free multiplexed cytokine
Cryptosporidium: genomic and biochemical features.

PMID 19187778 · PMC2819285 · Experimental parasitology · 2010 · 8 claims · 8 setups

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C. parvum lacks a plastid and mitochondrial genome, unlike other apicomplexans, limiting plastid-targeted drug strategies

parvum yeast recombinant gp40 pulsed-field happy genome
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

Has reproduction · 62

Immature (day 7) CASK KO induced neurons show increased dendritic complexity/neurite overgrowth and upregulated gene networks for cell adhesion, neurite outgrowth, and cytoskeletal organization.

day mature bulk qrt-pcr gene
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

Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer.

Next-generation high-density self-assembling functional protein arrays.

From single cells to whole organisms.

Proteomics in alcohol research.

Oligomeric protein structure networks: insights into protein-protein interactions.

Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.

The role of positive selection in determining the molecular cause of species differences in disease.

Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

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

Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

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

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

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

Genetical genomics: spotlight on QTL hotspots.

The Proteomic Code: a molecular recognition code for proteins.

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

Research Spotlight: New multiparameter bioanalytical technologies for applications in personalized medicine, drug discovery and fundamental biology.

Cryptosporidium: genomic and biochemical features.

CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

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