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 19

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

ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.

PMID 41820617 · PMC13084044 · The EMBO journal · 2026 · 8 claims · 7 setups

Has reproduction · 50

ZAP (ZC3HAV1/PARP13) is a key component of the RAPP quality control pathway

k562 zap-s rt-qpcr western immunofluorescence
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
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

PMID 15892868 · PMC1175952 · Genome biology · 2005 · 8 claims · 6 setups

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Two quantitative benchmarks (functional-annotation-based and physical-interaction-based log likelihood ratio scores) can measure relative accuracy of human PPI datasets

medline annotated interactions consolidated conditional co-citation bayesian
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
Pathway analysis of kidney cancer using proteomics and metabolic profiling.

PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

ccrcc rcc computational random gel immunoblotting immunohistochemistry
Analysis of protein sequence and interaction data for candidate disease gene prediction.

PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

ophid biocarta kegg pfam-annotated common benchmarking multiple-interval
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
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
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

PMID 16630345 · PMC1489951 · BMC bioinformatics · 2006 · 8 claims · 7 setups

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Sequence conservation (PSIC score difference) at the nsSNP position is the single most useful attribute for predicting deleterious vs neutral status.

swissprot nssnp-containing nssnps machine single-attribute sequence
Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.

PMID 19834888 · PMC4302342 · Proteomics · 2009 · 7 claims · 7 setups

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BioCAT (biotin tagging + AACT) enables highly sensitive and accurate single-step screening of mammalian protein-protein interactions without establishing a stable cell line

293t standard nk92mi list western sds-page nanolc-ms
The Hellenic type of nondeletional hereditary persistence of fetal hemoglobin results from a novel mutation (g.-109G>T) in the HBG2 gene promoter.

PMID 19050890 · PMC2690858 · Annals of hematology · 2009 · 7 claims · 7 setups

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HBG2:g.-109G>T is a novel promoter mutation causing a distinct ('Hellenic type') nd-HPFH

peripheral genomic nuclear mel cation reverse-phase denaturing
Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 8 claims · 8 setups

Has reproduction · 79

Meta-analysis confirmed a positive association between DED and DEP occurrence

patients taiwan biobank twb meta-analysis genome-wide score
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
Cohesin regulates alternative splicing.

PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups

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Cohesin regulates alternative splicing independently of its effects on transcription.

hct116rmac hct116 recombinant hek293 bulk rt-pcr proximity
A surrogate-based approach for post-genomic partner identification.

PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups

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Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.

biotinylated tnf-β analysis secondary phage sequence secondary
Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

PMID 18281699 · PMC2367731 · Nucleic acids research · 2008 · 8 claims · 7 setups

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H3t/H4 forms nucleosomes with H2A/H2B via the salt-dialysis method, similar to conventional H3.1/H4

recombinant reconstituted his6-tagged hnap1 salt-dialysis micrococcal chaperone-mediated
Point mutations in GLI3 lead to misregulation of its subcellular localization.

PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

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The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

hela immunofluorescence real-time luciferase
Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 8 setups

Has reproduction · 72

edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.

ffpe same nanostring tnbc nanostring immunohistochemistry differential

Experiments

ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.

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

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

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

Pathway analysis of kidney cancer using proteomics and metabolic profiling.

Analysis of protein sequence and interaction data for candidate disease gene prediction.

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.

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

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.

The Hellenic type of nondeletional hereditary persistence of fetal hemoglobin results from a novel mutation (g.-109G>T) in the HBG2 gene promoter.

Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

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

Cohesin regulates alternative splicing.

A surrogate-based approach for post-genomic partner identification.

Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

Point mutations in GLI3 lead to misregulation of its subcellular localization.

Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.