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 21

System / cell line: proteins ✕ Assay: receptor ✕ Clear

G2Cdb: the Genes to Cognition database.

PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

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G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

brain nervous genome synaptic proteomic large-scale sequence
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
Phosphoproteomics: new insights into cellular signaling.

PMID 16168091 · PMC1242200 · Genome biology · 2005 · 8 claims · 8 setups

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Protein kinases are one of the largest gene families in humans and mice, accounting for 1.7% of the human genome

yeast hela beta2-adrenergic erk phosphopeptide targeted silac
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

chicken comparative amino phylogenetic
Tipping the balance in autoimmune disease.

PMID 18001485 · PMC2246277 · Genome biology · 2007 · 8 claims · 8 setups

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Human autoimmune diseases are fundamentally diseases of immune dysfunction, evidenced by predisposing genes being immune-function genes, some shared and some unique across MS, T1D, SLE, CD and RA

patients congenic nzm2410 mrl-lpr snp induced genetic
Human protein reference database--2006 update.

PMID 16381900 · PMC1347503 · Nucleic acids research · 2006 · 7 claims · 6 setups

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HPRD is a comprehensive, continually expanded resource cataloging human protein domains, PTMs, protein-protein interactions, and other annotations.

proteins hela nucleolus signaling literature mass subcellular
An "omics" approach to uropathogenic Escherichia coli vaccinology.

PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups

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An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates

upec vaccination comparative two-dimensional
Protein microarray technology.

PMID 17126887 · PMC1828913 · Mechanisms of ageing and development · 2007 · 8 claims · 8 setups

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Protein microarrays enable high-throughput characterization of protein biochemical activities across an entire proteome in a single experiment

yeast sh2 protein-protein protein-dna chromatin
CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.

PMID 16892042 · PMC2360640 · British journal of cancer · 2006 · 6 claims · 6 setups

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CD70 was identified by proteomic analysis of plasma membrane preparations as highly expressed in A498 and SW839 RCC-derived cell lines

a498 frozen normal proteomics flow immunohistochemistry
TreeFam: a curated database of phylogenetic trees of animal gene families.

PMID 16381935 · PMC1347480 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Tree-based inference of orthologs and paralogs is more robust than BLAST-based methods because evolutionary rates (and thus pairwise BLAST scores) vary across gene family members

sequences animal treefam-b lamin phylogenetic homology sequence
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
Phagosome maturation: going through the acid test.

PMID 18813294 · PMC2908392 · Nature reviews. Molecular cell biology · 2008 · 8 claims · 8 setups

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Maturation of apoptotic cell-containing phagosomes proceeds via machinery mechanistically distinct from receptor-mediated endocytosis

caenorhabditis elegans swiss phagosomes rnai genetic acridine
Contributions of proteomics to understanding phagosome maturation.

PMID 18331591 · PMC2613258 · Cellular microbiology · 2008 · 8 claims · 8 setups

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Proteomic studies across many species have identified hundreds of proteins associated with phagosomes, revealing conserved functional classes (vATPase subunits, GTPases, hydrolases, SNAREs, Rabs, cytoskeletal proteins).

macrophage dictyostelium drosophila entamoeba quantitative 2dge prefractionation
SNAP: predict effect of non-synonymous polymorphisms on function.

PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

combined escherichia bacteriophage hiv-1 neural benchmark comparative
Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

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A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

library database oligovalent b-cells glycan bioinformatics one-pot
Mining the draft human genome.

PMID 11236999 · PMC2658632 · Nature · 2001 · 8 claims · 7 setups

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Protein-coding exons account for only about 3% of the human genome DNA, with repeat sequences making up around 46%.

genome unfinished drosophila tetraodon psi-blast domain sequence
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry
Discovery and hypothesis generation through bioinformatics.

PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

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Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

genome chemokine gene-expression proteins genome-wide phylogenetic microarray
MODBASE, a database of annotated comparative protein structure models and associated resources.

PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

sequences chains template chain comparative pairwise ligand
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 20

AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

ipf common key rats microarray network protein-protein

Experiments

G2Cdb: the Genes to Cognition database.

Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

Phosphoproteomics: new insights into cellular signaling.

Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

Tipping the balance in autoimmune disease.

Human protein reference database--2006 update.

An "omics" approach to uropathogenic Escherichia coli vaccinology.

Protein microarray technology.

CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.

TreeFam: a curated database of phylogenetic trees of animal gene families.

The Proteomic Code: a molecular recognition code for proteins.

Phagosome maturation: going through the acid test.

Contributions of proteomics to understanding phagosome maturation.

SNAP: predict effect of non-synonymous polymorphisms on function.

Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

Mining the draft human genome.

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

Discovery and hypothesis generation through bioinformatics.

MODBASE, a database of annotated comparative protein structure models and associated resources.

Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.