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 16

System / cell line: real ✕ Assay: mass ✕ Clear

On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.

PMID 18076765 · PMC2211327 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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The TGDR-AUC algorithm regularizes the empirical AUC by replacing the non-differentiable 0-1 loss with a smooth sigmoid surrogate function and applies constrained threshold gradient descent regularization

simulated serum preprocessed simulation mass high-resolution
A proteomic strategy to identify novel serum biomarkers for liver cirrhosis and hepatocellular cancer in individuals with fatty liver disease.

PMID 19656391 · PMC2729079 · BMC cancer · 2009 · 8 claims · 4 setups

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2D gel proteomic profiling of immunodepleted serum reveals protein spot patterns that differentiate pre-cirrhotic NAFLD, cirrhotic NAFLD, and cirrhotic NAFLD with HCC

immunodepleted serum liver gel direct semi-quantitative
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
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.

PMID 15005801 · PMC341449 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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An XML schema called Annotated Gel Markup Language (AGML) is proposed to manage, analyze, and disseminate annotated 2D gel electrophoresis and MS results.

biological 2de agml gel mass visualization
Proteomic analyses of the effects of drugs of abuse on monocyte-derived mature dendritic cells.

PMID 19811410 · PMC2812871 · Immunological investigations · 2009 · 6 claims · 7 setups

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Cocaine differentially regulates expression of several functional classes of proteins (apoptosis, protein folding, kinase activity, metabolism, signal transduction) in monocyte-derived mature dendritic cells

monocyte-derived excised difference hplc-tandem western
Human microglial cells synthesize albumin in brain.

PMID 18665237 · PMC2483733 · PloS one · 2008 · 8 claims · 8 setups

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Human microglial cells synthesize albumin de novo in the brain.

hmo6 microglial fetal alzheimer's immunocytochemistry immunohistochemistry tandem
Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.

PMID 19693676 · PMC2824116 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 7 setups

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Proteomic screening of human synaptosomes identifies a set of proteins differentially expressed in HIV/AIDS brain

frontal excised synaptosome paraffin-embedded 2d-page maldi-tof western
The dietary bioflavonoid, quercetin, selectively induces apoptosis of prostate cancer cells by down-regulating the expression of heat shock protein 90.

PMID 18726985 · PMC2826114 · The Prostate · 2008 · 7 claims · 8 setups

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Quercetin treatment of prostate cancer cells decreases cell proliferation and viability in a dose-dependent manner

pc-3 excised prostate viability difference nano
Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

PMID 18477650 · PMC2443277 · Carcinogenesis · 2008 · 8 claims · 7 setups

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HBx C-terminal deletion mutants (HBx3'-30 and HBx3'-40) produce differentially expressed gene and protein profiles in transfected Huh7 HCC cells, mostly involving transcriptional regulation, oncogenes/tumor suppressors, cell junctions, signal transduction, metabolism and immune response

huh7 frozen hcc genomic cdna two-dimensional western
Chips to hits.

PMID 11983055 · PMC139346 · Genome biology · 2002 · 8 claims · 8 setups

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Illumina's fiber-optic bead array technology allows ~2,000 oligonucleotide-based assays per bead array for high-throughput genotyping

individual yeast pools lncap cell-based affymetrix automated
The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

PMID 28930663 · PMC5719893 · Immunity · 2017 · 8 claims · 8 setups

Has reproduction · 67

A common APOE-dependent microglial molecular signature (MGnD) — loss of homeostatic genes plus induction of inflammatory genes with Apoe among the most upregulated — occurs in ALS, MS and AD mouse models and around neuritic Aβ-plaques in human AD brain.

facs-isolated fcrls+ sorted app-ps1 nanostring sequencing quantitative
WNT10B mutations in human obesity.

PMID 16477437 · PMC4304000 · Diabetologia · 2006 · 8 claims · 8 setups

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The WNT10B C256Y missense mutation abrogates the protein's ability to activate canonical WNT signalling and block adipogenesis

genomic 3t3-l1 subject proband dhplc top-flash western
New strategies in drug discovery.

PMID 16671397 · PMC7120019 · Methods in molecular biology (Clifton, N.J.) · 2006 · 8 claims · 8 setups

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A new integrated drug discovery paradigm has emerged combining clinical, genetic, genomic, and molecular phenotype data with cheminformatics, managed via informatics

animal normal low-abundance mice situ microarray taqman
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
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

PMID 18053132 · PMC2254445 · BMC bioinformatics · 2007 · 6 claims · 5 setups

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The paired oligo-border kernel (POBK) combined with SVMs predicts peptide adsorption/elution in SAX-SPE and retention time in IP-RP-HPLC more accurately than existing methods.

peptides peptide sax-spe ip-rp-hplc cross-run
Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

porcine paec umbilical huvec methyltransferase sds-page fragmentation

Experiments

On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.

A proteomic strategy to identify novel serum biomarkers for liver cirrhosis and hepatocellular cancer in individuals with fatty liver disease.

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

An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.

Proteomic analyses of the effects of drugs of abuse on monocyte-derived mature dendritic cells.

Human microglial cells synthesize albumin in brain.

Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.

The dietary bioflavonoid, quercetin, selectively induces apoptosis of prostate cancer cells by down-regulating the expression of heat shock protein 90.

Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

Chips to hits.

The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.

WNT10B mutations in human obesity.

New strategies in drug discovery.

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

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.