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 14

System / cell line: sections ✕ Assay: proteomics ✕ Clear

Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.

PMID 18922159 · PMC2614521 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

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PGRMC1 protein spots are differentially abundant between ER-negative and ER-positive breast tumors, with two of three spots more abundant in ER-negative tumors

sections pooled mcf7 paraffin-embedded 2d-page shrimp viability
Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

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Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

serum frozen ig-depleted clinical seldi-tof maldi lc-ms
A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

PMID 19725976 · PMC2742551 · BMC cancer · 2009 · 7 claims · 5 setups

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Three protein spots (beta-actin, HSP60, PDI) show low expression variability across tumourous, non-tumourous cirrhotic, and normal liver tissues by 2-DE (ANOVA p>0.99 ranking)

liver 2-de western immunohistochemistry
Proteomics technologies and challenges.

PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

serum myeloid formalin-fixed general maldi-tof phage maldi
Liver fatty acid binding protein expression in colorectal neoplasia.

PMID 15138477 · PMC2409459 · British journal of cancer · 2004 · 8 claims · 5 setups

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L-FABP is consistently lost/decreased in colorectal cancer compared with paired normal colon tissue

paired excised formalin-fixed normal gel maldi-tof immunohistochemistry
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
Proteomics analysis reveals novel components in the detergent-insoluble subproteome in Alzheimer's disease.

PMID 19746990 · PMC2784247 · Journal of proteome research · 2009 · 8 claims · 5 setups

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A label-free XIC-based LC-MS/MS quantitation strategy, combined with an FTLD-U comparator cohort, can be used to identify AD-specific changes in the detergent-insoluble brain subproteome.

pooled postmortem individual detergent-insoluble lc-ms sequential sds-page
Characterization of detergent-insoluble proteins in ALS indicates a causal link between nitrative stress and aggregation in pathogenesis.

PMID 19956584 · PMC2780298 · PloS one · 2009 · 8 claims · 8 setups

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The Triton X-100-insoluble fraction (TIF) from spinal cord of G93A SOD1 mice is enriched in specific proteins (cytoskeletal, chaperone, mitochondrial, metabolic, signaling) compared to WT mice, already at a preclinical stage.

spinal tif lumbar ventral gel maldi-tof western
Quantitative mass spectrometry of diabetic kidney tubules identifies GRAP as a novel regulator of TGF-beta signaling.

PMID 19836472 · PMC2829334 · Biochimica et biophysica acta · 2010 · 8 claims · 7 setups

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Label-free 2D-LC-MS/MS quantitative proteomics identified 476 significantly differentially expressed proteins in kidney tubules of diabetic OVE26 mice versus control mice

kidney hk11 list 2d-lc-ms immunoblot immunohistochemistry
MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.

PMID 40450001 · PMC12126529 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 70

MACanalyzeR is a novel computational scRNAseq framework (with FoamSpotteR, MacPolarizeR, and PathAnalyzeR modules) for comprehensive monocyte/macrophage metabolic and phenotypic profiling

bat stromal paraffin-embedded aortic bulk proteomics scrnaseq
An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

Has reproduction · 85

Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor
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
Neuroscience in the era of functional genomics and systems biology.

PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

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Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

developing hippocampus bac-transgenic fetal situ gene bac-transgenic
Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.

PMID 19889237 · PMC2783166 · BMC genomics · 2009 · 8 claims · 8 setups

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scNT-MUC exhibit complete occlusive thrombi and absence of columnar epithelial layers not seen in control or scNT-N umbilical cords

umbilical porcine puvec histology immunostaining real-time

Experiments

Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.

Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

Proteomics technologies and challenges.

Liver fatty acid binding protein expression in colorectal neoplasia.

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

Proteomics analysis reveals novel components in the detergent-insoluble subproteome in Alzheimer's disease.

Characterization of detergent-insoluble proteins in ALS indicates a causal link between nitrative stress and aggregation in pathogenesis.

Quantitative mass spectrometry of diabetic kidney tubules identifies GRAP as a novel regulator of TGF-beta signaling.

MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.

An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

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.

Neuroscience in the era of functional genomics and systems biology.

Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.