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 29

System / cell line: cancer ✕ Assay: spot ✕ Clear

Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

PMID 17303479 · PMC7105233 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 5 claims · 5 setups

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Pre-fractionation of plasma with immuno-affinity depletion and anion-exchange chromatography prior to 2D-DIGE substantially increases the number of detectable protein spots compared with unfractionated plasma.

plasma excised fractionated 2d-dige multi-dimensional lc-ms
sCellST predicts single-cell gene expression from H& E images.

PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

ovarian kidney prostate breast simulation spot-level nucleus
Proteomics as a tool for biomarker discovery.

PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

serum laser ovarian seldi-tof two-dimensional gene
Contribution of oncoproteomics to cancer biomarker discovery.

PMID 17407558 · PMC1852117 · Molecular cancer · 2007 · 6 claims · 8 setups

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Oncoproteomic biomarker panels (2-DE/MS-based) show higher sensitivity and specificity than currently used single tumor markers across multiple cancer types (Table 1)

serum bladder nipple colorectal 2-de isotope-coded immunoblotting
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
Proteomic analysis identifies MMP-9, DJ-1 and A1BG as overexpressed proteins in pancreatic juice from pancreatic ductal adenocarcinoma patients.

PMID 18706098 · PMC2528014 · BMC cancer · 2008 · 7 claims · 6 setups

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MMP-9, DJ-1 and A1BG are overexpressed in pancreatic juice and tissue from PDAC patients compared with cancer-free/normal controls

pooled individual trypsin-digested pancreatic two-dimensional difference maldi-tof-ms
Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups

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Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid

bxpc-3 2-d maldi-tof-ms western
Detection of p53 mutations in precancerous gastric tissue.

PMID 14520466 · PMC2394306 · British journal of cancer · 2003 · 8 claims · 6 setups

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p53 mutations can be detected in precancerous gastritis and intestinal metaplasia tissue using the restriction site mutation (RSM) assay

gastric enzyme-resistant gastritis pylori-positive restriction sequencing electron
Proteomic-based identification of haptoglobin-1 precursor as a novel circulating biomarker of ovarian cancer.

PMID 15199385 · PMC2364749 · British journal of cancer · 2004 · 7 claims · 7 setups

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Six serum protein spots (~40 kDa, pI 5.9–6.6) significantly overexpressed in grade 1, 2 and 3 ovarian cancer patients were identified by MALDI-TOFMS and n-ESIQ(q)TOFMS as isoforms of haptoglobin-1 precursor (HAP1)

serum tryptic 2de-separated paraffin-embedded two-dimensional affi-gel maldi-tofms
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
Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human.

PMID 17127214 · PMC5054074 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 7 setups

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15 differential protein spots were detected in 11 of 12 (91.7%) breast cancer tissue samples compared with adjacent normal tissue

breast spots 2d-page stained sds-page 2d-page maldi-tof
Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource.

PMID 16507150 · PMC1413975 · Breast cancer research : BCR · 2006 · 6 claims · 7 setups

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kConFab is a collaborative resource providing epidemiological, clinical, and biospecimen data from high-risk familial breast/ovarian cancer families, available to researchers worldwide for ethically approved, peer-reviewed projects.

germline unaffected index randomly brca1 tyrer-cuzick strp
Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

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Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

apc-deficient heart ileum fresh-frozen spatial high-resolution bulk
Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues.

PMID 12865921 · PMC2394238 · British journal of cancer · 2003 · 6 claims · 3 setups

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Hierarchical cluster analysis of 2-DE proteome data can distinguish normal breast, benign breast, and breast cancer tissues based on protein expression profiles

breast two-dimensional hierarchical mann-whitney
Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner.

PMID 41760664 · PMC13066420 · Nature communications · 2026 · 8 claims · 8 setups

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CellRefiner is a physical/particle-based model (subcellular element method) that integrates scRNA-seq and spatial transcriptomics data to reconstruct single-cell resolution spatial data

hypothalamic embryo hippocampus visual merfish seqfish slide-seqv2
Protein expression patterns in primary carcinoma of the vagina.

PMID 15199389 · PMC2409807 · British journal of cancer · 2004 · 5 claims · 4 setups

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Cluster analysis of 2-DE proteomic data allows accurate discrimination between normal vaginal mucosa, primary vaginal carcinoma and primary cervical carcinoma

fresh-frozen excised normal same two-dimensional matrix-assisted hierarchical
A novel approach for determining cancer genomic breakpoints in the presence of normal DNA.

PMID 17440616 · PMC1847701 · PloS one · 2007 · 8 claims · 6 setups

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PAMP enriches deletion-breakpoint-spanning DNA because shorter mutant amplicons are preferentially amplified over much longer wild-type sequences when using approximated flanking primer pairs.

detroit serial hs578t pamp individual nested
transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics.

PMID 41645434 · PMC12930851 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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transFusion is a comprehensive, web-based platform for integrated analysis of scRNA-seq and 10x Visium spatial transcriptomics data requiring no parameter configuration

breast scrna-seq 10x cellphonedb
PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.

PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 7 claims · 6 setups

Has reproduction · 75

The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival

pbmcs sorted expanded cancer multiparameter receptor targeted
Validation of reverse phase protein array for practical screening of potential biomarkers in serum and plasma: accurate detection of CA19-9 levels in pancreatic cancer.

PMID 18615426 · PMC2992687 · Proteomics · 2008 · 8 claims · 6 setups

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RPPA-measured CA19-9 levels correlate strongly with ELISA-measured levels in the same patient samples

serum same pancreatic candidate reverse elisa rppa

Experiments

Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

sCellST predicts single-cell gene expression from H& E images.

Proteomics as a tool for biomarker discovery.

Contribution of oncoproteomics to cancer biomarker discovery.

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

Proteomic analysis identifies MMP-9, DJ-1 and A1BG as overexpressed proteins in pancreatic juice from pancreatic ductal adenocarcinoma patients.

Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

Detection of p53 mutations in precancerous gastric tissue.

Proteomic-based identification of haptoglobin-1 precursor as a novel circulating biomarker of ovarian cancer.

Liver fatty acid binding protein expression in colorectal neoplasia.

Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human.

Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource.

Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues.

Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner.

Protein expression patterns in primary carcinoma of the vagina.

A novel approach for determining cancer genomic breakpoints in the presence of normal DNA.

transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics.

PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.

Validation of reverse phase protein array for practical screening of potential biomarkers in serum and plasma: accurate detection of CA19-9 levels in pancreatic cancer.