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).

• 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

• Proteomic analysis of serum in lung cancer induced by 3-methylcholanthrene.

  PMID 19794824 · PMC2753780 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 4 setups

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  141 protein spots are differentially expressed between normal rat sera and MCA-induced lung cancer rat sera (82 overexpressed, 59 underexpressed)

  serum lung excised two-dimensional maldi-tof-ms histopathology

• Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

  PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

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  85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

  paired list differentially oscc 2-de gene interaction

• Three-dimensional neuroblastoma cell culture: proteomic analysis between monolayer and multicellular tumor spheroids.

  PMID 18797883 · PMC2804865 · Pediatric surgery international · 2008 · 7 claims · 3 setups

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  18 protein spots were differentially over-expressed in neuroblastoma spheroids compared to monolayers

  neuroblastoma excised monolayer 2-d lc-ms fractionation

• A statistical model to identify differentially expressed proteins in 2D PAGE gels.

  PMID 19763172 · PMC2734266 · PLoS computational biology · 2009 · 7 claims · 5 setups

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  A mixture likelihood model incorporating both detected and non-detected proteins has higher statistical power to detect differential expression than standard approaches like the Student's t-test.

  plasma simulated page simulated

• The effects of quercetin on SW480 human colon carcinoma cells: a proteomic study.

  PMID 15748282 · PMC555539 · Nutrition journal · 2005 · 8 claims · 4 setups

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  20 μM quercetin treatment of SW480 cells for 48 h consistently decreased expression of three proteins and increased expression of one protein across four independent experiments.

  sw480 excised two-dimensional quantitative mass

• 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

• An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis.

  PMID 18179696 · PMC2231339 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  AGML 2.0 is a comprehensive XML representation for 2-DE experiments comprising identification, protocol (MI2DG), and gel sections

  general gel excised clinical 2-dimensional differential mass

• Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.

  PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups

  Has reproduction · 80

  Combining WGCNA hub genes and VAE 10-dimensional representation as features for an SVM classifier achieves high accuracy in predicting CRC

  colorectal same combined meturquoise microarray differential batch

• Human neuronal cell protein responses to Nipah virus infection.

  PMID 17553172 · PMC1896155 · Virology journal · 2007 · 8 claims · 4 setups

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  NiV infection induces differential protein expression in SK-N-MC human neuronal cells detectable by 2D-PAGE

  sk-n-mc spots 2d-page maldi-tof tandem

• Application of proteomics methods for pathogen discovery.

  PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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  Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

  hlf sequences synthetic conventional 2d-dige gelc-ms

• Proteomic approaches for studying alcoholism and alcohol-induced organ damage.

  PMID 23584750 · PMC3860448 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 8 claims · 7 setups

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  Chronic alcohol abuse produces persistent changes in brain function (tolerance, dependence, craving) likely resulting from alterations in gene and protein expression

  extracts trypsin-digested more yeast two-dimensional liquid mudpit

• Molecular markers of preterm labor in the choriodecidua.

  PMID 20009011 · PMC2852874 · Reproductive sciences (Thousand Oaks, Calif.) · 2010 · 8 claims · 4 setups

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  Preterm choriodecidua displays distinct gene and protein expression patterns associated with preterm labor

  choriodecidual excised differentially microarray two-dimensional mass

• Multidimensional proteomics analysis of amniotic fluid to provide insight into the mechanisms of idiopathic preterm birth.

  PMID 18431506 · PMC2315798 · PloS one · 2008 · 7 claims · 7 setups

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  A novel 5-peak SELDI proteomic signature (Q-profile) in the 10-12.5 kDa mass range identifies a subgroup of women at risk for preterm birth without intra-amniotic inflammation or bleeding.

  amniotic excised spot differentially seldi-tof fluorescence robotic

• 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

• The proteogenomic path towards biomarker discovery.

  PMID 18764911 · PMC2574627 · Pediatric transplantation · 2008 · 8 claims · 8 setups

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  Serum creatinine is a widely used but non-ideal biomarker for renal transplant monitoring because it lacks specificity and sensitivity for graft injury

  renal urine breast chronic microarray immunoassay gel

• Autoencoder Networks Decipher the Association between Lung Cancer and Alzheimer's Disease.

  PMID 36518809 · PMC9744611 · Computational intelligence and neuroscience · 2022 · 7 claims · 6 setups

  Has reproduction · 74

  AE networks trained on the 266 shared DEGs reveal a comorbidity (positive correlation) relationship between Alzheimer's disease and lung cancer, rather than the inverse relationship suggested by prior epidemiological studies.

  integrated expression overlapped moderated autoencoder pathway

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential

• Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

  PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

  lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell

• The diagnosis and management of pre-invasive breast disease: promise of new technologies in understanding pre-invasive breast lesions.

  PMID 14580250 · PMC314415 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

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  ADH and ductal carcinoma in situ (DCIS) are precursor lesions molecularly similar to adjacent invasive breast cancer

  locally adh brca1 malignant array chromosome-based cdna