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).

• 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

• 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

• Pathway analysis of kidney cancer using proteomics and metabolic profiling.

  PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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  31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

  ccrcc rcc computational random gel immunoblotting immunohistochemistry

• Alcohol consumption and breast tumor mitochondrial DNA mutations.

  PMID 19847642 · PMC4403627 · Breast cancer research and treatment · 2010 · 8 claims · 6 setups

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  Somatic mtDNA mutations are a frequent occurrence in breast tumors

  breast paraffin-embedded blood study ttge sequencing immunohistochemistry

• 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

• Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer.

  PMID 16620376 · PMC1459869 · BMC cancer · 2006 · 8 claims · 3 setups

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  Somatic mtDNA mutations are frequent in esophageal cancer, found in 55% (11/20) of tumors analyzed

  paired fragments ttge direct real-time

• Characterisation and protein expression profiling of annexins in colorectal cancer.

  PMID 18071363 · PMC2361450 · British journal of cancer · 2008 · 7 claims · 5 setups

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  Annexins A1, A2, A4 and A11 are overexpressed in primary colorectal cancer compared with normal colon

  dukes colorectal immunised whole-cell gel immunohistochemistry elisa

• Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

  PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups

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  Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung

  matched excised additional formalin-fixed 2-d lc-ms quantitative

• High rates of loss of heterozygosity on chromosome 19p13 in human breast cancer.

  PMID 11207044 · PMC2363776 · British journal of cancer · 2001 · 8 claims · 4 setups

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  The SAFB locus region on chromosome 19p13.2-3 shows a very high rate of loss of heterozygosity (LOH) in primary breast cancer, indicating presence of a breast tumour-suppressor gene locus

  breast microdissected loh rt-pcr pcr

• Comparing protein abundance and mRNA expression levels on a genomic scale.

  PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

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  Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

  yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded

• 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

• 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 RCL2 paraffin-embedded tissues.

  PMID 19012729 · PMC4506168 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

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  RCL2-fixed paraffin-embedded (RCL2P) tissue consistently gives the highest protein yield compared to FFPE and frozen tissue across extraction protocols

  normal rcl2p ffpe frozen yield 1-dimensional 2-dimensional

• Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

  PMID 19011008 · PMC2719557 · Investigative ophthalmology & visual science · 2009 · 6 claims · 5 setups

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  TGFBIp (multiple molecular weight forms) is significantly overexpressed in FECD HCEC-DM complex compared to normal endothelium

  pooled hcec-dm corneal 2-d western real-time

• Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

  PMID 10389971 · PMC2363009 · British journal of cancer · 1999 · 6 claims · 5 setups

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  Microsatellite instability is common in sporadic pancreatic cancer but occurs at a uniformly low rate and is not accompanied by hMLH1/hMSH2 alterations, suggesting it does not drive pancreatic tumorigenesis.

  sporadic msi-positive tumour unstable microsatellite denaturing sequencing

• Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

  PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

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  B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

  paraffin-embedded cloned same predicted pcr cloning blastx

• Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma.

  PMID 18672925 · PMC2680441 · Journal of proteome research · 2008 · 8 claims · 6 setups

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  34 immunoreactive protein spots were detected in 2DE Western blots probed with HCC patient sera but not normal sera

  hepg2 excised identified recombinant two-dimensional western in-gel

• The spectrum of ATM missense variants and their contribution to contralateral breast cancer.

  PMID 17393301 · PMC2137941 · Breast cancer research and treatment · 2008 · 6 claims · 3 setups

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  ATM missense variant frequency does not differ significantly between CBC and UBC patients, indicating no major impact on overall CBC risk

  germline breast denaturing sanger case-control

• Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

  PMID 16515697 · PMC1448207 · BMC medical genetics · 2006 · 8 claims · 7 setups

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  CMS compares IBS allele/genotype sharing between distantly related (beyond grandparental) affected and unaffected individuals from founder populations to detect disease loci while reducing confounding from population stratification and genetic heterogeneity.

  amish unrelated same overall microsatellite combinatorial permutation

• Fucosylated glycoproteins as markers of liver disease.

  PMID 19126969 · PMC3827789 · Disease markers · 2008 · 8 claims · 6 setups

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  Core alpha 1,6-linked fucosylation of AFP (AFP-L3) is increased in HCC and is a more specific marker of HCC than total AFP

  afp pooled larger igg lectin fucose-specific immunoblot