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).

• Evidence for a minimal eukaryotic phosphoproteome?

  PMID 17712425 · PMC1945084 · PloS one · 2007 · 8 claims · 3 setups

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  Divergence in eukaryotic kinases at the primary sequence level is not reflected at the level of substrate phosphorylation.

  lysates lysate pepchip peptide labelling statistical

• Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

  PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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  Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

  lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry

• Functional proteomics of failed filtering blebs.

  PMID 20019882 · PMC2793902 · Molecular vision · 2009 · 8 claims · 6 setups

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  Eight proteins are differentially expressed between failed filtering bleb Tenon's tissue and control Tenon's capsule, identified by 2D-electrophoresis proteomics and MALDI-TOF MS

  tenon's nih3t3 gel western immunohistochemistry

• 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

• Identification of proteins differentially expressed in the conventional renal cell carcinoma by proteomic analysis.

  PMID 15953868 · PMC2782202 · Journal of Korean medical science · 2005 · 6 claims · 4 setups

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  Eight proteins from 11 differentially expressed spots were identified in conventional RCC versus normal kidney tissue by 2D-PAGE and MALDI-TOF-MS

  conventional trypsin-digested lysates 2d-page maldi-tof bradford

• 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

• Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma.

  PMID 18839982 · PMC3204659 · Journal of proteome research · 2008 · 7 claims · 4 setups

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  Golgi membrane protein 1 (GOLM1/GP73), Annexin IV, and Eps8 are validated candidate biomarkers for cholangiocarcinoma

  membrane bile 18o-labeling sds-page western

• A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma.

  PMID 18715028 · PMC3769105 · Journal of proteome research · 2008 · 8 claims · 3 setups

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  iTRAQ-based quantitative LC-MS/MS proteomics can identify and quantitate differentially expressed proteins between HCC tumor and adjacent noncancerous liver tissue

  hcv-associated hcc formalin-fixed itraq western immunohistochemical

• Increase in endoplasmic reticulum stress-related proteins and genes in adipose tissue of obese, insulin-resistant individuals.

  PMID 18567819 · PMC2518495 · Diabetes · 2008 · 8 claims · 3 setups

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  UPR/ER stress-related proteins (calreticulin, PDI A3, glutathione-S-transferase P) are upregulated in adipose tissue of obese versus lean humans

  subcutaneous same adipose two-dimensional western real-time

• Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks.

  PMID 19011694 · PMC2582945 · PloS one · 2008 · 8 claims · 8 setups

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  A 16-microRNA signature (9 up, 7 down) distinguishes osteoarthritic from normal cartilage.

  patient-derived normal integrated taqman qrt-pcr northern

• Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

  PMID 18212748 · PMC2243141 · British journal of cancer · 2008 · 5 claims · 6 setups

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  LC-MS/MS proteomic analysis of stage I lung adenocarcinoma specimens identified myosin IIA and vimentin as candidate biomarker proteins with signal intensities that differed significantly among patient outcome groups

  surgically tryptic set lysates lc-ms mascot immunohistochemistry

• Immunohistochemical and proteomic evaluation of nuclear ubiquitous casein and cyclin-dependent kinases substrate in invasive ductal carcinoma of the breast.

  PMID 20069058 · PMC2801467 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 5 setups

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  NUCKS is highly overexpressed in invasive ductal carcinoma (IDC) of the breast compared to matched normal tissue.

  matched idc nucks rabbits lc-ms sds-page western

• The use of neuroproteomics in drug abuse research.

  PMID 19926406 · PMC3947580 · Drug and alcohol dependence · 2010 · 8 claims · 8 setups

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  Neuroproteomic technologies (2D-DIGE, iTRAQ, ICAT, etc.) enable identification of protein-level changes underlying effects of drugs of abuse such as amphetamine, morphine, cocaine, and alcohol.

  rodent brain postmortem sectioned 2d-dige itraq heat

• Proteomic studies of cholangiocarcinoma and hepatocellular carcinoma cell secretomes.

  PMID 20069059 · PMC2801507 · Journal of biomedicine & biotechnology · 2010 · 7 claims · 5 setups

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  The secretomes of cholangiocarcinoma (HuCCA-1) and four hepatocellular carcinoma cell lines show distinct, differing protein profiles.

  hucca-1 same conditioned paired sds-page trypan 1-de

• GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

  PMID 16919418 · PMC2842930 · Genomics · 2006 · 8 claims · 8 setups

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  Human FXN YAC transgenes containing GAA repeat expansions (YG22, YG8) rescue the embryonic lethality of homozygous Fxn knockout mice

  yg22 tissues lysates sciatic breeding semiquantitative western

• Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

  PMID 19936259 · PMC2775948 · PloS one · 2009 · 8 claims · 8 setups

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  Integrated proteomic analysis of a cancer mouse model and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

  k-ras ovarian lists tumor quantitative pathway immunoblot

• Serum S100A6 concentration predicts peritoneal tumor burden in mice with epithelial ovarian cancer and is associated with advanced stage in patients.

  PMID 19888321 · PMC2765613 · PloS one · 2009 · 8 claims · 8 setups

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  Serum S100A6 concentration correlates with peritoneal tumor burden in a mouse OVCA xenograft model, based on inverse regression calibration against bioluminescent imaging data.

  serum skov-3 pooled ovca lc-ms antigen whole-animal