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 alteration in gastic adenocarcinomas from Japanese patients.

  PMID 17187689 · PMC1774573 · Molecular cancer · 2006 · 7 claims · 2 setups

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  2D-EP and LC-ESI-MS/MS identified 69 different proteins in gastric tumor tissue, classifiable into cytoskeletal, stress/chaperone, glycolytic, metabolic, tumor suppressor, and stomach-specific categories.

  paired two-dimensional rt-pcr

• Toxicoproteomics: a parallel approach to identifying biomarkers.

  PMID 12940285 · PMC1241639 · Environmental health perspectives · 2003 · 8 claims · 8 setups

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  Combining parallel DNA microarray and proteomic analyses on the same tissues merges microarray's gene discovery power with proteomics' ability to exploit post-translational modifications for biomarker identification.

  liver serum peptide digested two-dimensional seldi maldi

• PHProteomicDB: a module for two-dimensional gel electrophoresis database creation on personal web sites.

  PMID 16970552 · PMC5054057 · Genomics, proteomics & bioinformatics · 2006 · 6 claims · 1 setups

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  PHProteomicDB is a PHP-written module that lets researchers share two-dimensional gel electrophoresis (2-DE) data on personal web sites without needing PHP or database expertise.

  umbilical two-dimensional

• 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

• Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

  PMID 17127212 · PMC5054077 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 6 setups

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  GMFG is a cytokine-responsive protein in EPO-induced (erythroid) and G-CSF-induced (myeloid) hematopoietic lineage development

  ac133+ excised e14 tissues 2-de lc-ms rt-pcr

• Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

  PMID 16403238 · PMC1351203 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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  No NPC proteome database existed prior to this work despite availability of other cancer proteome databases

  nasopharyngeal excised subset monoisotopic 2-de maldi-tof q-tof

• 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

• In vivo pharmaco-proteomic analysis of hydroxyurea induced changes in the sickle red blood cell membrane proteome.

  PMID 19914412 · PMC2818491 · Journal of proteomics · 2010 · 8 claims · 4 setups

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  2D-DIGE combined with tandem mass spectrometry identified 32 distinct sickle RBC membrane proteins that significantly changed in abundance after in vivo HU therapy

  sickle excised patients 2d-dige tandem immunoblot

• 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

• 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

• Human blood plasma preparation for two-dimensional gel electrophoresis.

  PMID 17174613 · PMC7105212 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 8 claims · 6 setups

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  Plasma protein concentrations reflect the physiological/health state of an individual and can serve as disease biomarkers

  serum blood plasma maldi-ms orthogonal peptidomic

• BRCA1 and BRCA2 mutation carriers in the Breast Cancer Family Registry: an open resource for collaborative research.

  PMID 18704680 · PMC2775077 · Breast cancer research and treatment · 2009 · 8 claims · 8 setups

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  The Breast Cancer Family Registry is an open resource for collaborative interdisciplinary and translational studies of the genetic epidemiology of breast cancer.

  breast california ashkenazi full two-dimensional denaturing

• Proteomic analysis of aqueous humor from patients with myopia.

  PMID 18334949 · PMC2268849 · Molecular vision · 2008 · 7 claims · 6 setups

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  Total protein concentration in AH is significantly greater in high myopia patients than in non-myopic controls

  aqueous gels silver-stained trypsin-digested bradford two-dimensional silver

• Proteomics as a method for early detection of cancer: a review of proteomics, exhaled breath condensate, and lung cancer screening.

  PMID 18095050 · PMC2150625 · Journal of general internal medicine · 2008 · 8 claims · 7 setups

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  Protein expression is closely aligned with cellular activity, unlike genomic changes which may have no functional significance

  serum resected plasma lower microarray two-dimensional proteomic

• 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

• Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.

  PMID 18267303 · PMC5054231 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  Gene expression of INSR, VDR, IDE, Akt, IRS-1, IRS-2, GLUT4, and glycolytic pathway enzymes is decreased at least 50% in T2DM muscle and activated T-cells versus non-diabetic controls

  activated skeletal muscle altered affymetrix quantitative sirna

• 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

• Global proteome analysis of Leptospira interrogans.

  PMID 19663501 · PMC2757032 · Journal of proteome research · 2009 · 8 claims · 5 setups

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  563 proteins were identified in L. interrogans via combined iTRAQ and 2DGE proteomic analysis

  leptospira serum liver itraq two-dimensional immunoblot

• Chemical genomics: what will it take and who gets to play?

  PMID 11423004 · PMC138939 · Genome biology · 2001 · 8 claims · 8 setups

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  Scaling chemical genetics to a genome-wide 'chemical genomics' requires large, well-funded, multidisciplinary centers that integrate compound libraries, protein resources, automation, and profiling technology, and freely distribute data and reagents.

  iccb fluorescently yeast engineered cell-based small-molecule expression