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 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

• 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

• 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

• 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

• 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

• Characterization of detergent-insoluble proteins in ALS indicates a causal link between nitrative stress and aggregation in pathogenesis.

  PMID 19956584 · PMC2780298 · PloS one · 2009 · 8 claims · 8 setups

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  The Triton X-100-insoluble fraction (TIF) from spinal cord of G93A SOD1 mice is enriched in specific proteins (cytoskeletal, chaperone, mitochondrial, metabolic, signaling) compared to WT mice, already at a preclinical stage.

  spinal tif lumbar ventral gel maldi-tof western

• The current state of proteomics in GI oncology.

  PMID 19104933 · PMC3045515 · Digestive diseases and sciences · 2009 · 8 claims · 8 setups

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  More than 130 exploratory proteomic studies have defined candidate biomarkers in serum, GI fluids, or cancer tissue for GI oncology

  serum laser-capture-microdissected seldi-ms 2-de antibody

• 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

• 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

• Adipose proteome analysis: focus on mediators of insulin resistance.

  PMID 19086862 · PMC2651673 · Expert review of proteomics · 2008 · 8 claims · 5 setups

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  Ectopic lipid accumulation in liver and muscle, resulting from impaired adipose tissue lipid-storage capacity, is more directly associated with insulin resistance than adipose tissue mass itself.

  3t3-l1 adipose visceral 35s-radiolabeling gel seldi-tof

• KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

  PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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  KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

  diffuse-type liver renal anaplastic differential proteomic proteomics

• 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

• Transcriptional and proteomic profiling in a cellular model of DYT1 dystonia.

  PMID 19665049 · PMC2774817 · Neuroscience · 2009 · 8 claims · 7 setups

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  Accumulation of mutant torsinA(ΔE) in the nuclear envelope is not sufficient to cause transcriptional dysregulation

  pc6-3 hek293 microarray 2-dige mass

• 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

• 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