ArticleJournal of the American Society for Mass Spectrometry2020
PINE: An Automation Tool to Extract and Visualize Protein-Centric Functional Networks.
Article in Journal of the American Society for Mass Spectrometry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed, 34 citations in OpenAlex.
- Evaluating the mechanism of action behind controlled hypothermic preservation of donor hearts: A randomized pilot study.The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation · 2025Trial
- Dynamic Remodeling of the Human Milk Serum Proteome Across Lactation: A Paired Two-Stage DIA Proteomic Study in Term and Preterm Mothers.Nutrients · 2026Article
- Time-resolved urinary proteomics reveals heme-associated oxidative stress responses in neonatal hypoxic-ischaemic encephalopathy.Molecular and cellular pediatrics · 2026Article
- Takotsubo Syndrome: The First Non-Acute Proteomic Analysis by Remote Dried Blood Microsampling.Journal of cardiovascular translational research · 2026Article
- Preterm functional outcomes are reflected in early postnatal proteome changes.Pediatric research · 2026Article
- Uncovering Urinary Proteome Differences in Very Preterm Infants with and without Preterm Brain Injury.Journal of proteome research · 2025Article
- Targeting the Opioid System in Cardiovascular Disease: Liver Proteomic and Lipid Profile Effects of Naloxone in Atherosclerosis.Biomedicines · 2025Article
- Dysregulation of protein SUMOylation networks in Huntington's disease R6/2 mouse striatum.Brain : a journal of neurology · 2025Article
- Integrated Profiling Identifies Long-Term Molecular Consequences of Prenatal Dexamethasone Treatment in the Rat Brain-Potential Triggers of Depressive Phenotype and Cognitive Impairment.Molecular neurobiology · 2025Article
- Article
- Identification of Disease-Relevant, Sex-Based Proteomic Differences in iPSC-Derived Vascular Smooth Muscle Cells.International journal of molecular sciences · 2024Article
- Alterations in plasma proteome during acute COVID-19 and recovery.Molecular medicine (Cambridge, Mass.) · 2024Article
- The Influence of the FFAR4 Agonist TUG-891 on Liver Steatosis in ApoE-Knockout Mice.Cardiovascular drugs and therapy · 2024Article
- Proteomics of the heart.Physiological reviews · 2024Review
- Physiological healing of chronic gastric ulcer is not impaired by the hydrogen sulphide (HInflammopharmacology · 2024Article
- Article
- High-Field Asymmetric Waveform Ion Mobility Spectrometry: Practical Alternative for Cardiac Proteome Sample Processing.Journal of proteome research · 2023Article
- A panel of blood biomarkers unique to sudden cardiac arrest.Heart rhythm · 2023Article
- Hyperphosphorylation of hepatic proteome characterizes nonalcoholic fatty liver disease in S-adenosylmethionine deficiency.iScience · 2023Article
- Proteomics research in forest trees: A 2012-2022 update.Frontiers in plant science · 2023Review
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Recent surges in mass spectrometry-based proteomics studies demand a concurrent rise in speedy and optimized data processing tools and pipelines. Although several stand-alone bioinformatics tools exist that provide protein-protein interaction (PPI) data, we developed Protein Interaction Network Extractor (PINE) as a fully automated, user-friendly, graphical user interface application for visualization and exploration of global proteome and post-translational modification (PTM) based networks. PINE also supports overlaying differential expression, statistical significance thresholds, and PTM sites on functionally enriched visualization networks to gain insights into proteome-wide regulatory mechanisms and PTM-mediated networks. To illustrate the relevance of the tool, we explore the total proteome and its PTM-associated relationships in two different nonalcoholic steatohepatitis (NASH) mouse models to demonstrate different context-specific case studies. The strength of this tool relies in its ability to (1) perform accurate protein identifier mapping to resolve ambiguity, (2) retrieve interaction data from multiple publicly available PPI databases, and (3) assimilate these complex networks into functionally enriched pathways, ontology categories, and terms. Ultimately, PINE can be used as an extremely powerful tool for novel hypothesis generation to understand underlying disease mechanisms.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.