ArticleNucleic acids research2020
piNET: a versatile web platform for downstream analysis and visualization of proteomics data.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 25 citations in OpenAlex.
- Recent advances in phosphoproteomics based on mass spectrometry and its clinical application prospects.Frontiers in pharmacology · 2026Review
- PTM encoding: decoding the mechanisms of exercise-induced metabolic memory through spatiotemporal modification networks.Frontiers in sports and active living · 2026Review
- Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data.Molecular & cellular proteomics : MCP · 2025Article
- Mice lacking acid-sensing ion channel 2 in the medial prefrontal cortex exhibit social dominance.Science advances · 2024Article
- Phosphoproteomic Characterization and Kinase Signature Predict Response to Venetoclax Plus 3+7 Chemotherapy in Acute Myeloid Leukemia.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Proteomics of novel induced pluripotent stem cell-derived vascular endothelial cells reveal extensive similarity with an immortalized human endothelial cell line.Physiological genomics · 2023Article
- PrIntMap-R: An Online Application for Intraprotein Intensity and Peptide Visualization from Bottom-Up Proteomics.Journal of proteome research · 2023Article
- From single- to multi-omics: future research trends in medicinal plants.Briefings in bioinformatics · 2023Article
- NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency.Scientific data · 2023Article
- qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast.Nucleic acids research · 2023Article
- Mass Spectrometric-Based Proteomics for Biomarker Discovery in Osteosarcoma: Current Status and Future Direction.International journal of molecular sciences · 2022Review
- Connecting omics signatures and revealing biological mechanisms with iLINCS.Nature communications · 2022Article
- Novel Molecular Networks and Regulatory MicroRNAs in Type 2 Diabetes Mellitus: Multiomics Integration and Interactomics Study.JMIR bioinformatics and biotechnology · 2022Article
- Article
- Tobacco smoking induces metabolic reprogramming of renal cell carcinoma.The Journal of clinical investigation · 2021Article
- Transcriptional Regulation of Cancer Immune Checkpoints: Emerging Strategies for Immunotherapy.Vaccines · 2020Review
- Argonaut: A Web Platform for Collaborative Multi-omic Data Visualization and Exploration.Patterns (New York, N.Y.) · 2020Article
- PINE: An Automation Tool to Extract and Visualize Protein-Centric Functional Networks.Journal of the American Society for Mass Spectrometry · 2020Article
- Multi-omics integration and interactomics reveals molecular networks and regulators of the beneficial effect of yoga and exercise.International journal of yogaArticle
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Authors and funding
22 authors at 13 institutions in 2 countries.
Funding
Abstract
Rapid progress in proteomics and large-scale profiling of biological systems at the protein level necessitates the continued development of efficient computational tools for the analysis and interpretation of proteomics data. Here, we present the piNET server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. The primary input for the server consists of a set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Several interconnected workflows can be used to generate: (i) interactive graphs and tables providing comprehensive annotation and mapping between peptides and proteins with PTM sites; (ii) high resolution and interactive visualization for enzyme-substrate networks, including kinases and their phospho-peptide targets; (iii) mapping and visualization of LINCS signature connectivity for chemical inhibitors or genetic knockdown of enzymes upstream of their target PTM sites. piNET has been built using a modular Spring-Boot JAVA platform as a fast, versatile and easy to use tool. The Apache Lucene indexing is used for fast mapping of peptides into UniProt entries for the human, mouse and other commonly used model organism proteomes. PTM-centric network analyses combine PhosphoSitePlus, iPTMnet and SIGNOR databases of validated enzyme-substrate relationships, for kinase networks augmented by DeepPhos predictions and sequence-based mapping of PhosphoSitePlus consensus motifs. Concordant LINCS signatures are mapped using iLINCS. For each workflow, a RESTful API counterpart can be used to generate the results programmatically in the json format. The server is available at http://pinet-server.org, and it is free and open to all users without login requirement.
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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.