ArticleNucleic acids research2011
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 78 citations in OpenAlex.
- Manganese availability determines insulin sensitivity by enhancing Akt activity.bioRxiv : the preprint server for biology · 2026Article
- Phosphoproteomics Data-Driven Integrative Analysis of Autophosphorylation Sites in the Human Kinome.International journal of molecular sciences · 2026Article
- EPSD 2.0: An Updated Database of Protein Phosphorylation Sites Across Eukaryotic Species.Genomics, proteomics & bioinformatics · 2025Article
- Inferring kinase-phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasets.Briefings in bioinformatics · 2025Article
- SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation.Nature communications · 2025Article
- Insight into Protein Engineering: FromCurrent pharmaceutical design · 2025Review
- A web portal for exploring kinase-substrate interactions.NPJ systems biology and applications · 2024Article
- Unique ligand and kinase-independent roles of the insulin receptor in regulation of cell cycle, senescence and apoptosis.Nature communications · 2023Article
- An integrated network representation of multiple cancer-specific data for graph-based machine learning.NPJ systems biology and applications · 2022Article
- dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.Nucleic acids research · 2022Article
- Signaling defects associated with insulin resistance in nondiabetic and diabetic individuals and modification by sex.The Journal of clinical investigation · 2021Article
- Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA).BMC cancer · 2021Article
- Temporal dynamics of the host molecular responses underlying severe COVID-19 progression and disease resolution.EBioMedicine · 2021Article
- A Cell-Autonomous Signature of Dysregulated Protein Phosphorylation Underlies Muscle Insulin Resistance in Type 2 Diabetes.Cell metabolism · 2020Article
- GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System.International journal of molecular sciences · 2020Article
- KSP: an integrated method for predicting catalyzing kinases of phosphorylation sites in proteins.BMC genomics · 2020Article
- piNET: a versatile web platform for downstream analysis and visualization of proteomics data.Nucleic acids research · 2020Article
- Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources.Clinical proteomics · 2020Review
- Capsule network for protein post-translational modification site prediction.Bioinformatics (Oxford, England) · 2019Article
- dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.Nucleic acids research · 2019Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of experimental phosphorylation sites that has been identified by mass spectrometry-based proteomics, the desire to explore the networks of protein kinases and substrates is motivated. Manning et al. have identified 518 human kinase genes, which provide a starting point for comprehensive analysis of protein phosphorylation networks. In this study, a knowledgebase is developed to integrate experimentally verified protein phosphorylation data and protein-protein interaction data for constructing the protein kinase-substrate phosphorylation networks in human. A total of 21,110 experimental verified phosphorylation sites within 5092 human proteins are collected. However, only 4138 phosphorylation sites (∼20%) have the annotation of catalytic kinases from public domain. In order to fully investigate how protein kinases regulate the intracellular processes, a published kinase-specific phosphorylation site prediction tool, named KinasePhos is incorporated for assigning the potential kinase. The web-based system, RegPhos, can let users input a group of human proteins; consequently, the phosphorylation network associated with the protein subcellular localization can be explored. Additionally, time-coursed microarray expression data is subsequently used to represent the degree of similarity in the expression profiles of network members. A case study demonstrates that the proposed scheme not only identify the correct network of insulin signaling but also detect a novel signaling pathway that may cross-talk with insulin signaling network. This effective system is now freely available at http://RegPhos.mbc.nctu.edu.tw.
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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.