ArticleBioinformatics (Oxford, England)2019
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 1 of them a synthesis that pooled it.
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Who cites it
42 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of cellular phosphoproteome datasets exploring phospho-signaling associated with the RNA-binding protein RAVER1.Scientific reports · 2026Pooled it
- Phosphoproteomic Data Integration Reveals Paralog-Specific Co-Regulatory Networks of Rho-Associated Kinases ROCK1 and ROCK2.International journal of molecular sciences · 2026Article
- Systematic Analysis of MRTFB Phosphoproteomic Datasets Reveals Co-Regulated Kinase Networks and Co-Occurring Phosphosites Associated with the Actin Cytoskeleton Pathway.Current issues in molecular biology · 2026Article
- Decoding MTSS2 phosphoregulation: its role in cytoskeletal dynamics and clinical implications.Protoplasma · 2026Review
- Phosphoproteomics Data-Driven Integrative Analysis of Autophosphorylation Sites in the Human Kinome.International journal of molecular sciences · 2026Article
- Deciphering Site-Specific Regulatory Networks of the Kinesin Protein KIF21A Through Integrative Phosphoproteomic Analysis.International journal of molecular sciences · 2026Article
- Co-Phosphoregulatory Network Underlying Functional Coherence of TLK1 and TLK2 Kinase Paralogs.International journal of molecular sciences · 2026Article
- Exploring the AAK1 Phospho-signaling Landscape Through Phospho-centric Co-regulation Network.Cell biochemistry and biophysics · 2026Article
- Phosphosite-specific co-regulation networks of MELK kinase: insights from integrative global phosphoproteomes.Journal, genetic engineering & biotechnology · 2026Article
- Site-Specific Phosphoproteomic Profiling of CAV1 Reveals Co-Regulatory Kinase Networks in Cancer Signaling.International journal of molecular sciences · 2026Article
- Integrative phosphoproteomic network analysis identifies CAMK2D as a shared regulator of TPD52 family proteins in cancer.Protoplasma · 2026Article
- Exploring the Phosphoregulatory Network of Human Sucrose Non-Fermenting 1-Related Kinase.Biology · 2026Article
- Computational Phosphosite-Specific Network Analysis of YES1 Y426 Reveals Cancer-Associated Phosphorylation Patterns.Proteomes · 2026Article
- Integrative phosphoproteomic analysis reveals co-regulatory phosphorylation networks of rhotekin in cancer progression.Discover oncology · 2026Article
- Emergence of Catalytic Activity in VRK3: Phosphoproteomic Insights into the Regulatory Network of a Former Pseudokinase.Proteomes · 2026Review
- Phosphorylation-dependent regulation of Eleven Lysine Rich Leukemia (ELL) uncovered by quantitative global phosphoproteomic analysis.Molecular genetics and genomics : MGG · 2026Article
- Comparative Phosphoproteomic Profiling and Network-based Interactome Analysis of GRK5 and GRK6.Cell biochemistry and biophysics · 2026Article
- Dissecting the Phospho-Regulatory Landscape of Protein Kinase N1 (PKN1) and Its Downstream Signaling: Functional Insights into the Activity-Dependent and Disease-Relevant Phosphosites.International journal of molecular sciences · 2026Article
- Phosphoproteomic Landscape of HDLBP: Insights into Function and Disease Associations.International journal of molecular sciences · 2026Article
- Proteome-Wide Analysis of Functional Phosphosites in the FGFR Family of Proteins: Insights from Large-Scale Phosphoproteomic Analysis.Proteomes · 2026Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Signaling and metabolic pathways are finely regulated by a network of protein phosphorylation events. Unraveling the nature of this intricate network, composed of kinases, target proteins and their interactions, is therefore of crucial importance. Although thousands of kinase-specific phosphorylations (KsP) have been annotated in model organisms their kinase-target network is far from being complete, with less studied organisms lagging behind. Results: In this work, we achieved an automated and accurate identification of kinase domains, inferring the residues that most likely contribute to peptide specificity. We integrated this information with the target peptides of known human KsP to predict kinase-specific interactions in other eukaryotes through a deep neural network, outperforming similar methods. We analyzed the differential conservation of kinase specificity among eukaryotes revealing the high conservation of the specificity of tyrosine kinases. With this approach we discovered 1590 novel KsP of potential clinical relevance in the human proteome. Availability and implementation: http://akid.bio.uniroma2.it. Supplementary information: Supplementary data are available at Bioinformatics online.
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