ArticleMolecular & cellular proteomics : MCP2008
GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy.
Article in Molecular & cellular proteomics : MCP, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 357 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
357 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identification of IDUA and WNT16 Phosphorylation-Related Non-Synonymous Polymorphisms for Bone Mineral Density in Meta-Analyses of Genome-Wide Association Studies.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2016Pooled it
- KSDiffusion: conditional diffusion for kinase-specific phosphorylation site prediction under data-limited and imbalanced regimes.Briefings in bioinformatics · 2026Article
- KRAS-Driven Hypertranscription and Metastatic Dissemination in Colorectal Cancer Could be Overcome by Targeting the NMHC IIA/ PLK1 Signaling Axis with a Novel Acridine Derivative.International journal of biological sciences · 2026Article
- Exploring Deleterious Nonsynonymous SNPs in theGenetics research · 2026Article
- Delving Into the Depths ofHuman mutation · 2026Article
- A multi-omics landscape of programmed cell death in acetaminophen-induced acute kidney injury.Renal failure · 2025Article
- DNA-PKcs-Driven YAP1 Phosphorylation and Nuclear Translocation: a Key Regulator of Ferroptosis in Hyperglycemia-Induced Cardiac Dysfunction in Type 1 Diabetes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Inferring kinase-phosphosite regulation from phosphoproteome-enriched cancer multi-omics datasets.Briefings in bioinformatics · 2025Article
- p38α-eIF6-Nsun2 axis promotes ILC3's rapid response to protect host from intestinal inflammation.The Journal of experimental medicine · 2025Article
- Omic AI reveals new autophagy regulators from the Atg1 interactome inFrontiers in cell and developmental biology · 2025Article
- Kinase-substrate prediction using an autoregressive model.Computational and structural biotechnology journal · 2025Article
- GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis.Genomics, proteomics & bioinformatics · 2024Article
- Analysis of damaging non-synonymous SNPs in GPx1 gene associated with the progression of diverse cancers through a comprehensive in silico approach.Scientific reports · 2024Article
- Increased translation driven by non-canonical EZH2 creates a synthetic vulnerability in enzalutamide-resistant prostate cancer.Nature communications · 2024Article
- PI3K-AKT-mediated phosphorylation of Thr260 in CgCaspase-3/6/7 regulates heat-induced activation in oysters.Communications biology · 2024Article
- Mice lacking acid-sensing ion channel 2 in the medial prefrontal cortex exhibit social dominance.Science advances · 2024Article
- GBMPhos: A Gating Mechanism and Bi-GRU-Based Method for Identifying Phosphorylation Sites of SARS-CoV-2 Infection.Biology · 2024Article
- Attenphos: General Phosphorylation Site Prediction Model Based on Attention Mechanism.International journal of molecular sciences · 2024Article
- Cell Cycle-Specific Protein Phosphatase 1 (PP1) Substrates Identification Using Genetically Modified Cell Lines.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction.Genomics, proteomics & bioinformatics · 2023Review
297 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Identification of protein phosphorylation sites with their cognate protein kinases (PKs) is a key step to delineate molecular dynamics and plasticity underlying a variety of cellular processes. Although nearly 10 kinase-specific prediction programs have been developed, numerous PKs have been casually classified into subgroups without a standard rule. For large scale predictions, the false positive rate has also never been addressed. In this work, we adopted a well established rule to classify PKs into a hierarchical structure with four levels, including group, family, subfamily, and single PK. In addition, we developed a simple approach to estimate the theoretically maximal false positive rates. The on-line service and local packages of the GPS (Group-based Prediction System) 2.0 were implemented in Java with the modified version of the Group-based Phosphorylation Scoring algorithm. As the first stand alone software for predicting phosphorylation, GPS 2.0 can predict kinase-specific phosphorylation sites for 408 human PKs in hierarchy. A large scale prediction of more than 13,000 mammalian phosphorylation sites by GPS 2.0 was exhibited with great performance and remarkable accuracy. Using Aurora-B as an example, we also conducted a proteome-wide search and provided systematic prediction of Aurora-B-specific substrates including protein-protein interaction information. Thus, the GPS 2.0 is a useful tool for predicting protein phosphorylation sites and their cognate kinases and is freely available on line.
Indexed as
Identifiers
What OpenQuestion holds
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.