ArticleBioinformatics (Oxford, England)2013
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 6 citations in OpenAlex.
- Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources.Methods in molecular biology (Clifton, N.J.) · 2021Article
- A Mini-review of the Computational Methods Used in Identifying RNA 5-Methylcytosine Sites.Current genomics · 2020Review
- Article
- A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.Nucleic acids research · 2014Article
- A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
motivationProtein phosphorylation is critical for regulating cellular activities by controlling protein activities, localization and turnover, and by transmitting information within cells through signaling networks. However, predictions of protein phosphorylation and signaling networks remain a significant challenge, lagging behind predictions of transcriptional regulatory networks into which they often feed.
resultsWe developed PhosphoChain to predict kinases, phosphatases and chains of phosphorylation events in signaling networks by combining mRNA expression levels of regulators and targets with a motif detection algorithm and optional prior information. PhosphoChain correctly reconstructed ∼78% of the yeast mitogen-activated protein kinase pathway from publicly available data. When tested on yeast phosphoproteomic data from large-scale mass spectrometry experiments, PhosphoChain correctly identified ∼27% more phosphorylation sites than existing motif detection tools (NetPhosYeast and GPS2.0), and predictions of kinase-phosphatase interactions overlapped with ∼59% of known interactions present in yeast databases. PhosphoChain provides a valuable framework for predicting condition-specific phosphorylation events from high-throughput data. AVAILABILITY: PhosphoChain is implemented in Java and available at http://virgo.csie.ncku.edu.tw/PhosphoChain/ or http://aitchisonlab.com/PhosphoChain
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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.