ArticleBioinformatics (Oxford, England)2017
Benchmarking substrate-based kinase activity inference using phosphoproteomic data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 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
54 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry.Nature communications · 2023Pooled it
- Multi-omics profiling identifies triciribine as a biomarker-guided antimetabolite therapy for acute lymphoblastic leukemia.NPJ precision oncology · 2026Article
- A cell-impermeable kinase inhibitor uncovers outside-in signaling pathways that promote HIV-1 infection.Journal of virology · 2026Article
- Integrative multi-omics analysisiScience · 2025Article
- HIV-1 latency reversing agents converge on phosphoregulation of nuclear protein complexes.bioRxiv : the preprint server for biology · 2025Article
- Proteomic sensors for quantitative multiplexed and spatial monitoring of kinase signaling.Nature communications · 2025Article
- Sex-specific phosphoproteome responses to calorie restriction and insulin in skeletal muscle from older rats.The journals of gerontology. Series A, Biological sciences and medical sciences · 2025Article
- An integrated proteomics approach identifies phosphorylation sites on viral and host proteins that regulate West Nile virus infection.Cell reports · 2025Article
- Comprehensive evaluation of phosphoproteomic-based kinase activity inference.Nature communications · 2025Article
- A computational tool to infer enzyme activity using post-translational modification profiling data.Communications biology · 2025Article
- PhosNetVis: A web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data.Patterns (New York, N.Y.) · 2025Article
- Article
- ERK synchronizes embryonic cleavages in Drosophila.Developmental cell · 2024Article
- PhosX: data-driven kinase activity inference from phosphoproteomics experiments.Bioinformatics (Oxford, England) · 2024Article
- Proteogenomic analysis reveals non-small cell lung cancer subtypes predicting chromosome instability, and tumor microenvironment.Nature communications · 2024Article
- Calorie restriction and rapamycin distinctly mitigate aging-associated protein phosphorylation changes in mouse muscles.Communications biology · 2024Article
- Comprehensive multi-omics analysis reveals WEE1 as a synergistic lethal target with hyperthermia through CDK1 super-activation.Nature communications · 2024Article
- Article
- Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.Nature communications · 2023Article
- Defining blood-induced microglia functions in neurodegeneration through multiomic profiling.Nature immunology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationPhosphoproteomic experiments are increasingly used to study the changes in signaling occurring across different conditions. It has been proposed that changes in phosphorylation of kinase target sites can be used to infer when a kinase activity is under regulation. However, these approaches have not yet been benchmarked due to a lack of appropriate benchmarking strategies.
resultsWe used curated phosphoproteomic experiments and a gold standard dataset containing a total of 184 kinase-condition pairs where regulation is expected to occur to benchmark and compare different kinase activity inference strategies: Z-test, Kolmogorov Smirnov test, Wilcoxon rank sum test, gene set enrichment analysis (GSEA), and a multiple linear regression model. We also tested weighted variants of the Z-test and GSEA that include information on kinase sequence specificity as proxy for affinity. Finally, we tested how the number of known substrates and the type of evidence ( in vivo , in vitro or in silico ) supporting these influence the predictions.
conclusionsMost models performed well with the Z-test and the GSEA performing best as determined by the area under the ROC curve (Mean AUC = 0.722). Weighting kinase targets by the kinase target sequence preference improves the results marginally. However, the number of known substrates and the evidence supporting the interactions has a strong effect on the predictions. AVAILABILITY AND IMPLEMENTATION: The KSEA implementation is available in https://github.com/ evocellnet/ksea. Additional data is available in http://phosfate.com. CONTACT: pbeltrao@ebi.ac.uk or ochoa@ebi.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.