The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics

Bioinformatics
Danica WiredjaMark R Chance

Abstract

Computational characterization of differential kinase activity from phosphoproteomics datasets is critical for correctly inferring cellular circuitry and how signaling cascades are altered in drug treatment and/or disease. Kinase-Substrate Enrichment Analysis (KSEA) offers a powerful approach to estimating changes in a kinase's activity based on the collective phosphorylation changes of its identified substrates. However, KSEA has been limited to programmers who are able to implement the algorithms. Thus, to make it accessible to the larger scientific community, we present a web-based application of this method: the KSEA App. Overall, we expect that this tool will offer a quick and user-friendly way of generating kinase activity estimates from high-throughput phosphoproteomics datasets. the KSEA App is a free online tool: casecpb.shinyapps.io/ksea/. The source code is on GitHub: github.com/casecpb/KSEA/. The application is also available as the R package "KSEAapp" on CRAN: CRAN.R-project.org/package=KSEAapp/. mark.chance@case.edu. Supplementary data are available at Bioinformatics online.

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Citations

Dec 20, 2018·Molecular & Cellular Proteomics : MCP·Karsten KrugD R Mani
Jul 24, 2019·Molecular & Cellular Proteomics : MCP·Anja M BillingJohannes Graumann
Jun 1, 2019·NPJ Systems Biology and Applications·Daniel LillBoris N Kholodenko
Oct 17, 2019·Integrative Biology : Quantitative Biosciences From Nano to Macro·Samantha Dale StrasserKevin M Haigis
Mar 21, 2020·Cancers·Elise AasebøMaria Hernandez-Valladares
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Jun 25, 2020·Cell Communication and Signaling : CCS·Tamara ScheidtChristian G Huber
Apr 25, 2020·International Journal of Molecular Sciences·Chen ChenJianlin Cheng
Jan 9, 2020·Molecular Cancer Research : MCR·Christina StanglW P Kloosterman
Jan 28, 2021·Molecular Systems Biology·Aurelien DugourdJulio Saez-Rodriguez
Nov 11, 2020·Molecular and Cellular Biology·Christine A MillsMichael J Emanuele
Feb 3, 2021·Mechanisms of Ageing and Development·Akshay BarejaJames P White
Oct 1, 2019·Molecular & Cellular Proteomics : MCP·Anja M BillingJohannes Graumann
Mar 1, 2019·Molecular & Cellular Proteomics : MCP·Karsten KrugD R Mani
Feb 21, 2021·Nature Communications·Serhan YılmazMehmet Koyutürk

Related Concepts

Pharmacotherapy
Phosphorylation
Phosphotransferases
Software Tools
Neuronal Circuitry
Inference
Proteomics
Analysis
Kinase Activity
Computer Program Package

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