{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,29]],"date-time":"2023-01-29T05:21:50Z","timestamp":1674969710307},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein 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.<\/jats:p>\n               <jats:p>Results: We 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 \u223c78% 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 \u223c27% more phosphorylation sites than existing motif detection tools (NetPhosYeast and GPS2.0), and predictions of kinase\u2013phosphatase interactions overlapped with \u223c59% of known interactions present in yeast databases. PhosphoChain provides a valuable framework for predicting condition-specific phosphorylation events from high-throughput data.<\/jats:p>\n               <jats:p>Availability: PhosphoChain is implemented in Java and available at http:\/\/virgo.csie.ncku.edu.tw\/PhosphoChain\/ or http:\/\/aitchisonlab.com\/PhosphoChain<\/jats:p>\n               <jats:p>Contact: \u00a0john.aitchison@systemsbiology.org or jchiang@mail.ncku.edu.tw<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt387","type":"journal-article","created":{"date-parts":[[2013,7,6]],"date-time":"2013-07-06T01:10:10Z","timestamp":1373073010000},"page":"2435-2444","source":"Crossref","is-referenced-by-count":6,"title":["PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data"],"prefix":"10.1093","volume":"29","author":[{"given":"Wei-Ming","family":"Chen","sequence":"first","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, WA 98109-5234, USA, 2Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan and 3Seattle Biomedical Research Institute, Seattle, WA 98109-5219, USA"},{"name":"1 Institute for Systems Biology, Seattle, WA 98109-5234, USA, 2Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan and 3Seattle Biomedical Research Institute, Seattle, WA 98109-5219, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel A.","family":"Danziger","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, WA 98109-5234, USA, 2Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan and 3Seattle Biomedical Research Institute, Seattle, WA 98109-5219, USA"},{"name":"1 Institute for Systems Biology, Seattle, WA 98109-5234, USA, 2Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan and 3Seattle Biomedical Research Institute, Seattle, WA 98109-5219, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jung-Hsien","family":"Chiang","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, WA 98109-5234, USA, 2Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan and 3Seattle Biomedical Research Institute, Seattle, WA 98109-5219, USA"},{"name":"1 Institute for Systems Biology, Seattle, WA 98109-5234, USA, 2Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan and 3Seattle Biomedical Research Institute, Seattle, WA 98109-5219, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John D.","family":"Aitchison","sequence":"additional","affiliation":[{"name":"1 Institute for Systems Biology, Seattle, WA 98109-5234, USA, 2Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan and 3Seattle Biomedical Research Institute, Seattle, WA 98109-5219, USA"},{"name":"1 Institute for Systems Biology, Seattle, WA 98109-5234, USA, 2Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan and 3Seattle Biomedical Research Institute, Seattle, WA 98109-5219, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,7,5]]},"reference":[{"key":"2023012810464103500_btt387-B1","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkq964","article-title":"YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface","volume":"39","author":"Abdulrehman","year":"2011","journal-title":"Nucleic Acids Res."},{"issue":"Pt. 1","key":"2023012810464103500_btt387-B2","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1042\/bj3080181","article-title":"Insulin increases mRNA levels of protein kinase C-alpha and -beta in rat adipocytes and protein kinase C-alpha, -beta and -theta in rat skeletal muscle","volume":"308","author":"Avignon","year":"1995","journal-title":"Biochem. 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