2018
DOI: 10.1111/gtc.12655
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Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data

Abstract: Cellular signaling regulates various cellular functions via protein phosphorylation.Phosphoproteomic data potentially include information for a global regulatory network from signaling to cellular functions, but a procedure to reconstruct this network using such data has yet to be established. In this paper, we provide a procedure to reconstruct a global regulatory network from signaling to cellular functions from phosphoproteomic data by integrating prior knowledge of cellular functions and inference of the k… Show more

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Cited by 7 publications
(4 citation statements)
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“…KEGG and WikiPathways were both found to have a moderate coverage of the proteome but could not be investigated in depth for their use in phosphoproteomics data analysis due to the absence of accessible phosphosite-specific annotation. Nonetheless, today both databases continue to be used in pathway analysis of phosphoproteomic data, largely as a source of gene sets for enrichment type studies ( Abe et al, 2020 ; Park et al, 2015 ; Kwon et al, 2015 ; Kawata et al, 2019 ).…”
Section: Discussionmentioning
confidence: 99%
“…KEGG and WikiPathways were both found to have a moderate coverage of the proteome but could not be investigated in depth for their use in phosphoproteomics data analysis due to the absence of accessible phosphosite-specific annotation. Nonetheless, today both databases continue to be used in pathway analysis of phosphoproteomic data, largely as a source of gene sets for enrichment type studies ( Abe et al, 2020 ; Park et al, 2015 ; Kwon et al, 2015 ; Kawata et al, 2019 ).…”
Section: Discussionmentioning
confidence: 99%
“…Therefore, it will be interesting to determine whether the regulation of the Sema4C-mediated E-cadherin expression and migratory ability in LECs are activated by ERK. We focused on protein phosphorylation, a post-translational modification (PTM) with a prevalent role in the control of protein activity and signal transduction) ( 36 ). p-ERK could not be tested at the RNA level, so total ERK was tested at the RNA level to reveal the regulation of Sema4C in the present study.…”
Section: Discussionmentioning
confidence: 99%
“…Insulin and other metabolic hormones mediate downstream metabolic events, including TFs and protein kinases activity 5,[25][26][27][28][29] . Previously, we proposed the concept of "transomic", a global biochemical network for revealing molecular interactions and regulations [30][31][32][33] . We constructed a differential regulatory trans-omic network of metabolic reactions in the liver of wild-type (WT) and ob/ob mice at 16 h-fasting 34 .…”
Section: Introductionmentioning
confidence: 99%