Publication: Identification of novel components of target-of-rapamycin signaling pathway by network-based multi-omics integrative analysis
dc.contributor.coauthor | Eke, Elif Dereli | |
dc.contributor.coauthor | Arga, Kazim Yalcin | |
dc.contributor.coauthor | Dikicioglu, Duygu | |
dc.contributor.coauthor | Eraslan, Serpil | |
dc.contributor.coauthor | Erkol, Emir | |
dc.contributor.coauthor | Celik, Arzu | |
dc.contributor.coauthor | Kirdar, Betul | |
dc.contributor.coauthor | Di Camillo, Barbara | |
dc.contributor.department | KUTTAM (Koç University Research Center for Translational Medicine) | |
dc.contributor.department | School of Medicine | |
dc.contributor.kuauthor | Eraslan, Serpil | |
dc.contributor.schoolcollegeinstitute | Research Center | |
dc.contributor.schoolcollegeinstitute | SCHOOL OF MEDICINE | |
dc.date.accessioned | 2024-11-09T23:19:20Z | |
dc.date.issued | 2019 | |
dc.description.abstract | Target of rapamycin (TOR) is a major signaling pathway and regulator of cell growth. TOR serves as a hub of many signaling routes, and is implicated in the pathophysiology of numerous human diseases, including cancer, diabetes, and neurodegeneration. Therefore, elucidation of unknown components of TOR signaling that could serve as potential biomarkers and drug targets has a great clinical importance. In this study, our aim is to integrate transcriptomics, interactomics, and regulomics data in Saccharomyces cerevisiae using a network-based multiomics approach to enlighten previously unidentified, potential components of TOR signaling. We constructed the TOR-signaling protein interaction network, which was used as a template to search for TOR-mediated rapamycin and caffeine signaling paths. We scored the paths passing from at least one component of TOR Complex 1 or 2 (TORC1/TORC2) using the co-expression levels of the genes in the transcriptome data of the cells grown in the presence of rapamycin or caffeine. The resultant network revealed seven hitherto unannotated proteins, namely, Atg14p, Rim20p, Ret2p, Spt21p, Ylr257wp, Ymr295cp, and Ygr017wp, as potential components of TOR-mediated rapamycin and caffeine signaling in yeast. Among these proteins, we suggest further deciphering of the role of Ylr257wp will be particularly informative in the future because it was the only protein whose removal from the constructed network hindered the signal transduction to the TORC1 effector kinase Npr1p. In conclusion, this study underlines the value of network-based multiomics integrative data analysis in discovering previously unidentified components of the signaling networks by revealing potential components of TOR signaling for future experimental validation. | |
dc.description.indexedby | WOS | |
dc.description.indexedby | Scopus | |
dc.description.indexedby | PubMed | |
dc.description.issue | 5 | |
dc.description.openaccess | YES | |
dc.description.publisherscope | International | |
dc.description.sponsoredbyTubitakEu | N/A | |
dc.description.sponsorship | Marmara University Research Fund (BAPKO) [FEN-A-091116-0496] | |
dc.description.sponsorship | University of Padova Junior Project Grants: "Dynamic Modeling of TOR signaling pathway through systems biology approaches" [TUBITAK110M692] | |
dc.description.sponsorship | Turkish State Planning Organization [DPT-09 K120520] | |
dc.description.sponsorship | Boazici University Research Fund 1932 project | |
dc.description.sponsorship | Leverhulme Trust [ECF-2016-681] This work was supported by Marmara University Research Fund (BAPKO) through FEN-A-091116-0496 project, University of Padova Junior Project Grants: "Dynamic Modeling of TOR signaling pathway through systems biology approaches," TUBITAK110M692 project, Turkish State Planning Organization DPT-09 K120520 project, and the Boazici University Research Fund 1932 project. Duygu Dikiciolu would like to thank the Leverhulme Trust (ECF-2016-681) and the Isaac Newton Trust. The authors thank Tiziana Sanavia for comments and assistance in this study. | |
dc.description.volume | 23 | |
dc.identifier.doi | 10.1089/omi.2019.0021 | |
dc.identifier.eissn | 1557-8100 | |
dc.identifier.issn | 1536-2310 | |
dc.identifier.quartile | Q2 | |
dc.identifier.scopus | 2-s2.0-85065881694 | |
dc.identifier.uri | https://doi.org/10.1089/omi.2019.0021 | |
dc.identifier.uri | https://hdl.handle.net/20.500.14288/10536 | |
dc.identifier.wos | 464560900001 | |
dc.keywords | Drug targets | |
dc.keywords | Target of rapamycin (TOR) signaling | |
dc.keywords | Biomarkers | |
dc.keywords | Multiomics | |
dc.keywords | Caffeine | |
dc.keywords | Network-based analysis tor function | |
dc.keywords | Growth | |
dc.keywords | Autophagy | |
dc.keywords | Database | |
dc.keywords | Reveals | |
dc.keywords | MTORC2 | |
dc.keywords | Enhancement | |
dc.keywords | Information | |
dc.keywords | Metabolism | |
dc.keywords | Complexes | |
dc.language.iso | eng | |
dc.publisher | Mary Ann Liebert, Inc. | |
dc.relation.ispartof | Omics-A Journal of Integrative Biology | |
dc.subject | Biotechnology | |
dc.subject | Applied microbiology | |
dc.subject | Genetics | |
dc.subject | Heredity | |
dc.title | Identification of novel components of target-of-rapamycin signaling pathway by network-based multi-omics integrative analysis | |
dc.type | Journal Article | |
dspace.entity.type | Publication | |
local.contributor.kuauthor | Eraslan, Serpil | |
local.publication.orgunit1 | SCHOOL OF MEDICINE | |
local.publication.orgunit1 | Research Center | |
local.publication.orgunit2 | KUTTAM (Koç University Research Center for Translational Medicine) | |
local.publication.orgunit2 | School of Medicine | |
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