[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-detail-120853-en":3,"doc-seo-120853-105":30,"detail-sidebar-cat-0-en-105":92},{"code":4,"msg":5,"data":6},0,"success",{"doc_id":7,"user_id":8,"nickname":9,"user_avatar":10,"doc_module":4,"category_id":11,"category_name":12,"doc_title":13,"doc_description":14,"doc_content":15,"file_id":16,"file_url":17,"file_type":18,"file_size":19,"view_count":20,"is_deleted":4,"is_public":20,"is_downloadable":20,"audit_status":20,"page_count":21,"language":22,"language_code":23,"site_id":24,"html_lang":23,"table_of_contents":25,"faqs":26,"seo_title":27,"seo_description":14,"update_tm":28,"read_time":29},120853,1649267921044,"Ava Thompson","https://us-avatar.wpscdn.com/avatar/1800007509477c92dfb?_k=1782875107921204101",8,"Research & Report","Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera - Research Article Summary","Climate change increases the need to clarify how cultivated grapevine Vitis vinifera defends against cold. This study applies Self Organizing Maps to leaf gene-expression profiles from five cultivars exposed to four temperature regimes, producing temperature-specific patterns in normalized expression data. Results connect vitamin B1 (thiamine) biosynthesis with temperature regulation and thiamine-linked stress responses. Findings also indicate epigenetic regulation of stress-responsive gene expression under low temperatures, highlighting cold-stress co-regulated modules.","TYPE Original Research PUBLISHED 06 December 2023 DOI 10.3389/fpls.2023.1303542  \nOPEN ACCESS  \nEDITED BY  \nYuriy L Orlov,  \nI.M.Sechenov First Moscow State Medical University, Russia  \nREVIEWED BY  \nSamuel Coulbourn Flores, Stockholm University, Sweden  \nVladimir Aleksandrovich Ivanisenko, Russian Academy of Sciences (RAS), Russia Massimo Guazzini,  \nUniversity of Udine, Italy  \n*CORRESPONDENCE Tomas Konecny  \n [tomas.konecny@abi.am](tomas.konecny@abi.am)  \nRECEIVED 28 September 2023  \nACCEPTED 14 November 2023  \nPUBLISHED 06 December 2023  \nCITATION  \nKonecny T, Nikoghosyan M and Binder H (2023) Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera.  \nFront. Plant Sci. 14:1303542 .  \ndoi: 10.3389/fpls.2023.1303542  \nCOPYRIGHT  \n© 2023 Konecny, Nikoghosyan and Binder. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.  \nMachine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera  \nTomas Konecny 1,2*, Maria Nikoghosyan 1,3 and Hans Binder 1,2  \n1Armenian Bioinformatics Institute, Yerevan, Armenia, 2 Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany, 3 Bioinformatics Group, Institute of Molecular Biology Institute of National Academy of Sciences RA, Yerevan, Armenia  \nIntroduction: The escalating challenge of climate change has underscored the critical need to understand cold defense mechanisms in cultivated grapevine Vitis vinifera. Temperature variations can affect the growth and overall health of vine.  \nMethods: We used Self Organizing Maps machine learning method to analyze gene expression data from leaves of five Vitis vinifera cultivars each treated by four different temperature conditions. The algorithm generated sample-specific“portraits” of the normalized gene expression data, revealing distinct patterns related to the temperature conditions applied.  \nResults: Our analysis unveiled a connection with vitamin B1 (thiamine) biosynthesis, suggesting a link between temperature regulation and thiamine metabolism, in agreement with thiamine related stress response established in Arabidopsis before. Furthermore, we found that epigenetic mechanisms play a crucial role in regulating the expression of stress-responsive genes at low temperatures in grapevines.  \nDiscussion: Application of Self Organizing Maps portrayal to vine transcriptomicsidentified modules of coregulated genes triggered under cold stress. Our machine learning approach provides a promising option for transcriptomics studies in plants.  \nKEYWORDS  \nSelf organizing maps, grapevine, temperature stress, vitamin B1, epigenetics, climate change  \nAbbreviations: SOM, self-organizing map; CPM, counts per million; GO, gene ontology; PANTHER, protein analysis through evolutionary relationships; REVIGO, reduce + visualize gene ontology; CIRGO, circular gene ontology; KEGG, kyoto encyclopedia of genes and genomes; BRITE, biomolecular relationship information transfer encyclopedia; AP2, apetala 2; ICE1, inducer of cbf expression 1; CBF, c-repeat binding factors; FLC, flowering locus c; PRMT10, protein arginine n-methyltransferase 10; CHR10, chromatin remodeling 10; THI1-1, thiamine thiazole synthase 1; THI1-2, thiamine thiazole synthase 2; THI1, cysteine-dependent adenosine diphosphate thiazole synthase; THIC, phosphomethylpyrimidine synthase; TPK1/THIN, thiamine pyrophosphokinase; DXS, 1-deoxy-d-xylulose-5-phosphate synthase; TH1, thiamine biosynthetic bifunctional enzyme; TH2, thiamine phosphate phosphatase/aminohmp aminohydrolase.  \nFrontiers ","cbCaikFUjcPTZLP6","https://ap.wps.com/l/cbCaikFUjcPTZLP6","pdf",12920564,1,12,"English","en",105,"# Introduction\n# Methods\n# Results\n# Discussion\n# Keywords and Abbreviations","[{\"question\":\"What machine learning method was used to analyze grapevine transcriptome data?\",\"answer\":\"Self Organizing Maps (SOM) was used to analyze normalized gene expression data from grapevine leaves under different temperature conditions.\"},{\"question\":\"How does the study relate temperature stress to thiamine in Vitis vinifera?\",\"answer\":\"The analysis revealed a connection with vitamin B1 (thiamine) biosynthesis, suggesting a link between temperature regulation and thiamine metabolism during cold acclimation.\"},{\"question\":\"What role do epigenetic mechanisms play according to the results?\",\"answer\":\"Epigenetic mechanisms are proposed to play a crucial role in regulating the expression of stress-responsive genes under low-temperature conditions in grapevines.\"}]","Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera - 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