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dc.contributor.authorPulvirenti, Alfredo
dc.contributor.authorGiugno, Rosalba
dc.contributor.authorDistefano, Rosario
dc.contributor.authorPigola, Giuseppe
dc.contributor.authorMongiovi, Misael
dc.contributor.authorGiudice, Girolamo 
dc.contributor.authorVendramin, Vera
dc.contributor.authorLombardo, Alessandro
dc.contributor.authorCattonaro, Federica
dc.contributor.authorFerro, Alfredo
dc.date.accessioned2017-11-27T13:49:51Z
dc.date.available2017-11-27T13:49:51Z
dc.date.issued2015
dc.identifierISI:000367623900005
dc.identifier.citationBMC Syst Biol. 2015; 9 Suppl 3:S5
dc.identifier.issn1752-0509
dc.identifier.urihttp://hdl.handle.net/20.500.12105/5402
dc.description.abstractBackground: Vitis vinifera (Grapevine) is the most important fruit species in the modern world. Wine and table grapes sales contribute significantly to the economy of major wine producing countries. The most relevant goals in wine production concern quality and safety. In order to significantly improve the achievement of these objectives and to gain biological knowledge about cultivars, a genomic approach is the most reliable strategy. The recent grapevine genome sequencing offers the opportunity to study the potential roles of genes and microRNAs in fruit maturation and other physiological and pathological processes. Although several systems allowing the analysis of plant genomes have been reported, none of them has been designed specifically for the functional analysis of grapevine genomes of cultivars under environmental stress in connection with microRNA data. Description: Here we introduce a novel knowledge base, called BIOWINE, designed for the functional analysis of Vitis vinifera genomes of cultivars present in Sicily. The system allows the analysis of RNA-seq experiments of two different cultivars, namely Nero d'Avola and Nerello Mascalese. Samples were taken under different climatic conditions of phenological phases, diseases, and geographic locations. The BIOWINE web interface is equipped with data analysis modules for grapevine genomes. In particular users may analyze the current genome assembly together with the RNA-seq data through a customized version of GBrowse. The web interface allows users to perform gene set enrichment by exploiting third-party databases. Conclusions: BIOWINE is a knowledge base implementing a set of bioinformatics tools for the analysis of grapevine genomes. The system aims to increase our understanding of the grapevine varieties and species of Sicilian products focusing on adaptability to different climatic conditions, phenological phases, diseases, and geographic locations.
dc.description.sponsorshipThis work has been partially founded by Programma Operativo Fondo Europeo per lo Sviluppo Regionale (PO-FESR 2007-2013), Linea di intervento 4.1.1.2. Grant number: CUP G23F11000840004. AP, RG, and AF were also partially supported by ``Progetto di Ricerca GNCS - INDAM 2014´´.
dc.language.isoeng
dc.publisherBioMed Central (BMC) 
dc.type.hasVersionVoR
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectEXPRESSION ANALYSIS
dc.subjectMETABOLITE ANALYSIS
dc.subjectGRAPEVINE GENOME
dc.subjectGENE-EXPRESSION
dc.subjectBAC LIBRARY
dc.subjectSEQUENCE
dc.subjectIDENTIFICATION
dc.subjectTRANSCRIPTOME
dc.subjectSTRESS
dc.subjectBERRY
dc.titleA knowledge base for Vitis vinifera functional analysis
dc.typejournal article
dc.rights.licenseAtribución 4.0 Internacional*
dc.identifier.pubmedID26050794
dc.format.volume9
dc.identifier.doi10.1186/1752-0509-9-S3-S5
dc.contributor.funderUnión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF) 
dc.description.peerreviewed
dc.relation.publisherversionhttps://doi.org/10.1186/1752-0509-9-S3-S5
dc.identifier.journalBMC Systems Biology
dc.repisalud.orgCNICCNIC::Grupos de investigación::Regulación Molecular de la Insuficiencia Cardiaca
dc.repisalud.institucionCNIC
dc.rights.accessRightsopen accesses_ES


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