VitisNet: “Omics” Integration through Grapevine Molecular Networks

dc.contributor.author Grimplet, Jérôme
dc.contributor.author Cramer, Grant
dc.contributor.author Dickerson, Julie
dc.contributor.author Mathiason, Kathy
dc.contributor.author Van Hemert, John
dc.contributor.author Fennell, Anne
dc.contributor.department Department of Electrical and Computer Engineering
dc.contributor.department Bioinformatics and Computational Biology Program
dc.date 2018-02-17T11:06:21.000
dc.date.accessioned 2020-06-30T02:03:39Z
dc.date.available 2020-06-30T02:03:39Z
dc.date.copyright Thu Jan 01 00:00:00 UTC 2009
dc.date.issued 2009-12-21
dc.description.abstract <p><strong>Background</strong></p> <p>Genomic data release for the grapevine has increased exponentially in the last five years. The Vitis vinifera genome has been sequenced and Vitis EST, transcriptomic, proteomic, and metabolomic tools and data sets continue to be developed. The next critical challenge is to provide biological meaning to this tremendous amount of data by annotating genes and integrating them within their biological context. We have developed and validated a system of Grapevine Molecular Networks (VitisNet).</p> <p><strong>Methodology/Principal Findings</strong></p> <p>The sequences from the Vitis vinifera (cv. Pinot Noir PN40024) genome sequencing project and ESTs from the Vitis genus have been paired and the 39,424 resulting unique sequences have been manually annotated. Among these, 13,145 genes have been assigned to 219 networks. The pathway sets include 88 “Metabolic”, 15 “Genetic Information Processing”, 12 “Environmental Information Processing”, 3 “Cellular Processes”, 21 “Transport”, and 80 “Transcription Factors”. The quantitative data is loaded onto molecular networks, allowing the simultaneous visualization of changes in the transcriptome, proteome, and metabolome for a given experiment.</p> <p><strong>Conclusions/Significance</strong></p> <p>VitisNet uses manually annotated networks in SBML or XML format, enabling the integration of large datasets, streamlining biological functional processing, and improving the understanding of dynamic processes in systems biology experiments. VitisNet is grounded in the Vitis vinifera genome (currently at 8x coverage) and can be readily updated with subsequent updates of the genome or biochemical discoveries. The molecular network files can be dynamically searched by pathway name or individual genes, proteins, or metabolites through the MetNet Pathway database and web-portal at http://metnet3.vrac.iastate.edu/. All VitisNet files including the manual annotation of the grape genome encompassing pathway names, individual genes, their genome identifier, and chromosome location can be accessed and downloaded from the VitisNet tab at http://vitis-dormancy.sdstate.org.</p>
dc.description.comments <p>This article is from PLoS ONE 4(12): e8365. doi:<a href="http://dx.doi.org/10.1371/journal.pone.0008365" target="_blank">10.1371/journal.pone.0008365</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/ece_pubs/84/
dc.identifier.articleid 1083
dc.identifier.contextkey 8041315
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath ece_pubs/84
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/21146
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/ece_pubs/84/2009_Grimplet_VitisNetOmics.pdf|||Sat Jan 15 02:10:54 UTC 2022
dc.source.uri 10.1371/journal.pone.0008365
dc.subject.disciplines Bioinformatics
dc.subject.disciplines Computational Biology
dc.subject.disciplines Systems and Communications
dc.subject.keywords Genetic networks
dc.subject.keywords Grapevine
dc.subject.keywords Genomic databases
dc.subject.keywords Protein metabolism
dc.subject.keywords Transcription factors
dc.subject.keywords Metabolic networks
dc.subject.keywords Grapes
dc.subject.keywords Metabolic pathways
dc.title VitisNet: “Omics” Integration through Grapevine Molecular Networks
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isOrgUnitOfPublication a75a044c-d11e-44cd-af4f-dab1d83339ff
relation.isOrgUnitOfPublication c331f825-0643-499a-9eeb-592c7b43b1f5
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