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PMID: 20027228 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

VitisNet: "Omics" integration through grapevine molecular networks.

PloS one ·Vol. 4 ·No. 12 ·2009-12-21 ·Pages e8365

Grimplet J, Cramer GR, Dickerson JA, Mathiason K, Van Hemert J, Fennell AY

Abstract

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). 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. 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.

MeSH Terms
Base Sequence Biological Transport Computational Biology/methods Environment Expressed Sequence Tags Gene Regulatory Networks/genetics Metabolic Networks and Pathways/genetics Software Transcription Factors/metabolism Vitis/genetics
Chemicals
Transcription Factors
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Grimplet Jérôme
Horticulture, Forestry, Landscape, and Parks Department, South Dakota State University, Brookings, South Dakota, USA.
Cramer Grant R
Dickerson Julie A
Mathiason Kathy
Van Hemert John
Fennell Anne Y
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Article Info
Journal
PloS one
Abbr.
PLoS One
ISSN
1932-6203
DOI
10.1371/journal.pone.0008365
Published
2009-12-21
Epub
2009-00-21
Pages
e8365
Language
English
Region
United States
NLM ID
101285081
PMCID
PMC2791446
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pone.0008365 PMC Full Text View journal details
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