VitisNet, Vitis vinifera, Grapevine Molecular Networks, grape genome
Background: 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). Methodology/Principal Findings: 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. Conclusions/Significance: 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/
DOI of Published Version
Copyright: © 2009 Grimplet et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Grimplet, Jerome; Cramer, Grant R.; Dickerson, Julie A.; Mathiason, Kathy; Van Hemert, John; and Fennell, Anne Y. Dr, "VitisNet: ‘‘Omics’’ Integration through Grapevine Molecular Networks" (2009). Agronomy, Horticulture and Plant Science Faculty Publications. 53.
Zip files contains all VitisNet files
AdditionalFile2_2_VitisNet_12X.xlsx (7426 kB)
Additional File 2_2_VVitisNet_12X
journal.pone.0008365.s001.XLS (10040 kB)
Table S1: The complete grape gene annotation based on the 8X assembly (Jaillon et al., 2007) of transcript sequences. Unique Gene: Genoscope ID (Jaillon et al., 2007) is used if a genome sequence has been identified, otherwise VVGI 5 TC (Tentative Consensus sequences) number or EST GenBank ID is used. Unique transcript: VVGI 5 TC number or EST GenBank ID is used if a transcript has been identified, otherwise the Genoscope ID is used. Function: tentative functional annotation. Network ID: the identifier that is used in the networks. Network or simplified category: list of the networks where the genes appear, otherwise a short description of the biological role. In Network: the gene is present in at least one network. Probeset: probeset ID for the Affymetrix GeneChip® Vitis vinifera (Grape) Genome Array. Best Arabidopsis match: best matched hit in Arabidopsis putative proteins. InterPro domain ID: list of the domains detected from InterPro (Hunter et al., 2009). Gene Ontology ID: list of the identified GO terms. Gene Ontology description: description of the GO term (The Gene Ontology Consortium, 2009). Accession UniProt: UniProt ID for the genome sequences (Apweiler et al., 2004). Accession UniProt for published grapevine protein: UniProt ID for grapevine proteins individually published apart of the genome sequencing. EST probeset: EST from which the probeset was designed. IASMA gene: ID from the heterozygote Vitis genome (Velasco et al., 2007). Chromosome position: position of the gene on chromosome retrieved from Gramene.org. Other Vitis: presence in non-vinifera Vitis species. cDNA array: ID used in the cDNA array from Mathiason et al., (2009). Other TC from VVGI5: list of other TC from the DFCI matching the gene. Other probesets: other Affymetrix probesets matching the gene.
journal.pone.0008365.s002.DOC (26 kB)
Table S2:List of pathways constructed from bibliographic data and the corresponding journal articles used.
journal.pone.0008365.s003.DOC (57 kB)
Text S1: References for supporting material.
journal.pone.0008365.s004.DOC (3429 kB)
Text S2: Tutorial for Using VitisNet, a database for the grapevine molecular networks.