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Protocols

VitisNet specifications

Information


Unique identifier OMICS_10376
Name VitisNet
Restrictions to use None
Maintained Yes

Taxon


  • Plants and Fungi
    • Vitis vinifera

Publication for VitisNet

VitisNet citations

 (8)
library_books

Lipopolysaccharide O antigen delays plant innate immune recognition of Xylella fastidiosa

2018
Nat Commun
PMCID: 5786101
PMID: 29374171
DOI: 10.1038/s41467-018-02861-5

[…] echnical variation using DESeq2, which was also used for statistical testing. Functional annotations and biological processes associated to the differentially expressed grape genes were obtained from VitisNet (https://www.sdstate.edu/ps/research/vitis/pathways.cfm). Enrichment analyses of grape biological processes were performed in R using a hypergeometric test with a significant cut-off of P < 0 […]

library_books

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

2018
BMC Genomics
PMCID: 5773036
PMID: 29343235
DOI: 10.1186/s12864-018-4434-2

[…] uences of BLASTX and BLASTP were then searched as described previously, using Blast2GO [] with BLASTX and BLASTP. Predicted genes were then functionally annotated using the V. vinifera annotation and VitisNet pathways [] providing seedless transcriptomic resources. Transcription factors were identified using PlantTFDB []. The RAV transcription factor subfamily of AP2/ERF TF family was examined usi […]

library_books

Neofusicoccum parvum Colonization of the Grapevine Woody Stem Triggers Asynchronous Host Responses at the Site of Infection and in the Leaves

2017
Front Plant Sci
PMCID: 5487829
PMID: 28702038
DOI: 10.3389/fpls.2017.01117

[…] g the PlantTFDB v4.0 database (Jin et al., ). Motifs were annotated by comparison with PlantTFDB v4.0 database (Jin et al., ) using tomtom v4.11.1 with the following parameters: -e-value -no-ssc. The VitisNet functional annotations were used to assign grape genes to functional categories (Grimplet et al., ). Enrichment analyses of grape biological functions were computed in R using the classic Fis […]

library_books

A Concise Review on Multi Omics Data Integration for Terroir Analysis in Vitis vinifera

2017
Front Plant Sci
PMCID: 5477006
PMID: 28676813
DOI: 10.3389/fpls.2017.01065

[…] les) that may be relevant for the control of berry transition between development and ripening.There are also online resources available that can help analyze omic data from V. vinifera. For example, VitisNet (, ) offers manually annotated molecular networks (16,000 genes and 247 networks) where omics data can be loaded to visualize changes in the transcriptome, proteome and metabolome for a given […]

library_books

Phylloxera (Daktulosphaira vitifoliae Fitch) alters the carbohydrate metabolism in root galls to allowing the compatible interaction with grapevine (Vitis ssp.) roots

2015
Plant Sci
PMCID: 4388344
PMID: 25804808
DOI: 10.1016/j.plantsci.2015.02.002

[…] Index still holds the most comprehensive cDNA collection based on experimental evidence to date, the associated functional annotation has been updated less frequently. Therefore, information from the VitisNet platform was used to transfer putative functional gene annotations for targets differentially expressed in our analysis by mapping the target sequences to the latest VitisNet annotation (Refe […]

call_split

Identification of a Plastid Localized Bifunctional Nerolidol/Linalool Synthase in Relation to Linalool Biosynthesis in Young Grape Berries

2014
Int J Mol Sci
PMCID: 4284690
PMID: 25470020
DOI: 10.3390/ijms151221992
call_split See protocol

[…] The gene models which were annotated as putative linalool synthase genes (LIN) were obtained from database of VitisNet [] and FLAGdb++ [] both based on grape genome []. The redundant sequences, together with imperfect models caused by insert/deletion mutation and frame shift, were dropped. The amino acid sequ […]

Citations

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VitisNet institution(s)
Horticulture, Forestry, Landscape, and Parks Department, South Dakota State University, Brookings, SD, USA

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