Tools

The VESPUCCI compendium is a complete and comprehensive database of nearly all transcriptomic experiments performed on grapevines using both microarray and RNA-seq data. It is organized as a single coherent expression matrix in which each row represents a gene and each column represents a condition. Data are normalized using different strategies, either log ratios for both microarray and RNA-seq, to compare coexpression patterns across all conditions, or TPM for RNA-seq experiments only. The database can be queried programmatically using the GraphQL interface (COMPASS, http://vespucci.fmach.it/compass), the Python or R packages (https://pypi.org/project/pyCOMPASS/ and https://github.com/onertipaday/rcompass).

Website: https://vespucci.readthedocs.io/en/latest/

References: 

Moretto, M. et al. (2022). A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape. Frontiers in plant science, 13:815443. 10.3389/fpls.2022.815443

Moretto, M. et al. (2016). VESPUCCI: exploring patterns of gene expression in grapevine. Frontiers in plant science, 7, 633. doi 10.3389/fpls.2016.00633

Provider:

Web-based platform with several tools to visualize gene expression data in the form of expression heatmaps of a desired list of genes, and gene- or list-centered coexpression networks. The platform also includes genome browsers and a search engine for looking correspondencies between all PN40024 genome annotations and the Grape Reference Catalogue. 

Website: http://www.vitviz.tomsbiolab.com/

The platform includes the following tools: (1) Expression Atlases App: To visualize the expression of a gene or a set of genes in form of heatmaps or bar plots. (2) Gene co-expression network App: Gene or List-Centered Aggregated Networks (GCNs) . (3) EXHARA: Expression across SRA runs used in networks. (4) Gene Cards & Conversions Apps: Tools to explore the Grape Gene Reference Catalogue and find correspondencies between V1 and VCost annotation versions. (5) DAP-Browse App: for the visualization of DAP-seq data in Genome Browsers (JBrowse).

Provider:

José Tomás Matus  / Luis Orduña / Antonio Santiago / David Navarro-Payá

Primary contact | tomas.matus (at) uv.es 

GREAT (GRape Expression ATlas) is an RNA-seq data analysis workflow developed with Snakemake and a web application developed with R Shiny, which allows to analyze and visualize public RNA-seq data from Vitis vinifera species. It allows to explore gene expression in about 2000 public RNA-seq samples with interactive heatmaps or expression tables. Also, this application performs some statistical analyses, like genes clustering with MFuzz or differential gene expression analysis with askoR (edgeR). You can get functional information for your genes of interest. The tools can be interrogated using a gene list or a genomic region.

Website: https://great.colmar.inrae.fr/ (request an account by email to contact-GREAT-colmar (at) inrae.fr)

References: Velt et al., in prep.

Provider:

Camille Rustenholz / Amandine Velt
Primary contact | camille.rustenholz (at) inrae.fr | amandine.velt (at) inrae.fr

OneGenE uses a causality-based method to find genes directly interacting with the input gene(s). The website allows to make single and multiple gene queries and retrieve the list(s) of interacting genes. It allows also to analyze the network formed by input genes as well as to expand this network to find new interacting genes.

Website: vitis.onegenexp.eu

Reference: Pilati, S.; Malacarne, G.; Navarro-Payá, D.; Tomè, G.; Riscica, L.; Cavecchia, V.; Matus, J.T.; Moser, C.; Blanzieri, E. Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families. Biomolecules 2021, 11, 1744. https://doi.org/10.3390/biom11121744

Provider: 

Stefania Pilati / Valter Cavecchia

University of Trento, IMEM-CNR Trento, Fondazione Edmund Mach, S. Michele all’Adige (Italy)

Primary contact | stefania.pilati (at) fmach.it 

VTC-Agg (v1.1) is a tool to quickly interrogate the co-expressed gene lists of your gene(s) of interest. Two gene co-expression networks constructed from 1,359 microarray samples (33 experiments) are available for querying – based rank of correlation (i.e. mutual rank, MR) and aggregation networks. The top 300 co-expressed genes, their associated functional annotation (i.e. mapman BIN category, VitisNet annotation, and homology to Arabidopsis genes), as well as enrichment of BIN and cis-regulatory elements (when available) can be downloaded for further analysis. Bulk download of the entire datasets are also available for local query.

Website: https://sites.google.com/view/vtc-agg

Reference: Wong DCJ. Network aggregation improves gene function prediction of grapevine gene co-expression networks. Plant Mol Biol. 2020 Jul;103(4-5):425-441. doi: 10.1007/s11103-020-01001-2. Epub 2020 Apr 7. PMID: 32266646. DOI: 10.1007/s11103-020-01001-2

Provider:

Darren C. J. Wong 

Primary contact | wongdcj (at) gmail.com 

Gramene is an integrated resource for reference genomes and comparative functional analyses in plants, currently hosting reference genome assemblies, gene annotation, gene expression, genetic variation, phylogenomic analyses (e.g., gene family trees, whole-genome DNA alignments and synteny maps), and pathways for 150 genomes to date, including grapevine PN40024 (as of its 68th release in Nov 2023)

Website: www.gramene.org

Reference: Tello-Ruiz et al (2021). Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res. 49(D1):D1452-D1463. https://doi.org/10.1093/nar/gkaa979

Provider:

Doreen Ware

Contact:  www.gramene.org/feedback

USDA-ARS and Cold Spring Harbor Laboratory 

The Vitis pangenome browser is a Gramene portal focused on Vitis vinifera genomes. The site hosts genome assemblies, gene annotations and phylogenetic analyses for each of the 29 hosted grapevine genomes (4th release, Feb 2024) and a selection of reference plant model organisms from Gramene.

Website: http://vitis.gramene.org

Provider:

Doreen Ware

Contact: www.vitis.gramene.org/feedback

USDA-ARS and Cold Spring Harbor Laboratory

This tool helps explore the transcriptional programs controlling the development of different organ in Vitis vinifera (cv. Corvina). The atlas consists in 54 grapevine samples (including different developmental stages of bud, inflorescence, tendril, leaf, stem, root, developing berry, withering berries, seed, rachis, anther, carpel, petal, pollen, and seedling) with three biological replicates for each sample. 

Website efP Browser: click here

Reference (Atlas): Fasoli et al. (2012). The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program. The Plant Cell, 24(9), 3489–3505. https://doi.org/10.1105/tpc.112.100230

Albeit not an online tool, this resource provides a manually curated MapMan ontology file specific to grapevine (Vitis vinifera). MapMan is a widely used tool for the visualization of systems biology data sets, offering a structured ontology for categorizing genes based on their biological functions. This helps researchers in interpreting large-scale genomic data by mapping genes to specific biological pathways and processes.

The file is in GMT (Gene Matrix Transposed) format, a text-based file type commonly used for gene set enrichment analysis that lists gene sets along with their associated gene identifiers and categories, facilitating the organization and analysis of gene expression data. This curated GMT file can be utilized with the R package gprofiler2, enabling users to conduct enrichment analysis with this specialized grape ontology. This way, researchers can identify overrepresented biological categories within their gene lists, providing deeper insights into the functional implications of their data.

DOWNLOAD FILE HERE

Provider:

Kristina Gruden / Živa Ramšak / Tomás Matus

Primary contact | tomas.matus (at) gmail.com

Grape RNA is a expression database of the grape world. The main purpose of this database is to collect, store, treatment and share the Transcriptome data of the vitis genus. Grape RNA database aimed to make full use of the high throughout data, and make the data more convenient to be used for the researchers.

What can you find in Grape RNA?

1. The raw data of these samples.
2. The expression data of vitis.
3. The assembled transcriptome of 51 accessions.
4. The GO, KEGG and NCBI annotation of all version.
5. Webtools of the related analysis.