Online tools

 

Online Tools for the Analysis of Genomics Data 

The scope of this repository is to serve the grapevine community with a list of tools for genomics/transcriptomics analyses, including the visualization of gene expression data across publicly available data, generation of gene co-expression networks, etc.

 

VESPUCCI - Vitis Expression Study Platform Using Command Compendium Instance

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://compass.fmach.it/graphql), the Python or R packages (https://pypi.org/project/pyCOMPASS/ and https://github.com/onertipaday/rcompass) or with the Dash web-application (http://compass.fmach.it/dashcompass)

Website: http://compass.fmach.it/vespucci

Reference: 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:

Marco Moretto
Primary contact | marco.moretto (at) fmach.it
Computational Biology Unit, Fondazione E. Mach, Italy

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GREAT platform (under construction)

Definition of Acronym:

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Provider:

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

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VTC-Agg. -  Aggregate and correlation rank grapevine gene co-expression networks

VTC-Agg is hosting an updated co-expression matrix constructed from 1,359 samples (33 experiments) using the mutual rank (MR) as the similarity metric to replace VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx) which will be retiring very soon. To help guide future hypothesis-driven studies aimed at understanding the function and transcriptional regulatory networks of grapevine genes,  aggregate networks are created and metadata (e.g. functional BIN and CRE enrichment results) associated. Network aggregation will offer new and unique opportunities for superior gene function prediction in future grapevine functional genomics studies.

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 

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OneGenE (under construction)

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Website: Under construction

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Primary contact |

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Grape eFP Browser

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Website: http://bar.utoronto.ca/efp_grape/cgi-bin/efpWeb.cgi

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Provider:

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VitisCyc

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Website: www.pathways.cgrb.oregonstate.edu

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Provider:

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Mapman Tools adapted for Grapevine (under construction)

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Download latest mapping file (V.Cost + Stilbenoid pathway update)

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Provider:

Kristina Gruden / Živa Ramšak

Primary contact | This email address is being protected from spambots. You need JavaScript enabled to view it. 

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GRAMENE DATABASE -

Description

Website: http://www.gramene.org

Reference: 

Provider:

Doreen Ware
Primary contact | (at)
Affiliation 
 
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If you wish do add your own tool or analysis resource send a mail to tomas.matus (at) uv.es with your request.

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