University of Nottingham

vSeed
The Virtual Seed Web Resource
vseed.nottingham.ac.uk
  
 
 
 

This site contains web-based tools for analysis of gene expression occurring during seed maturation, dormancy and germination.

  
 

Related Resources:

The Seed Biology Place

tair

BAR

GeneMANIA

Infobiotics


Online Network Query Tools:

  
 

SeedNet

SeedNet - Genome-wide transcription network in seeds (original reference: Bassel et al PNAS (USA) 2011):
A queryable interface for SeedNet, a genome-wide network model describing transcriptional interactions in dormant and germinating Arabidopsis seeds.

  
 

SCoPNetSeed Co-Prediction Network - SCoPNet for seed dormancy and germination (original reference: Bassel et al The Plant Cell, 2011 doi: 10.1105/tpc.111.088153.):
A queryable interface for SCoPNet, a genome-wide network model describing transcriptional interactions in germinating and dormant Arabidopsis seeds, generated through machine learning.

 
 

People:

Mike Holdsworth

Natalio Krasnogor

Alex Marshall

Enrico Glaab

Pawel Widera

James Gilbert

George Bassel



Micropylar Endosperm-(END)net (original reference: Dekkers et al. Submitted):
A queryable interface for ENDnet, a genome-wide network model describing transcriptional interactions in the micropylar endosperm of germinating Arabidopsis seeds.

 
 

Radicle-(RAD)net (original reference: Dekkers et al. Submitted):
A queryable interface for RADnet, a genome-wide network model describing transcriptional interactions in the lower axis of germinating Arabidopsis seeds.

 


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Gene expression visualisations
(eFP browsers):

  
 

eFPLepidiumHigh resolution time-course course of germination in Arabidopsis (original reference: Dekkers et al. Submitted):
An eFP Browser of seed germination, analysing expression in separated radicle, cotyledon, lateral and micropylar endosperm.

 




 

Other resources:

  
 

TAGGITTAGGIT analysis of seed transcriptome datasets: (original reference: Carrera et al Plant Physiology 2007): TAGGIT uses a seed germination/dormancy ontology to annotate 'omics datasets, thus allowing more biologically informed analysis. A guide and most up-to-date version (although not updated since 2009, you can also use your own gene lists) of the TAGGIT workflow.

  
   

vSEED


vSEED Web Portal:
Web portal for the ERANET-PG funded vSEED project.

  
 
 
 

The vSEED Web Resource is associated with:

The ERANET-PG vSEED project and Infobiotics (University of Nottingham).

This project is a collaboration between Professor Michael Holdsworth and Professor Nat Krasnogor, School of Computer Science; University of Nottingham.

Funding for this project was originally from ERANET-PG (BB/G02488X/1), BBSRC.

Site managed by Professor Michael Holdsworth with a great deal of help from MyCIB.
Last update 01 March 2013.