vseed.nottingham.ac.uk
This site contains web-based tools for analysis of gene expression occurring during seed maturation, dormancy and germination.
Related Resources:
Online Network Query
Tools:
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.
Seed
Co-Predicition 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.
Micropylar
Endosperm-(ME)Net (original reference: vSEED consortium,
Unpublished):
A queryable interface for MENet, a genome-wide network
model describing transcriptional interactions in the
micropylar endosperm of germinating Arabidopsis seeds.
>>Coming soon.
People:
Axis-(AXIS)Net
(original reference: vSEED consortium, Unpublished):
A queryable interface for AXIS-Net, a genome-wide network
model describing transcriptional interactions in the lower
axis of germinating Arabidopsis seeds.
>>Coming soon.
Wheat-Net
(original reference: vSEED consortium, Unpublished and
Wan et. al.;
BMC Genomics 2008 9: 121):
A queryable interface for Wheat-Net, a genome-wide network
model describing transcriptional interactions during wheat
seed development and in response to abiotic stress.
>>Coming soon.
Gene expression
visualisations
(eFP browsers):
High resolution time-course course of
germination in Arabidopsis and Lepidium: An eFP
Browser of seed germination, analysing expression in
separated radicle, cotyledon, lateral and micropylar
endosperm.
>>Coming soon.
Other resources:
TAGGIT
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 Web
Portal:
Web portal for the ERANET-PG funded vSEED project.
The
vSEED Web Resource is associated with:
The ERANET-PG vSEED
project, the Centre for Plant
Integrative Biology and Infobiotics (University of
Nottingham) and The Bio-Array Resource
for Plant Functional Genomics (University of Toronto).
This project is a collaboration between Professor
Michael Holdsworth and Dr George Bassel, School
of Biosciences and CPIB, MyCIB
(Multidisciplinary Centre for Integrative Biology
especially Dr. Alex Marshall), Professor Nat
Krasnogor and Dr. Enrico Glaab, School
of Computer Science; University of
Nottingham, and Professor
Nicholas J. Provart, Arabidopsis Research Group at
the Department of
Cell and Systems Biology, University of Toronto.
Funding for this project is
from ERANET-PG
(BB/G02488X/1), BBSRC,
EU Marie Curie Fellowship scheme.
Site managed by Professor
Michael Holdsworth with a great deal of help from
Dr Alex Marshall and John Veasey (MyCIB).
Last update 7 September 2011.