Arabidopsis Affymetrix Data-Mining Tool Links
This page contains a list of tools which I think are useful for mining
useful information from the Arabidopsis Affymetrix data that is publicly
available on the internet. I have tried to arrange the tools in an order
which may be intuitive from the point of view of the user, and titled
each one with the question that they may want to ask.
The
tools are collected from the following websites:
NASCArrays
(University of Nottingham)
GenevestigATor
(ETH Zurich)
University
of Leeds
BBC:
Botany Beowulf Cluster (University of Toronto)
EBI:
European Bioinformatics Institute
AREX:
The Arabidopsis Gene Expression Database
PlantCARE
NASCArrays, GenevestigATor, Leeds, BBC and AREX each use their own different but largely overlapping datasets, although many BBC tools can also use the NASC or AtGenExpress datasets. EBI's epclust tool uses your inputted dataset. AREX uses the a root tissue only dataset but includes data from other expression experiments (in situ hybridisations, promoter::reporter constructs etc) in addition to the Affy data.
To use the GenevestigATor tools you need to register first, but this is both free and fast. Some of the Beowulf tools require AGI codes to be give with a capital A and a small t and g. You also need to register with AREX if you want to be able to enter data or view restricted access data.
I doubt the list is comprehensive, and I will gladly add more tools as and when I find them. Email me at to recommend another tool, or report a mistake in the content or the workings of this page. The next set of tools i plan to incorporate can be accessed at BioConductor.
I now have too many to comfortably fit on one page, so click on a link below:
I
want to know about expression of my gene
- Expression Profile
- Cis-Elements
- Miscellaneous Information
I want to know about the relationship between the expression of 2 genes
I
want expression data on a list of genes
I want to select samples for a more specific dataset
- last updated on: 29/6/2005 -