NASC Genespring workgroup
We have obtained a grant from the BBSRC to implement a Genespring workgroup database (Agilent technologies). This will allow users to easily access all the data within the NASCArrays database (currently more than 3000 slides) and perform detailed statistical analysis on the data. Similar implementations of Genespring workgroup have been used by NERC, Finnish, and Swiss transcriptomic groups and numerous pharma companies.
Current status
Genespring have recently updated and accelerated their software, to version 11. We have updated our database to the current version and this can be accessed using Genspring GX11 clients (available to download here).All the data from the NASCArrays database is now available in the workgroup. The Genespring client server license is also up and running allowing users access to the full version of Genespring GX11.
Tomato metabolite data
The data presented in the publication, Kovacs et al, Effect of tomato pleiotropic mutations on flavour volatile biosynthesis, Phytochemistry 2009, is available in the workgroup. To download the raw data click here or access the data via the workgroup and use the following details to log on: Username = tommetab, password = tommetab.
Instructions for viewing the data in the workgroup can be found here. Detailed instructions on Genspring GX can be found under the Implementation and Training section.
Genespring GX features
Genespring GX is a powerful visualisation and analysis tool for use with a wide range of expression data including Affymetrix, Agilent, spotted-arrays and real-time PCR data.
Data can be visualised in a number of ways, including:
- Line graphs
- Box plots
- PCA analysis
- Volcano plots
- Pathway analysis
- Grouping by GO ontologies
Data can be analysed using a wide range of techniques:
- Volcano plots for differentially expressed genes
- One- and two-parameter ANOVA
- Clustering (Hierarchical, K-means, self organising maps, principal component analysis etc)
- Class prediction
- GSA / GSEA analysis
Genespring GX workgroup features
Genespring workgroup allows direct access to all experiments in the NASCArrays database. Whole experiments, individual or groups of .CEL files can be downloaded and analysed. Personal data (experiments, gene lists, analysis results) can be shared with the entire community or selected users.
An Introductory talk was given at GARNet 2007.
An article describing the Workgroup has been published in the June 2008 GARNet newsletter.
Implementation and Training
The implementation of the workgroup has been initiated and we launched the first trial at the 2007 Garnet meeting.
Training sessions will be initially held at NASC and at selected meetings. For more information or if you would like to arrange a local training session, please email genespring@arabidopsis.info
Latest training session:
A hands-on workshop was run at SEB/GARNet meeting at the Univerisyt of Nottingham, 2008.
This introductory talk given as part of the workshop.
Accessing Genespring workgroup
Access to Genespring workgroup is via the Genespring GX11 client. This is avalible for windows, MAC and Linux and co nbe downloaded from the Agilent website or our ftp site.
For a username and password and instructions for accessing the workgroup, please email genespring@arabidopsis.info