NASC Genespring workgroup
We have recently 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.
Go directly to workgroup
Current status
Genespring have recently updated and accelerated their software, so we are holding back on triggering our main licence and fully populating the database until then (May 08).This will ensure that the community have the maximum time available with the best product.
Currenttly a range of experiments are available on the provisional database inlcuding many of the AtGenExpress set. In additional an experiment performed on the Wheat Genome array is available.
A list of all the experiments accessible in the Workgroup can be found here.
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
- Chromosome maps
- 2D and 3D scatter plots
- Volcano plots
- Overlaid on pathway diagrams (KEGG etc)
- 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)
- Promoter motif identification
- Class prediction
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.
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 email genespring@arabidopsis.info
Documents written at NASC to help you get started:
Accessing Genespring workgroup
Access to Genespring workgroup can be through a number of ways:
- Full Genespring GX functionality (5 concurrent seats). Genespring can be installed on any computer and access is granted if a seat is free.
- Genespring workgroup viewer (100 concurrent seats). Allows existing data / experiments to be viewed and limited analysis tools. All Genespring viewing tools and filtering tools (volcano plots etc) are available to generate new gene lists.
- Web viewer. Allows viewing of genes lists / data via a web browser.