Development of analysis environment for microarray data

Project leader:   EIJA KORPELAINEN
CSC - Scientific computing, Bioinformatics services (www.csc.fi)

Doctoral students of the project: 

Other researchers of the project: 
Aleksi Kallio
Jarno Tuimala
Taavi Hupponen
Petri Klemelä
Mikko Koski
Janne Käki
Mika Rissanen
Arti Viitanen
Satu Nahkuri

Key words:  bioinformatics, systems biology, DNA-microarrays

Project desciption and main results:
In order to enable more researchers to benefit from the method development in the R/Bioconductor-project (http://www.bioconductor.org), we have created the Chipster analysis software for microarray data. Chipster (http://chipster.csc.fi/) offers an intuitive graphical user interface to a comprehensive collection of up-to-date analysis methods.

Chipster supports all major DNA microarray platforms and, being a Java program, it is compatible with Windows, Linux and MacOS. The usual analysis features such as preprocessing, statistical tests, clustering, and annotation are complemented with e.g. linear (mixed) models, bootstrapping hierarchical clustering results, finding periodically expressed genes from time series data, and promoter analysis tools.
Chipster also offers a simple way to use alternative annotations for Affymetrix arrays, and direct data export to the GEO and ArrayExpress databases. Analysis history is automatically recorded, and the analysis scripts can be viewed at the source code level.
In addition to showing images produced by the R/Bioconductor, Chipster can
also produce interactive  visualizations for hierarchical and SOM clustering, scatter plots, histograms and time series plots.

Graphical client software runs at the user's computer and connects to the CSC server environment through a front-end server. It is also possible to connect external Web Services to the system. New tools can be added using a simple annotation system, and no modifications or wrappers are needed.
The client software utilizes Java Web Start to make installation and version updates as easy as possible.

Publications: