Chipster (http://chipster.ctmm-trait.nl), a user-friendly, open-source, high-throughput data analysis software tool created and maintained by the IT Center for Science (CSC, Finland)1, has been released for use in CTMM-TraIT.
A workflow for array-Comparative Genomic Hybridization (aCGH) microarray analysis2 for analysing DNA copy number data has also been included within this tool, enabling easy and intuitive data (pre)processing and analysis.
With just a few mouse clicks researchers can process and examine their own data, or retrieve and process microarray data stored within the public database ‘Gene Expression Omnibus’ (GEO), hosted by The National Center for Biotechnology Information (NCBI). It is no longer necessary to have an extensive bio-informatics background or programming skills in order to be able to perform microarray data (pre)processing and analysis such as unsupervised hierarchical clustering, group comparisons and survival tests. Different data visualisation methods are available from within Chipster, depending on the selected data (e.g. view copy number aberrations at study or individual subject level in an interactive genome browser). Furthermore, analysis workflows can be stored and shared, allowing for an easy overview of the exact analysis settings that were used, facilitating reproducibility.
Whereas before Chipster, routine microarray data was largely limited to researchers with bio-informatics expertise, now a much larger group of researchers can easily apply established and validated bio-informatic workflows for mining microarray data, allowing them to derive meaningful information from (publicly) available data sources.
For each workflow tool in Chipster a short description is provided: what does a particular tool do and on what kind of data? How may some parameters be adjusted and in what manner will this affect the analysis? Additionally, more information on the tools is provided in the user manual and the available source codes.
1. M Aleksi Kallio, Jarno T Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, Mikko Koski, Janne Käki, Eija I Korpelainen. Chipster: user-friendly analysis software for microarray and other high-throughput data. (2011) BMC Genomics 12: 507
2. Mark A van de Wiel, Franck Picard, Wessel N van Wieringen and Bauke Ylstra. Preprocessing and downstream analysis of microarray DNA copy number profiles. (2011) Brief Bioinform. 12(1):10-21.