Integrative platform to translate gene sets to networks.
CONCLUSIONS
We have implemented a computational platform (Moksiskaan) that integrates pathway, protein-protein interaction, genome and literature mining data to result in comprehensive networks for a list of genes or proteins. Moksiskaan is able to generate hypothetical pathways for these genes or proteins as well as estimate their activation statuses using regulation information in pathway repositories. An automatically generated result document provides a detailed description of the query genes, biological processes and drug targets. Moksiskaan networks can be downloaded to Cytoscape for further analysis. To demonstrate the utility of Moksiskaan, we use gene microarray and clinical data from >200 glioblastoma multiforme primary tumor samples and translate the resulting set of 124 survival-associated genes to a network.


METHODS
Moksiskaan and user guide are freely available under GNU General Public License at http://csbi.ltdk.helsinki.fi/moksiskaan/
Laakso
Marko
M
Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Program, University of Helsinki, 00014 University of Helsinki, Finland.
Hautaniemi
Sampsa
S
D030541:Databases, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D005796:Genes; D016678:Genome; D023281:Genomics / Q000379:methods*; D012984:Software