Marko Laakso1, Sampsa Hautaniemi. 1. Computational Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Program, University of Helsinki, 00014 University of Helsinki, Finland.
Abstract
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: Moksiskaan and user guide are freely available under GNU General Public License at http://csbi.ltdk.helsinki.fi/moksiskaan/
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: Moksiskaan and user guide are freely available under GNU General Public License at http://csbi.ltdk.helsinki.fi/moksiskaan/
Authors: Ilkka Liikanen; Vladia Monsurrò; Laura Ahtiainen; Mari Raki; Tanja Hakkarainen; Iulia Diaconu; Sophie Escutenaire; Otto Hemminki; João D Dias; Vincenzo Cerullo; Anna Kanerva; Sari Pesonen; Daniela Marzioni; Marco Colombatti; Akseli Hemminki Journal: Mol Ther Date: 2011-07-26 Impact factor: 11.454
Authors: S Heinonen; L Saarinen; J Naukkarinen; A Rodríguez; G Frühbeck; A Hakkarainen; J Lundbom; N Lundbom; K Vuolteenaho; E Moilanen; P Arner; S Hautaniemi; A Suomalainen; J Kaprio; A Rissanen; K H Pietiläinen Journal: Int J Obes (Lond) Date: 2014-02-19 Impact factor: 5.095
Authors: Melody K Morris; Julio Saez-Rodriguez; David C Clarke; Peter K Sorger; Douglas A Lauffenburger Journal: PLoS Comput Biol Date: 2011-03-03 Impact factor: 4.475
Authors: Kristian Ovaska; Marko Laakso; Saija Haapa-Paananen; Riku Louhimo; Ping Chen; Viljami Aittomäki; Erkka Valo; Javier Núñez-Fontarnau; Ville Rantanen; Sirkku Karinen; Kari Nousiainen; Anna-Maria Lahesmaa-Korpinen; Minna Miettinen; Lilli Saarinen; Pekka Kohonen; Jianmin Wu; Jukka Westermarck; Sampsa Hautaniemi Journal: Genome Med Date: 2010-09-07 Impact factor: 11.117