title: Heterogeneous biological network visualization system: case study in context of medical image data.
abstract: We have developed a system called megNet for integrating and visualizing heterogeneous biological data in order to enable modeling biological phenomena using a systems approach. Herein we describe megNet, including a recently developed user interface for visualizing biological networks in three dimensions and a web user interface for taking input parameters from the user, and an in-house text mining system that utilizes an existing knowledge base. We demonstrate the software with a case study in which we integrate lipidomics data acquired in-house with interaction data from external databases, and then find novel interactions that could possibly explain our previous associations between biological data and medical images. The flexibility of megNet assures that the tool can be applied in diverse applications, from target discovery in medical applications to metabolic engineering in industrial biotechnology.
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, Espoo, Finland. Erno.Lindfors@vtt.fi
authors.forename: Erno
authors.initials: E
authors.lastname: Lindfors
authors.forename: Jussi
authors.initials: J
authors.lastname: Mattila
authors.forename: Peddinti V
authors.initials: PV
authors.lastname: Gopalacharyulu
authors.forename: Antti
authors.initials: A
authors.lastname: Pesonen
authors.forename: Jyrki
authors.initials: J
authors.lastname: Lötjönen
authors.forename: Matej
authors.initials: M
authors.lastname: Orešič
mesh_terms: D000818:Animals; D016208:Databases, Factual; D020869:Gene Expression Profiling / Q000379:methods; D023281:Genomics / Q000379:methods; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D034904:Lamin Type A / Q000235:genetics / Q000378:metabolism; D050356:Lipid Metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics / Q000502:physiology; D008954:Models, Biological; D011485:Protein Binding; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology*; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014584:User-Computer Interface
chemical_list: C494847:LMNA protein, human; D034904:Lamin Type A