title: Integrating Microarray Data and GRNs.
abstract: With the completion of the Human Genome Project and the emergence of high-throughput technologies, a vast amount of molecular and biological data are being produced. Two of the most important and significant data sources come from microarray gene-expression experiments and respective databanks (e,g., Gene Expression Omnibus-GEO (http://www.ncbi.nlm.nih.gov/geo)), and from molecular pathways and Gene Regulatory Networks (GRNs) stored and curated in public (e.g., Kyoto Encyclopedia of Genes and Genomes-KEGG (http://www.genome.jp/kegg/pathway.html), Reactome (http://www.reactome.org/ReactomeGWT/entrypoint.html)) as well as in commercial repositories (e.g., Ingenuity IPA (http://www.ingenuity.com/products/ipa)). The association of these two sources aims to give new insight in disease understanding and reveal new molecular targets in the treatment of specific phenotypes.Three major research lines and respective efforts that try to utilize and combine data from both of these sources could be identified, namely: (1) de novo reconstruction of GRNs, (2) identification of Gene-signatures, and (3) identification of differentially expressed GRN functional paths (i.e., sub-GRN paths that distinguish between different phenotypes). In this chapter, we give an overview of the existing methods that support the different types of gene-expression and GRN integration with a focus on methodologies that aim to identify phenotype-discriminant GRNs or subnetworks, and we also present our methodology.
authors.affiliation: Department of Production and Management Engineering, Technical University of Crete, Chania, 73100, Greece. koumakis@ics.forth.gr.|Foundation for Research and Technology-Hellas (FORTH), Institute of Computer Science, Vassilika Vouton, 71110, Heraklion, Greece. koumakis@ics.forth.gr.
authors.forename: L
authors.initials: L
authors.lastname: Koumakis
authors.affiliation: Foundation for Research and Technology-Hellas (FORTH), Institute of Computer Science, Vassilika Vouton, 71110, Heraklion, Greece.
authors.forename: G
authors.initials: G
authors.lastname: Potamias
authors.affiliation: Foundation for Research and Technology-Hellas (FORTH), Institute of Computer Science, Vassilika Vouton, 71110, Heraklion, Greece.|Department of Applied Informatics and Multimedia, Technological Educational Institute, Heraklion, Greece.
authors.forename: M
authors.initials: M
authors.lastname: Tsiknakis
authors.affiliation: Department of Electronic and Computer Engineering, Technical University of Crete, Chania, 73100, Greece.
authors.forename: M
authors.initials: M
authors.lastname: Zervakis
authors.affiliation: Department of Production and Management Engineering, Technical University of Crete, Chania, 73100, Greece.
authors.forename: V
authors.initials: V
authors.lastname: Moustakis
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks; D006801:Humans; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods
keywords: Bioinformatics; Functional pathways; Gene expression; Gene regulatory networks; Microarray; Pathways; Systems biology