title: KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments.
abstract: Gene expression analysis, using high throughput genomic technologies,has become an indispensable step for the meaningful interpretation of the underlying molecular complexity, which shapes the phenotypic manifestation of the investigated biological mechanism. The modularity of the cellular response to different experimental conditions can be comprehended through the exploitation of molecular pathway databases, which offer a controlled, curated background for statistical enrichment analysis. Existing tools enable pathway analysis, visualization, or pathway merging but none integrates a fully automated workflow, combining all above-mentioned modules and destined to non-programmer users. We introduce an online web application, named KEGG Enriched Network Visualizer (KENeV), which enables a fully automated workflow starting from a list of differentially expressed genes and deriving the enriched KEGG metabolic and signaling pathways, merged into two respective, non-redundant super-networks. The final networks can be downloaded as SBML files, for further analysis, or instantly visualized through an interactive visualization module. In conclusion, KENeV (available online at http://www.grissom.gr/kenev) provides an integrative tool, suitable for users with no programming experience, for the functional interpretation, at both the metabolic and signaling level, of differentially expressed gene subsets deriving from genomic experiments.
authors.affiliation: Metabolic Engineering and Bioinformatics Programme, Institute of Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
authors.forename: Eleftherios
authors.initials: E
authors.lastname: Pilalis
authors.affiliation: Metabolic Engineering and Bioinformatics Programme, Institute of Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
authors.forename: Theodoros
authors.initials: T
authors.lastname: Koutsandreas
authors.affiliation: Metabolic Engineering and Bioinformatics Programme, Institute of Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Valavanis
authors.affiliation: Biomedical Research Foundation, Academy of Athens, Athens, Greece.
authors.forename: Emmanouil
authors.initials: E
authors.lastname: Athanasiadis
authors.affiliation: Biomedical Research Foundation, Academy of Athens, Athens, Greece.
authors.forename: George
authors.initials: G
authors.lastname: Spyrou
authors.affiliation: Metabolic Engineering and Bioinformatics Programme, Institute of Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
authors.forename: Aristotelis
authors.initials: A
authors.lastname: Chatziioannou
keywords: Enrichment analysis; Gene expression; KEGG; Microarrays; Molecular pathways; Next generation sequencing