title: Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine development.
abstract: We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named "fight-club hubs" characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named "switch genes" was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops.
authors.affiliation: Institute for Computing Applications "Mauro Picone," National Research Council, 00185 Rome, Italy.
authors.forename: Maria Concetta
authors.initials: MC
authors.lastname: Palumbo
authors.affiliation: Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy.
authors.forename: Sara
authors.initials: S
authors.lastname: Zenoni
authors.affiliation: Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy.
authors.forename: Marianna
authors.initials: M
authors.lastname: Fasoli
authors.affiliation: Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy.
authors.forename: Mélanie
authors.initials: M
authors.lastname: Massonnet
authors.affiliation: Department of Computer, Control, and Management Engineering, "Sapienza" University of Rome, 00185 Rome, Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Farina
authors.affiliation: Institute for Computing Applications "Mauro Picone," National Research Council, 00185 Rome, Italy.
authors.forename: Filippo
authors.initials: F
authors.lastname: Castiglione
authors.affiliation: Dipartimento di Biotecnologie, Università degli Studi di Verona, 37134 Verona, Italy.
authors.forename: Mario
authors.initials: M
authors.lastname: Pezzotti
authors.affiliation: Institute for Systems Analysis and Computer Science "Antonio Ruberti," National Research Council, 00185 Rome, Italy SysBio Centre for Systems Biology, 00185 Rome, Italy paola.paci@iasi.cnr.it.
authors.forename: Paola
authors.initials: P
authors.lastname: Paci
mesh_terms: D005638:Fruit / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling / Q000379:methods; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005812:Genes, Switch; D018745:Genome, Plant; D018551:Solanum lycopersicum / Q000235:genetics*; D059467:Transcriptome; D027843:Vitis / Q000235:genetics* / Q000254:growth & development