Data from: 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

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.