Identification of a novel gene signature for neuroblastoma differentiation using a Boolean implication network

In this dataset, we report the analysis by RNA-sequencing (RNA-seq) of the transcriptional profile of neuroblastoma cell lines at baseline and after treatment with 13-cis-retinoic acid. Data from this study validated Boolean Implication Network derived differentiation signature in neuroblastoma. Our differentiation signature included a cluster of genes involved in intracellular signaling and growth factor receptor trafficking pathways that is strongly associated with neuroblastoma differentiation, and we validated the associations of UBE4B, a gene within this cluster, with neuroblastoma cell and tumor differentiation. Our findings demonstrate that Boolean network analyses of symmetric and asymmetric gene expression relationships can identify novel genes and pathways relevant for neuroblastoma tumor differentiation that could represent potential therapeutic targets. Overall design: Neuroblastoma cell lines were treated with 5µM 13-cis-retinoic acid for 48 hours, while control plates were left untreated.