TitleDifferential gene regulatory networks in development and disease.
Publication TypeJournal Article
Year of Publication2018
AuthorsSingh, AJ, Ramsey, SA, Filtz, TM, Kioussi, C
JournalCell Mol Life Sci
Date Published2018 03
KeywordsAnimals, Congenital Abnormalities, Embryo, Mammalian, Embryonic Development, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, High-Throughput Nucleotide Sequencing, Humans, Neoplasms, Signal Transduction, Single-Cell Analysis, Systems Biology, Transcriptome

Gene regulatory networks, in which differential expression of regulator genes induce differential expression of their target genes, underlie diverse biological processes such as embryonic development, organ formation and disease pathogenesis. An archetypical systems biology approach to mapping these networks involves the combined application of (1) high-throughput sequencing-based transcriptome profiling (RNA-seq) of biopsies under diverse network perturbations and (2) network inference based on gene-gene expression correlation analysis. The comparative analysis of such correlation networks across cell types or states, differential correlation network analysis, can identify specific molecular signatures and functional modules that underlie the state transition or have context-specific function. Here, we review the basic concepts of network biology and correlation network inference, and the prevailing methods for differential analysis of correlation networks. We discuss applications of gene expression network analysis in the context of embryonic development, cancer, and congenital diseases.

Alternate JournalCell Mol Life Sci
PubMed ID29018868
Grant List1553728-DBI / / National Science Foundation / International