Vision from next generation sequencing – Multi-dimensional genome-wide analysis for producing gene regulatory networks

Genomics and genetics have invaded all aspects of biology and medicine, opening uncharted territory for scientific exploration. The definition of “gene” itself has become ambiguous, and the central dogma is continuously being revised and expanded. Computational biology and computational medicine are no longer intellectual domains of the chosen few. Next generation sequencing (NGS) technology, together with novel methods of pattern recognition and network analyses, has revolutionized the way we think about fundamental biological mechanisms and cellular pathways.

In this review, the authors discuss NGS-based genome-wide approaches that can provide deeper insights into retinal development, aging and disease pathogenesis. They  first focus on gene regulatory networks (GRNs) that govern the differentiation of retinal photoreceptors and modulate adaptive response during aging. Then, they discuss NGS technology in the context of retinal disease and develop a vision for therapies based on network biology.

rna-seq

The authors believe that specific and uniform guidelines are required for generation of genome, transcriptome and epigenome data to facilitate comparative analysis and integration of multi-dimensional data sets, and for constructing networks underlying complex biological processes. As cellular homeostasis and organismal survival are dependent on gene-gene and gene-environment interactions, they believe that network-based biology will provide the foundation for deciphering disease mechanisms and discovering novel drug targets for retinal neurodegenerative diseases.

Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A. (2015) Vision from next generation sequencing: Multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res [Epub ahead of print]. [abstract]

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