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bioRxiv · 10.1101/593400

Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans

Ito, M.·Nomoto, Y.·Kubota, Y.·Kasahara, K.·Tomita, A.·Oshime, T.·Yamashita, H.·Fahmi, M.
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Abstract

Obtaining a comprehensive understanding of the gene regulatory networks, or gene cascades, involved in cell fate determination and cell lineage segregation in Caenorhabditis elegans is a long-standing challenge. Although RNA-sequencing (RNA-Seq) is a promising technique to resolve these questions, the bioinformatics tools to identify associated gene cascades from RNA-Seq data remain inadequate. To overcome these limitations, we developed Gene Cascade Finder (GCF) as a novel tool for building gene cascades by comparison of mutant and wild-type RNA-Seq data along with integrated information of protein-protein interactions, expression timing, and domains. Application of GCF to RNA-Seq data confirmed that SPN-4 and MEX-3 regulate the canonical Wnt pathway during embryonic development. Moreover, lin-35, hsp-3, and gpa-12 were found to be involved in MEX-1-dependent neurogenesis, and MEX-3 was found to control the gene cascade promoting neurogenesis through lin-35 and apl-1. Thus, GCF could be a useful tool for building gene cascades from RNA-Seq data.

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Ito, M., Nomoto, Y., Kubota, Y., Kasahara, K., Tomita, A., Oshime, T., Yamashita, H., Fahmi, M.. 2019-03-29. Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans. https://doi.org/10.1101/593400

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