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

English version

Autoři: Yusuke Nomoto ^aff001; Yukihiro Kubota ^aff002; Yuto Ohnishi ^aff001; Kota Kasahara ^aff002; Aimi Tomita ^aff001; Takehiro Oshime ^aff001; Hiroki Yamashita ^aff001; Muhamad Fahmi ^aff002; Masahiro Ito ^aff001
Působiště autorů: Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan ^aff001; Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan ^aff002
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0215187

Souhrn

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.

Klíčová slova:

Biology and life sciences – Genetics – Gene expression – Gene regulation – Genomics – Genome analysis – Gene prediction – Organisms – Eukaryota – Animals – Invertebrates – Nematoda – Caenorhabditis – Caenorhabditis elegans – Cell biology – Signal transduction – Cell signaling – Signaling cascades – Wnt signaling cascade – Stress signaling cascade – Computational biology – Molecular biology – Molecular biology techniques – Molecular biology assays and analysis techniques – Nucleic acid analysis – RNA analysis – Neuroscience – Developmental neuroscience – Research and analysis methods – Animal studies – Experimental organism systems – Model organisms – Animal models

Zdroje

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

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