論文 - 詳細
| RRC ID | 59564 |
|---|---|
| 著者 | Nomoto Y, Kubota Y, Ohnishi Y, Kasahara K, Tomita A, Oshime T, Yamashita H, Fahmi M, Ito M. |
| タイトル | Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans. |
| ジャーナル | PLoS One |
| 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. |
| 巻・号 | 14(9) |
| ページ | e0215187 |
| 公開日 | 2019-1-1 |
| DOI | 10.1371/journal.pone.0215187 |
| PII | PONE-D-19-08337 |
| PMID | 31504044 |
| PMC | PMC6736238 |
| MeSH | Animals Caenorhabditis elegans Caenorhabditis elegans Proteins / genetics* Caenorhabditis elegans Proteins / metabolism Gene Expression Regulation, Developmental Gene Regulatory Networks* Genomics / methods* Neurogenesis Protein Interaction Maps* Software* |
| IF | 2.776 |
| 引用数 | 1 |
| オルトメトリクス指標 |
オルトメトリクス指標項目
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| 最多言及媒体 | X(Twitter) |
| 各媒体での言及数の合計 | 2 |
| 過去6か月間でのオルトメトリクス指標の変動値 | 0.0 |
| リソース情報 | |
| 線虫 | tm1276 tm291 tm1476 |