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JustRNA: a database of plant long noncoding RNA expression profiles and functional network.
Tseng, Kuan-Chieh; Wu, Nai-Yun; Chow, Chi-Nga; Zheng, Han-Qin; Chou, Chin-Yuan; Yang, Chien-Wen; Wang, Ming-Jun; Chang, Song-Bin; Chang, Wen-Chi.
Afiliación
  • Tseng KC; Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
  • Wu NY; Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan.
  • Chow CN; Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan.
  • Zheng HQ; Yourgene Health, No. 376-5 Fuxing Rd, Shulin Dist., New Taipei City 238, Taiwan.
  • Chou CY; Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
  • Yang CW; Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan.
  • Wang MJ; Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
  • Chang SB; Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
  • Chang WC; Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
J Exp Bot ; 74(17): 4949-4958, 2023 09 13.
Article en En | MEDLINE | ID: mdl-37523674
Long noncoding RNAs (lncRNAs) are regulatory RNAs involved in numerous biological processes. Many plant lncRNAs have been identified, but their regulatory mechanisms remain largely unknown. A resource that enables the investigation of lncRNA activity under various conditions is required because the co-expression between lncRNAs and protein-coding genes may reveal the effects of lncRNAs. This study developed JustRNA, an expression profiling resource for plant lncRNAs. The platform currently contains 1 088 565 lncRNA annotations for 80 plant species. In addition, it includes 3692 RNA-seq samples derived from 825 conditions in six model plants. Functional network reconstruction provides insight into the regulatory roles of lncRNAs. Genomic association analysis and microRNA target prediction can be employed to depict potential interactions with nearby genes and microRNAs, respectively. Subsequent co-expression analysis can be employed to strengthen confidence in the interactions among genes. Chromatin immunoprecipitation sequencing data of transcription factors and histone modifications were integrated into the JustRNA platform to identify the transcriptional regulation of lncRNAs in several plant species. The JustRNA platform provides researchers with valuable insight into the regulatory mechanisms of plant lncRNAs. JustRNA is a free platform that can be accessed at http://JustRNA.itps.ncku.edu.tw.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: MicroARNs / ARN Largo no Codificante Tipo de estudio: Prognostic_studies Idioma: En Revista: J Exp Bot Asunto de la revista: BOTANICA Año: 2023 Tipo del documento: Article País de afiliación: Taiwán Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
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PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: MicroARNs / ARN Largo no Codificante Tipo de estudio: Prognostic_studies Idioma: En Revista: J Exp Bot Asunto de la revista: BOTANICA Año: 2023 Tipo del documento: Article País de afiliación: Taiwán Pais de publicación: Reino Unido