Dataset Information

PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks.

ABSTRACT: Circular RNA (circRNA) is a novel type of endogenous noncoding RNA with covalently closed loop structures, which are widely expressed in various tissues and have functional implications in cellular processes. Acting as competing endogenous RNAs (ceRNAs), circRNAs are important regulators of miRNA activities. The identification of these circRNAs underlines the increasing complexity of ncRNA-mediated regulatory networks. However, more biological evidence is required to infer direct circRNA-miRNA associations while little attention has been paid to circRNAs in plants as compared to the abundant research in mammals. PlantCircNet is presented as an integrated database that provides visualized plant circRNA-miRNA-mRNA regulatory networks containing identified circRNAs in eight model plants. The bioinformatics integration of data from multiple sources reveals circRNA-miRNA-mRNA regulatory networks and helps identify mechanisms underlying metabolic effects of circRNAs. An enrichment analysis tool was implemented to detect significantly overrepresented Gene Ontology categories of miRNA targets. The genomic annotations, sequences and isoforms of circRNAs were also investigated. PlantCircNet provides a user-friendly interface for querying detailed information of specific plant circRNAs. The database may serve as a resource to facilitate plant circRNA research. Several circRNAs were identified to play potential regulatory roles in flower development and response to environmental stress from regulatory networks related with miR156a and AT5G59720, respectively. This present research indicated that circRNAs could be involved in diverse biological processes. Database URL: http://bis.zju.edu.cn/plantcircnet/index.php.

SUBMITTER: Zhang P

PROVIDER: S-EPMC5727401 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks.

Zhang Peijing P Meng Xianwen X Chen Hongjun H Liu Yongjing Y Xue Jitong J Zhou Yincong Y Chen Ming M

Database : the journal of biological databases and curation 20170101

Circular RNA (circRNA) is a novel type of endogenous noncoding RNA with covalently closed loop structures, which are widely expressed in various tissues and have functional implications in cellular processes. Acting as competing endogenous RNAs (ceRNAs), circRNAs are important regulators of miRNA activities. The identification of these circRNAs underlines the increasing complexity of ncRNA-mediated regulatory networks. However, more biological evidence is required to infer direct circRNA-miRNA a ...[more]

PMID: 31725858

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Project description:BackgroundMacrophage play a crucial role in regulating tumor progression. This study intended to investigate the circular RNA (circRNA) regulatory network associated with macrophage infiltration in hepatocellular carcinoma (HCC).MethodsThe immune cell fractions of HCC from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium were calculated by Estimation of the Proportion of Immune and Cancer cells algorithm. The differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs) and circRNAs (DEcircRNAs) were identified from HCC and adjacent non-tumor cases of TCGA or Gene Expression Omnibus database. The DEmRNAs related to macrophage were selected by weighted gene co-expression network analysis and then utilized to generate the circRNA-miRNA-mRNA network. A hub circRNA regulatory network was established based on the co-expressed DEmiRNAs and DEmRNAs owning contrary correlation with the clinical characteristics, survival and macrophage infiltration level. A gene signature based on the DEmRNAs in hub network was also generated for further evaluation. The circRNA binding bite for miRNA was detected by luciferase assay.ResultsHigh macrophage fraction predicted good survival for HCC. A circRNA-miRNA-mRNA network was constructed by 27 macrophage related DEmRNAs, 21 DEmiRNAs, and 15 DEcircRNAs. Among this network, the expression of hsa-miR-139-5p was negatively correlated with CDCA8, KPNA2, PRC1 or TOP2A. Hsa-miR-139-5p low or targeted DEmRNA high expression was associated with low macrophage infiltration, high grade, advanced stage and poor prognosis of HCC. Additionally, the risk score generated by 4-DEmRNA signature could reflect the macrophage infiltration status and function as an independent prognostic factor for HCC. Finally, hsa_circ_0007456 acting on hsa-miR-139-5p related network was viewed as the hub circRNA regulatory network. Taken together, some circRNA regulatory networks may be associated with macrophage infiltration, which provides clues for mechanism study and therapeutic strategies of HCC.

Project description:Coxsackievirus A16 (CV-A16) has caused worldwide epidemics of hand, foot, and mouth disease (HFMD) in infants and preschool children. Circular RNAs (circRNAs), a class of noncoding RNA molecules, participate in the progression of viral infectious diseases. Although the function of circRNAs has been a heavily researched topic, their role in CV-A16 infection is still unclear. In this study, the viral effects of CV-A16 on the cellular circRNA transcriptome were investigated using next-generation sequencing technology. The results showed that a total of 8726, 8611, and 6826 circRNAs were identified at 0, 12, and 24 h postinfection, respectively. Moreover, it was found that 1769 and 1192 circRNAs were differentially expressed in at 12 and 24 h postinfection, respectively. The common differentially expressed circRNAs were used for functional annotation analysis, and it was found that the parent genes of differentially expressed circRNAs might be associated with the viral infection process, especially the "Immune system process" in GO analysis and the "Inflammation mediated by chemokine and cytokine signaling pathway" in KEGG analysis. Subsequently, circRNA-miRNA-mRNA regulatory networks were constructed, and the hsa_circ_0004447/hsa-miR-942-5p/MMP2, hsa_circ_0078617/hsa-miR-6780b-5p/MMP2 and hsa_circ_0078617/hsa-miR-5196-5p/MMP2 regulatory axes were identified by enrichment analysis as important networks during the progression of CV-A16 infection. Finally, six dysregulated circRNAs were selected for validation and were verified to be consistent with the sequencing results. Considering all of these results, to the best of our knowledge, this study is the first to present a comprehensive overview of circRNAs induced by CV-A16 infection, and this research demonstrated that a network of enriched circRNAs and circRNA-associated competitive endogenous RNAs (ceRNAs) is involved in the regulation of CV-A16 infection, thereby helping to elucidate the mechanisms underlying CV-A16-host interactions.

Dataset Information

PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks.

Publications

PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks.

Similar Datasets

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