靶向Wnt1的miRNA与circRNA及其靶基因间相互作用的生物信息学分析
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山东省罕少见病重点实验室,山东省医药生物技术研究中心,山东省医学科学院;济南大学-山东省医学科学院 医学与生命科学学院;,天津市武清区人民医院,山东省立医院小儿骨科,山东省罕少见病重点实验室,山东省医药生物技术研究中心,山东省医学科学院;济南大学-山东省医学科学院 医学与生命科学学院;,山东省罕少见病重点实验室,山东省医药生物技术研究中心,山东省医学科学院;济南大学-山东省医学科学院 医学与生命科学学院;,山东省罕少见病重点实验室,山东省医药生物技术研究中心,山东省医学科学院;济南大学-山东省医学科学院 医学与生命科学学院;,山东省罕少见病重点实验室,山东省医药生物技术研究中心,山东省医学科学院;济南大学-山东省医学科学院 医学与生命科学学院;

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山东省英才基金项目(2015ZRC03171)与山东省国际科技合作项目资助


Bioinformatics Interaction Analysis of Wnt1-Targeting miRNAs and Their Corresponding circRNAs and Target Genes
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School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences;Key Laboratory for Rare DdDd Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences,The People's Hospital of Wuqing District, Tianjin,Department of Pediatric Orthopaedics, Shandong Provincial Hospital , Shandong, Jinan,School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences;Key Laboratory for Rare DdDd Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences,School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences;Key Laboratory for Rare DdDd Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences,School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences;Key Laboratory for Rare DdDd Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences,School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences;Key Laboratory for Rare DdDd Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong Academy of Medical Sciences

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This work was supported by grants from The Talent Fund Project of Shandong Province(2015ZRC03171), and the International Cooperation Project for the Department of Science& Technology of Shandong Province

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    摘要:

    为对靶向Wnt1的7种miRNAs进行circRNAs及其靶基因的预测,同时分析其与circRNAs及靶基因间的相互作用,分别采用Starbase及miRWALK软件,对文献报道的靶向Wnt1基因的let-7e、miR-21、miR-34a、miR-122、miR-148a、miR-148b与miR-152等7种miRNAs的circRNAs和对应的靶基因进行生物信息学预测.利用Cytoscape 3.2.1对这7种miRNAs和预测所得到的circRNAs及对应的靶基因进行网络分析.并进一步对预测到的靶基因通过DAVID软件进行通路分析. Starbase软件对这7种不同miRNAs所预测的靶circRNAs的数量分别为58、15、41、20、28、28、28个.分别比较miRWALK中7~9个以上软件共有的miRNAs及其与靶基因的关系,发现CHD7基因是唯一一个在三种不同预测范围内与miR-21、 miR-148a、 miR-148b和miR-152等4种miRNAs相对应的靶基因.CNOT6、NBEA、ZFYVE26与ZDHHC17是在两种不同预测范围内与至少4个miRNAs相对应的靶基因.在7种miRNAs所预测靶基因相关的KEGG信号通路中,7~9个软件以上共有的信号通路为Focal adhesion信号通路、MAPK信号通路、Notch信号通路与TGF-beta信号通路.在MAPK信号通路中DUSP1与MRPS35_hsa_circ_001042 均分别是与miR-21、miR-148a、miR-148b及miR-152等4种miRNAs相互作用的靶基因与circRNA.本研究对靶向Wnt1的miRNAs及其相互作用的circRNAs、靶基因与信号通路等进行了网络分析与预测,为进一步分析它们之间的相互作用奠定了基础.

    Abstract:

    To predict circRNAs and target genes for seven known Wnt1-targeting miRNAs, then further analyze the interaction among these seven miRNAs and their corresponding circRNAs and target genes, seven reported Wnt1-targeting miRNAs including let-7e, miR-21, miR-34a, miR-122, miR-148a, miR-148b and miR-152 were predicted for their interacting circRNAs and target genes by Starbase and miRWALK softwares, respectively. Then the network analysis of miRNA and their interaction circRNAs and target genes was built by Cytoscape3.2.1 software. DAVID was performed to analyze singaling pathway according to miRNAs predicted target genes. The number of target circRNAs predicted by Starbase software for these 7 different miRNAs were 58, 15, 41, 20, 28, 28 and 28, respectively. Comparing the relationship between miRNAs and their target gene in more than 7~9 softwares predicted by miRWALK, we found that the CHD7 gene is the only one corresponding with miR-21, miR-148-a and miR-148 and miR-152 in more than 7 softwares predications. CNOT6, NBEA, ZFYVE26 and ZDHHC17 were the target genes equivalent with at least 4 miRNAs predicted by both 7 and 8 different softwares in miRWALK. For KEGG signaling pathways, Focl adhesion, MAPK, Notch and TGF-beta signaling pathways were all predicted by seven miRNAs’ target genes in more than 7 different predication softwares of miRWALK. In the MAPK signaling pathway, DUSP1 was found to have interaction with miR-21,miR-148a, miR-148b and miR-152 simultaneously, MRPS35_hsa_circ_001042 was also predicted to interact with these four miRNAs. We found that the DUSP1 and MRPS35_hsa_circ_001042 in the MAPK signaling pathway, are the target genes and circRNA, interacted with miR-21,miR-148a, miR-148b, and miR-152, respectively. In the study, we analyzed known Wnt1-targeting miRNAs and their corresponding circRNAs and predicted target genes, signaling pathway and interaction network were also involved. The study laid the foundation for the further analysis of the interaction among Wnt1-targeting miRNAs, circRNAs and target genes.

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张 遥,任秀智,王延宙,马 翔,左清利,韩金祥,鲁艳芹.靶向Wnt1的miRNA与circRNA及其靶基因间相互作用的生物信息学分析[J].生物化学与生物物理进展,2016,43(11):1094-1101

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  • 收稿日期:2016-08-01
  • 最后修改日期:2016-10-13
  • 接受日期:2016-10-20
  • 在线发布日期: 2016-11-22
  • 出版日期: 2016-11-20
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