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基于中值的JS散度可变剪接差异分析研究

刘文斌 王兵 方刚 石晓龙 许鹏

引用本文: 刘文斌, 王兵, 方刚, 石晓龙, 许鹏. 基于中值的JS散度可变剪接差异分析研究[J]. 电子与信息学报, doi: 10.11999/JEIT190941 shu
Citation:  Wenbin LIU, Bing WANG, Gang FANG, Xiaolong SHI, Peng XU. Study on the Differential Analysis of Alternative Splicing Based on the Median Value by Jensen-Shannon Divergence[J]. Journal of Electronics and Information Technology, doi: 10.11999/JEIT190941 shu

基于中值的JS散度可变剪接差异分析研究

    作者简介: 刘文斌: 男,1969年生,教授,研究方向为生物信息学;
    王兵: 男,1993年生,硕士生,研究方向为生物信息学;
    方刚: 男,1969年生,教授,研究方向为生物信息学;
    石晓龙: 男,1975年生,教授,研究方向为生物信息学;
    许鹏: 男,1986年生,博士后,研究方向为生物信息学
    通讯作者: 刘文斌,wbliu6910@126.com
  • 基金项目: 国家重点研发计划2019YFA0706402,国家自然科学基金(61572367, 61573017, 61972107, 61972109)

摘要: 可变剪接是一种广泛存在于生物体中造成蛋白质多样性的重要机制,它对细胞的增殖、分化、发育、凋亡等一系列重要的生物过程具有重要精细调控的作用。近年来,人们发现多种复杂疾病的产生往往伴随着剪接异构体的紊乱表达。为了研究剪接异构体在整体分布上的差异,该文提出一种基于中值的JS散度可变剪接差异分析方法。结果表明,该文的方法能够发现大量在剪接异构体整体分布上具有显著差异的基因。这些基因不仅富集在一些癌症密切相关的通路,而且也富集在一些基于可变剪接调控的信号通路、细胞分裂过程和蛋白质功能等通路。此外,与基因层次的差异分析相比,可变剪接显著差异的基因在生存分析方面也具有更好的性能。总之,该文提出基于中值的JS散度可变剪接差异分析方法,将为进一步揭示可变剪接在癌症中的机制奠定基础。

English

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  • 图 1  4种方法差异基因的韦恩图

    图 2  乳腺癌驱动基因的PPI网络

    图 3  癌症分类结果比较

    图 4  差异基因生存分析曲线

    表 1  癌症数据集统计信息

    癌症癌症样本正常样本基因个数异构体个数
    BRCA11001121017833481
    LIHC37350887126234
    UCEC11724976530953
    下载: 导出CSV

    表 2  KEGG通路分析

    癌症通路(Gen Model)通路(AS Model)
    Focal adhesionCell cycle
    PI3K-Akt signaling pathwayp53 signaling pathway
    Tight junctionPathways in cancer
    Regulation of lipolysis in adipocytesOocyte meiosis
    BRCAPathways in cancerViral carcinogenesis
    Rap1 signaling pathwayAdherens junction
    cAMP signaling pathwayPurine metabolism
    ABC transportersPI3K-Akt signaling pathway
    Cell adhesion molecules (CAMs)Hippo signaling pathway
    Leukocyte transendothelial migrationMetabolic pathways
    Metabolic pathwaysMetabolic pathways
    Fatty acid degradationPhagosome
    Protein processing in endoplasmic reticulumFc gamma R-mediated phagocytosis
    ProteasomeLeishmaniasis
    LIHCmTOR signaling pathwayHomologous recombination
    AMPK signaling pathwaySphingolipid metabolism
    Valine, leucine and isoleucine degradationECM-receptor interaction
    SpliceosomeCell cycle
    Ubiquitin mediated proteolysisFanconi anemia pathway
    Insulin signaling pathwayRibosome biogenesis in eukaryotes
    Vascular smooth muscle contractionOsteoclast differentiation
    cGMP-PKG signaling pathwayCell cycle
    Focal adhesionAdherens junction
    MAPK signaling pathwayAxon guidance
    UCECProteoglycans in cancerPhagosome
    Calcium signaling pathwayRheumatoid arthritis
    Platelet activationAMPK signaling pathway
    Adherens junctionPPAR signaling pathway
    Oxytocin signaling pathwayECM-receptor interaction
    Ras signaling pathwayPlatelet activation
    下载: 导出CSV
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  • 通讯作者:  刘文斌, wbliu6910@126.com
  • 收稿日期:  2019-11-22
  • 录用日期:  2020-04-24
  • 网络出版日期:  2020-05-13
通讯作者: 陈斌, bchen63@163.com
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