中文版 | English
题名

基于植物公共RNA-seq数据的数据整合、挖掘和可视化

其他题名
DATA INTEGRATION, MINING AND VISUALIZATION OF PUBLIC PLANT RNA-SEQ DATA
姓名
姓名拼音
ZHANG Hong
学号
12032141
学位类型
硕士
学位专业
071001 植物学
学科门类/专业学位类别
07 理学
导师
翟继先
导师单位
生物系
论文答辩日期
2023-05-16
论文提交日期
2023-06-25
学位授予单位
南方科技大学
学位授予地点
深圳
摘要
基因表达是生物体将遗传信息转化为生命活性物质(RNA 或者蛋白质)的重要过程,是研究生命活动的重要指标。作为基因表达研究的金标准,转录组测序(RNA-seq)数据在不同植物研究中均数以万计。为方便植物学者能充分利用已公开的海量植物转录组资源,本研究整合了拟南芥、水稻、玉米、大豆、棉花以及小麦的转录组原始数据,通过统一的标准化分析,分别构建了 ARSArabidopsis RNA-Seq Databasehttp://ipf.sustech.edu.cn/pub/athrdb/)和 PPRDPlant Public RNA-seq Databasehttp://ipf.sustech.edu.cn/pub/plantrna/)数据库,共涵盖六个物种的超72,000 RNA-seq 样本、2,000 多组遗传相关的突变体和 4,000 多组不同条件下处理的相关数据。这些资源对植物研究人员发掘感兴趣基因的组织特异性、发育动态、以及转录调控等提供了便利。
在此基础上,本研究进一步搭建了植物内含子剪接效率 PISEPlant Intron-Splicing Efffficiency Databasehttps://plantintron.com/)数据库。剪接是 mRNA 成熟的关键步骤,可变剪接是增加基因功能多样性的重要途径。作为可变剪接最常见的形式,内含子保留在植物响应环境信号中发挥重要作用。尽管存在海量公共RNA-seq数据,但并没可供查询单基因或者内含子剪接效率的资源。PISE 数据库包含了超57,000 个植物公共 RNA-seq 文库,覆盖了包括拟南芥、水稻、玉米和大豆已注释的约 160 万个内含子。用户可查看基因内含子在所有文库中的剪接效率。以上数据库均支持多形式的个性化查询选项,同时还提供多样式的图表来展示分析结果。综上,该研究为植物学者利用公共数据开展研究提供了便利。
关键词
语种
中文
培养类别
独立培养
入学年份
2020
学位授予年份
2023-06
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专题生命科学学院_生物系
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张洪. 基于植物公共RNA-seq数据的数据整合、挖掘和可视化[D]. 深圳. 南方科技大学,2023.
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