本篇我们将介绍miRNA与mRNA结合预测、LncRNA与miRNA结合预测、LncRNA与蛋白RNP结合预测相关内容
miRNA是非编码调控小分子,通过抑制基因表达发挥作用,前体pri-miRNA、pre-miRNA通过核内的drosa酶作用,由核孔复合体进入至胞浆中,在通过Dicer酶的剪切,形成成熟的miRNA,AGO2可介导miRNA结合至mRNA的3’UTR,进而对基因的表达进行抑制,可在mRNA、蛋白水平发生降解作用
我们对数据的整理,通过数据库查询分类、数据库功能及用途、示例结合分析、数据库优化等这四大项,进行阐述和演示数据库的查询和使用,希望对您的实验项目有所帮助
数据库查询分类
① microRNA.org:http://www.microrna.org/microrna/home.do
② TargetScan:http://www.targetscan.org/vert_70/
③ starbase: http://starbase.sysu.edu.cn/
④ Tarbase: http://www.tarbase.com/
⑤ deepBase:http://deepbase.sysu.edu.cn/
⑥ miRanda: http://www.microrna.org/microrna/home.do
⑦ RNAhybrid:https://bibiserv.cebitec.uni-bielefeld.de/
⑧ CoGeMiR:http://cogemir.tigem.it/
数据库功能及用途(常用数据库)
1. microRNA.org:
Predicted microRNA targets & targetdownregulation scores. Experimentally observed expression patterns
数据库功能:1. mirSVR predicted target site scoringmethod: Comprehensive modeling of microRNA targets predicts functionalnon-conserved and non-canonical sites
2. microRNA target predictions: ThemicroRNA.org resource: targets and expression.
3. miRanda application: Human MicroRNAtargets.
4. miRanda algorithm: MicroRNA targets inDrosophila.
2. TargetScan:
Search for predicted microRNA targets inmammals
数据库功能:Search for predicted microRNA targets inmammals
3. starbase:
CLIP-Seq, Pan-Cancer. Portal, Visualize,Analyze, Discover.
数据库功能:
1. starBase is designed for decodingPan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenousRNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq(HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data and tumor samples (14 cancer types,>6000 samples).
2. starBase is also developed fordeciphering Protein-RNA and miRNA-target interactions, such as protein-lncRNA,protein-sncRNA, protein-mRNA, protein-pseudogene, miRNA-lncRNA, miRNA-mRNA,miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA interactions and ceRNA networksfrom 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets.
3. starBase provides miRFunction andceRNAFunction web tools to predict the function of ncRNAs (miRNAs, lncRNAs,pseduogenes) and protein-coding genes from the miRNA-mediated (ceRNA)regulatory networks
示例结合分析:
microRNA.org:
预测已知mRNA结合的miRNA:以H19为例
1. 打开主页面
2. 点击“targetmRNA”,对话框输入h19,选择种属
3. 点击“GO”,即可获取得到预测结合的miRNA
已知miRNA,查询该miRNA调控的mRNA:以mir-9为例
1. 打开主页面
2. 点击“miRNA”,对话框输入miR-9,选择种属
3. 点击“go”,即可获取miR-9调控的mRNA
数据库优化:
microRNA.org是一款预测可以预测miRNA的靶标mRNA,以及引起靶标基因下调的得分值,以及miRNA的表达情况,也可以预测mRNA结合的miRNA,无法预测得到miRNA的调控网络
2. starBase:以mir-9为例
①打开主页面
②点击“miRNA-mRNA”,点击(两种查询:miRNA-mRNA intersections、miRNA-mRNAinteractions)
③这里我们演示miRNA-mRNA interactions的示例
数据库优化:
Starbase可查询miRNA、LncRNA、mRNA相互调控和结合的预测,存储了大量的互作网络结合的miRNA,ceRNA的竞争结合,RNA蛋白结合等数据
长链非编码RNA(Long-noncodingRNA,lncRNA)是一类转录本长度大于200bp的非编码RNA,可作为人类基因组中一类重要的调控分子通过多种方式发挥其生物学功能. 近年来的研究表明,lncRNA也可以作为一种竞争性内源性RNA(competing endogenous RNA),与miRNA互作结合,形成ceRNA的竞争机制
数据库查询分类
①lncRNABase:http://starbase.sysu.edu.cn/mirLncRNA.php
② starbase: http://starbase.sysu.edu.cn/
③RegRNA2.0:http://regrna2.mbc.nctu.edu.tw/detection.html
数据库功能及用途:
1. lncRNABase
数据库功能:
View the predicted miRNA-lncRNAinteractions by scanning lncRNA sequences overlapping with CLIP-Seq peaks forpotential microRNA targets (miRanda/mirSVR) and then output the detailedinformation. Here, we list predicted miRNA-target interactions overlapped withCLIP-Seq data
2. starbase:
数据库功能:
1. starBase is designed for decodingPan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenousRNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq(HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data and tumor samples (14 cancer types,>6000 samples).
2. starBase is also developed fordeciphering Protein-RNA and miRNA-target interactions, such as protein-lncRNA,protein-sncRNA, protein-mRNA, protein-pseudogene, miRNA-lncRNA, miRNA-mRNA,miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA interactions and ceRNA networksfrom 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets.
3. starBase provides miRFunction andceRNAFunction web tools to predict the function of ncRNAs (miRNAs, lncRNAs,pseduogenes) and protein-coding genes from the miRNA-mediated (ceRNA)regulatory networks
3. RegRNA2.0:
an integrated web server for identifyingfunctional RNA motifs and sites
示例结合分析:
以H19为例
lncRNABase:
1. 打开主页面
2. 在“lncRNAGene Symbol”对话框中输入H19
3. 点击“search”,查询即可获取
长链非编码RNAs(longnon-coding RNAs,lncRNAs)在表观遗传、转录和转录后水平上调控基因表达中起着重要作用,能够通过多种机制,包括遗传印记、染色质重塑、剪切调控、mRNA降解和翻译调控确定lncRNAs的功能,探索lncRNAs的主要工具包括微阵列、RNA测序(RNA-seq)、Northern blotting、实时定量逆转录聚合酶链式反应(qRT-PCR),荧光原位杂交(FISH)、RNA干扰(RNAi)、RNA-结合蛋白质免疫沉淀(RIP)、通过RNA纯化进行染色质分离(ChIRP)、交联免疫沉淀(CLIP)和生物信息学预测等方法,LncRNA可与蛋白互作结合,调控基因的表达、转录、修饰等生物学过程
以下是我们对数据的整理,通过数据库查询分类、数据库功能及用途、示例结合分析、数据库优化等这四大项,进行阐述和演示数据库的查询和使用,希望对您的实验项目有所帮助
数据库查询分类
RPISeq :http://pridb.gdcb.iastate.edu/RPISeq/
数据库功能及用途:
RPISeq
数据库功能:
Submit a protein sequence and an RNAsequence to predict the interaction probability.
实例分析:
以蛋白AGO2和LncRNA H19为例
Interaction probabilities
Prediction using RF classifier 0.55
Prediction using SVM classifier 0.54
两者数值均>0.5,表示预测会相互结合
数据库优化:
该网站可预测已知的蛋白和已知的RNA序列,通过RF值和SVM值,来评估RNA与蛋白的结合概率
微信ID:gzscbio
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