基于Linux的长非编码RNA信息系统
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摘要
长非编码RNA(long non-coding RNA,lncRNA)已成为生物信息学研究领域的热点,涉及lncRNA基因注释、结构预测、功能和机制等研究方向。研究也产生了大量分布零散的lncRNA信息(包括lncRNA知识、研究方法和数据库等),而现有的lncRNA信息平台功能单一,缺乏对信息资源的整合。针对这一问题,文章建立基于Linux的lncRNA信息系统。该系统主要由数据库模块、网页服务模块和软件工具模块等3部分构成。基于此架构,系统通过由lncRNA知识、GBrowse浏览器、分析和计算、工具信息和数据库信息等页面向网络用户提供信息服务。测试结果表明,系统能够提供lncRNA知识的展示、数据可视化、预测和转录分析、常用的工具和数据库信息等服务。该系统能有效整合lncRNA研究相关的多源信息,进而提高lncRNA研究的效率。
The study on long non-coding RNAs has been a hot topic in bioinformatic research area,which includes several directions,e.g.lncRNA gene annotation,structure prediction,function and mechanism study.This results in a large amount of distributed lncRNA information,e.g.lncRNA knowledge,research methods and databases,however current lncRNA information platforms that only have simple functions are lack of integration of various information.Focusing on this problem,we constructed a lncRNA information system based on Linux,which is composed of three models of database,web service and software tools.Based on the system framework,the lncRNA information is provided to network users by web pages of lncRNA knowledge,GBrowse,analysis,computation,tools and databases information.Testing result manifests that our system can provide users with services including lncRNA related knowledge presentation,data visualization,prediction and transcription analysis,and information of tools and databases.Our system can efficiently integrate multi-source information about the lncRNAs,therefore improving further lncRNA study.
The study on long non-coding RNAs has been a hot topic in bioinformatic research area,which includes several directions,e.g.lncRNA gene annotation,structure prediction,function and mechanism study.This results in a large amount of distributed lncRNA information,e.g.lncRNA knowledge,research methods and databases,however current lncRNA information platforms that only have simple functions are lack of integration of various information.Focusing on this problem,we constructed a lncRNA information system based on Linux,which is composed of three models of database,web service and software tools.Based on the system framework,the lncRNA information is provided to network users by web pages of lncRNA knowledge,GBrowse,analysis,computation,tools and databases information.Testing result manifests that our system can provide users with services including lncRNA related knowledge presentation,data visualization,prediction and transcription analysis,and information of tools and databases.Our system can efficiently integrate multi-source information about the lncRNAs,therefore improving further lncRNA study.
引文
[1]Mattick J S,Rinn J L.Discovery and annotation of long noncoding RNAs[J].Nat Struct Mol Biol,2015,22(01):5-7.
[2]Smith M A,Gesell T,Stadler P F,et al.Widespread purifying selection on RNA structure in mammals[J].Nucleic Acids Res,2013,41(17):8220-8236.
[3]MORRIS K V,MATTICK J S.The rise of regulatory RNA[J].Nat Rev Genet,2014,15(06):423-437.
[4]Ma L,Li A,Zou D,et al.LncRNAWiki:harnessing community knowledge in collaborative curation of human long non-coding RNAs[J].Nucleic Acids Research,2015,43(D1):D187-D192.
[5]Harrow J,Frankish A,Gonzalez J M,et al.GENCODE:The reference human genome annotation for The ENCODEProject[J].Genome research,2012,22(09):1760-1774.
[6]Xie C,Yuan J,Li H,et al.NONCODEv4:exploring the world of long non-coding RNA genes[J].Nucleic Acids Research,2014,42(D1):D98-D103.
[7]Jiang Q,Wang J,Wu X,et al.LncRNA2Target:a database for differentially expressed genes after lncRNA knockdown or overexpression[J].Nucleic Acids Research,2015,43(D1):D193-D196.
[8]Stein L D,Mungall C,Shu S,et al.The Generic Genome Browser:A Building Block for a Model Organism System Database[J].Genome research,2002,12(10):1599-1610.
[9]Sun L,Zhang Z,Bailey T,et al.Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1knockout study[J].BMC Bioinformatics,2012,13(01):331.
[10]Sun L,Liu H,Zhang L,et al.lncRScan-SVM:A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine[J].PLoS ONE,2015,10(10):e0139654.
[2]Smith M A,Gesell T,Stadler P F,et al.Widespread purifying selection on RNA structure in mammals[J].Nucleic Acids Res,2013,41(17):8220-8236.
[3]MORRIS K V,MATTICK J S.The rise of regulatory RNA[J].Nat Rev Genet,2014,15(06):423-437.
[4]Ma L,Li A,Zou D,et al.LncRNAWiki:harnessing community knowledge in collaborative curation of human long non-coding RNAs[J].Nucleic Acids Research,2015,43(D1):D187-D192.
[5]Harrow J,Frankish A,Gonzalez J M,et al.GENCODE:The reference human genome annotation for The ENCODEProject[J].Genome research,2012,22(09):1760-1774.
[6]Xie C,Yuan J,Li H,et al.NONCODEv4:exploring the world of long non-coding RNA genes[J].Nucleic Acids Research,2014,42(D1):D98-D103.
[7]Jiang Q,Wang J,Wu X,et al.LncRNA2Target:a database for differentially expressed genes after lncRNA knockdown or overexpression[J].Nucleic Acids Research,2015,43(D1):D193-D196.
[8]Stein L D,Mungall C,Shu S,et al.The Generic Genome Browser:A Building Block for a Model Organism System Database[J].Genome research,2002,12(10):1599-1610.
[9]Sun L,Zhang Z,Bailey T,et al.Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1knockout study[J].BMC Bioinformatics,2012,13(01):331.
[10]Sun L,Liu H,Zhang L,et al.lncRScan-SVM:A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine[J].PLoS ONE,2015,10(10):e0139654.