lncRNA与疾病关联关系预测研究进展
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摘要
lncRNAs(long noncoding RNAs)是一类长度超过200个核苷酸的非编码RNAs,越来越多的证据表明lncRNAs在许多生物过程中起关键作用。lncRNAs也与多种疾病的发生和发展有密切的联系。近年来,很多研究人员关注于预测lncRNA与疾病的关联预测的计算模型,这可以有效地减少生物实验的时间和成本。本文总结了近年来有关lncRNA与疾病关联预测的一些数据资源和有代表性的计算方法,并对当前存在的问题进行了分析,讨论了未来的挑战和发展方向。
lncRNAs( long noncoding RNAs) are the kind of noncoding RNAs with more than 200 nt nucleotides in length. There are increasing evidences showing that lncRNAs play key roles in many biological processes. In recent years,many researchers have focused on computation models for predicting lncRNA-disease association,which can effectively reduce the time and cost of biological experiments. The paper summarizes some data resources and representative computation methods related to the prediction of lncRNA-disease association in recent years. It also analyzes the existing problems and discusses future challenges and directions.
lncRNAs( long noncoding RNAs) are the kind of noncoding RNAs with more than 200 nt nucleotides in length. There are increasing evidences showing that lncRNAs play key roles in many biological processes. In recent years,many researchers have focused on computation models for predicting lncRNA-disease association,which can effectively reduce the time and cost of biological experiments. The paper summarizes some data resources and representative computation methods related to the prediction of lncRNA-disease association in recent years. It also analyzes the existing problems and discusses future challenges and directions.
引文
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[2]LOURO R,SMIRNOVA A S,VERJOVSKI-ALMEIDA S. Long intronic noncoding RNA transcription:Expression noise or expression choice?[J]. Genomics,2009,93(4):291-298.
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[4]CHEN X,YAN C C,ZHANG X,et al. Long non-coding RNAs and complex diseases:From experimental results to computational models[J]. Briefings in Bioinformatics,2016,18(4):558-576.
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[8] CHAKRABORTY S,DEB A,MAJI R K,et al. LncRBase:An enriched resource for lnc RNA information[J]. PloS One,2014,9(9):e108010.
[9]LYNN S,ARZE C,NADENDLA S,et al. Disease ontology:A backbone for disease semantic integration[J]. Nucleic Acids Research,2011,40(Database issue):940-946.
[10]AMBERGER J S,BOCCHINI C A,SCHIETTECATTE F,et al.OM IM.org:Online mendelian inheritance in man(OM IM),an online catalog of human genes and genetic disorders[J].Nucleic Acids Research,2015,43(Database issue):789-798.
[11]CHEN G,WANG Z,WANG D,et al. LncRNADisease:A database for long-non-coding RNA-associated diseases[J].Nucleic Acids Research,2013,41(Database issue):983-986.
[12]NING S,ZHANG J,WANG P,et al. Lnc2Cancer:A manually curated database of experimentally supported lncRNAs associated w ith various human cancers[J]. Nucleic Acids Research,2016,44(Database issue):D980-D985.
[13]WANG Y,CHEN L,CHEN B,et al. Mammalian nc RNAdisease repository:A global view of ncRNA-mediated disease netw ork[J]. Cell Death&Disease,2013,4(8):e765.
[14]SUN Jie,SHI Hongbo,WANG Zhenzhen,et al. Inferring novel lnc RNA-disease associations based on a random w alk model of a lnc RNA functional similarity netw ork[J]. M olecular Biosystems,2014,10(8):2074-2081.
[15]ZHOU M,WANG X,LI J,et al. Prioritizing candidate diseaserelated long non-coding RNAs by w alking on the heterogeneous lnc RNA and disease netw ork[J]. M olecular bioSystems,2015,11(3):760-769.
[16]YANG X,GAO L,GUO X,et al. A network based method for analysis of lncRNA-disease associations and prediction of lnc RNAs implicated in diseases[J]. PLoS One,2014,9(1):e87797.
[17]YAO Qianlan,WU Leilei,JIA Li,et al. Global prioritizing disease candidate lncRNAs via a multi-level composite netw ork[J]. Scientific Reports,2017,7:39516.
[18]ZHANG Jingpu, ZHANG Zuping, CHEN Zhigang, et al.Integrating multiple heterogeneous netw orks for novel LncRNAdisease association inference[J]. IEEE/ACM Transactions on Computational Biology&Bioinformatics,2017,PP(99):1.
[19]CHEN Xing,YAN Guiying. Novel human lncRNA-disease association inference based on lnc RNA expression profiles[J].Bioinformatics,2013,29(20):2617-2624.
[20]ZHAO T,XU J,LIU L,et al. Identification of cancer-related lnc RNAs through integrating genome,regulome and transcriptome features[J]. M olecular BioSystems,2014,11(1):126-136.
[21]BISWAS A K,KANG M,KIM D C,et al. Inferring disease associations of the long non-coding RNAs through non-negative matrix factorization[J]. Netw ork M odeling Analysis in Health Informatics&Bioinformatics,2015,4(1):1-17.
[22]LIU Mingxi,CHEN Xing,CHEN Geng,et al. A computational framew ork to infer human disease-associated long noncoding RNAs[J]. PLoS One,2014,9(1):e84408.
[23] LI Jianwei, CHENG Gao, WANG Yuchen, et al. A bioinformatics method for predicting long noncoding RNAs associated w ith vascular disease[J]. Science China Life Sciences,2014,57(8):852-857.
[24] Chen Xing. Predicting lnc RNA-disease associations and constructing lncRNA functional similarity netw ork based on the information of miRNA[J]. Scientific Reports,2015,5:13186.
[2]LOURO R,SMIRNOVA A S,VERJOVSKI-ALMEIDA S. Long intronic noncoding RNA transcription:Expression noise or expression choice?[J]. Genomics,2009,93(4):291-298.
[3]GEISLER S,COLLER J. RNA in unexpected places:Long noncoding RNA functions in diverse cellular contexts[J]. Nature Review s M olecular Cell Biology,2013,14(11):699-712.
[4]CHEN X,YAN C C,ZHANG X,et al. Long non-coding RNAs and complex diseases:From experimental results to computational models[J]. Briefings in Bioinformatics,2016,18(4):558-576.
[5]ZHAO Yi,LI Hui,FANG Shuangsang,et al. NONCODE 2016:An informative and valuable data source of long non-coding RNAs[J]. Nucleic Acids Research,2016,44(Database issue):D203-D208.
[6] VOLDERS P J,HELSENS K,WANG X,et al. LNCipedia:A database for annotated human lnc RNA transcript sequences and structures[J]. Nucleic Acids Research, 2013, 41(Database issue):D246-D251.
[7]QUEK X C,THOMSON D W,MAAG J L,et al. lnc RNAdb v2.0:Expanding the reference database for functional long noncoding RNAs[J]. Nucleic Acids Research,2015,43(Database issue):168-173.
[8] CHAKRABORTY S,DEB A,MAJI R K,et al. LncRBase:An enriched resource for lnc RNA information[J]. PloS One,2014,9(9):e108010.
[9]LYNN S,ARZE C,NADENDLA S,et al. Disease ontology:A backbone for disease semantic integration[J]. Nucleic Acids Research,2011,40(Database issue):940-946.
[10]AMBERGER J S,BOCCHINI C A,SCHIETTECATTE F,et al.OM IM.org:Online mendelian inheritance in man(OM IM),an online catalog of human genes and genetic disorders[J].Nucleic Acids Research,2015,43(Database issue):789-798.
[11]CHEN G,WANG Z,WANG D,et al. LncRNADisease:A database for long-non-coding RNA-associated diseases[J].Nucleic Acids Research,2013,41(Database issue):983-986.
[12]NING S,ZHANG J,WANG P,et al. Lnc2Cancer:A manually curated database of experimentally supported lncRNAs associated w ith various human cancers[J]. Nucleic Acids Research,2016,44(Database issue):D980-D985.
[13]WANG Y,CHEN L,CHEN B,et al. Mammalian nc RNAdisease repository:A global view of ncRNA-mediated disease netw ork[J]. Cell Death&Disease,2013,4(8):e765.
[14]SUN Jie,SHI Hongbo,WANG Zhenzhen,et al. Inferring novel lnc RNA-disease associations based on a random w alk model of a lnc RNA functional similarity netw ork[J]. M olecular Biosystems,2014,10(8):2074-2081.
[15]ZHOU M,WANG X,LI J,et al. Prioritizing candidate diseaserelated long non-coding RNAs by w alking on the heterogeneous lnc RNA and disease netw ork[J]. M olecular bioSystems,2015,11(3):760-769.
[16]YANG X,GAO L,GUO X,et al. A network based method for analysis of lncRNA-disease associations and prediction of lnc RNAs implicated in diseases[J]. PLoS One,2014,9(1):e87797.
[17]YAO Qianlan,WU Leilei,JIA Li,et al. Global prioritizing disease candidate lncRNAs via a multi-level composite netw ork[J]. Scientific Reports,2017,7:39516.
[18]ZHANG Jingpu, ZHANG Zuping, CHEN Zhigang, et al.Integrating multiple heterogeneous netw orks for novel LncRNAdisease association inference[J]. IEEE/ACM Transactions on Computational Biology&Bioinformatics,2017,PP(99):1.
[19]CHEN Xing,YAN Guiying. Novel human lncRNA-disease association inference based on lnc RNA expression profiles[J].Bioinformatics,2013,29(20):2617-2624.
[20]ZHAO T,XU J,LIU L,et al. Identification of cancer-related lnc RNAs through integrating genome,regulome and transcriptome features[J]. M olecular BioSystems,2014,11(1):126-136.
[21]BISWAS A K,KANG M,KIM D C,et al. Inferring disease associations of the long non-coding RNAs through non-negative matrix factorization[J]. Netw ork M odeling Analysis in Health Informatics&Bioinformatics,2015,4(1):1-17.
[22]LIU Mingxi,CHEN Xing,CHEN Geng,et al. A computational framew ork to infer human disease-associated long noncoding RNAs[J]. PLoS One,2014,9(1):e84408.
[23] LI Jianwei, CHENG Gao, WANG Yuchen, et al. A bioinformatics method for predicting long noncoding RNAs associated w ith vascular disease[J]. Science China Life Sciences,2014,57(8):852-857.
[24] Chen Xing. Predicting lnc RNA-disease associations and constructing lncRNA functional similarity netw ork based on the information of miRNA[J]. Scientific Reports,2015,5:13186.