circVAR database: genome-wide archive of genetic variants for human circular RNAs.
circVAR database: genome-wide archive of genetic variants for human circular RNAs.
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circVAR 数据库：人类环状 RNA 遗传变异的全基因组档案
DOI：
10.1186/s12864-020-07172-y
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发表时间：
2020-10-29
期刊：
影响因子：
4.4
通讯作者：
Qu H
中科院分区：
文献类型：
--
作者：
Zhao M;Qu H
研究背景环状RNA（CircRNA）通过与miRNA和RNA结合蛋白的结合在基因表达调控中发挥重要作用。circRNA的遗传变异可能通过改变其与靶miRNA和蛋白质的结合效率来影响复杂的性状/疾病。越来越多的人需要利用大规模的实验证据来研究遗传变化的功能。然而，有没有在线的遗传资源circRNA genes.ResultsWe集成从circBase，circNet和circRNAdb的295，526 circRNA进行了广泛的遗传注释。所有预先计算的遗传变异都在我们的在线资源circVAR上展示，并具有数据浏览和搜索功能。我们探索了circRNA及其相关变体的基于染色体的分布。我们发现，基于对1000个基因组和ClinVAR数据库的映射，17号染色体具有相对大量的circRNA和相关的常见和健康相关的遗传变异。在对基于全基因组关联研究（GWAS）的circRNA变体进行注释后，我们发现circRNA中存在许多非编码变体，这提示了GWAS研究中报告的常见疾病的新机制。对于癌症为基础的体细胞变异，我们发现，7号染色体有许多高度复杂的突变，已被忽视在以前的research.ConclusionWe使用的circVAR数据库收集SNPs和小插入和缺失（INDEL）在假定的circRNA区域，并确定其潜在的表型信息。为了给circRNA研究界提供一个可重复使用的资源，我们将所有关于circRNA和相关基因的预先计算的遗传数据以及数据查询和浏览功能发布在 http://soft.bioinfo-minzhao.org/circvar .
BackgroundCircular RNAs (circRNAs) play important roles in regulating gene expression through binding miRNAs and RNA binding proteins. Genetic variation of circRNAs may affect complex traits/diseases by changing their binding efficiency to target miRNAs and proteins. There is a growing demand for investigations of the functions of genetic changes using large-scale experimental evidence. However, there is no online genetic resource for circRNA genes.ResultsWe performed extensive genetic annotation of 295,526 circRNAs integrated from circBase, circNet and circRNAdb. All pre-computed genetic variants were presented at our online resource, circVAR, with data browsing and search functionality. We explored the chromosome-based distribution of circRNAs and their associated variants. We found that, based on mapping to the 1000 Genomes and ClinVAR databases, chromosome 17 has a relatively large number of circRNAs and associated common and health-related genetic variants. Following the annotation of genome wide association studies (GWAS)-based circRNA variants, we found many non-coding variants within circRNAs, suggesting novel mechanisms for common diseases reported from GWAS studies. For cancer-based somatic variants, we found that chromosome 7 has many highly complex mutations that have been overlooked in previous research.ConclusionWe used the circVAR database to collect SNPs and small insertions and deletions (INDELs) in putative circRNA regions and to identify their potential phenotypic information. To provide a reusable resource for the circRNA research community, we have published all the pre-computed genetic data concerning circRNAs and associated genes together with data query and browsing functions at http://soft.bioinfo-minzhao.org/circvar .
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
14.9
作者：
Rosenbloom KR;Armstrong J;Barber GP;Casper J;Clawson H;Diekhans M;Dreszer TR;Fujita PA;Guruvadoo L;Haeussler M;Harte RA;Heitner S;Hickey G;Hinrichs AS;Hubley R;Karolchik D;Learned K;Lee BT;Li CH;Miga KH;Nguyen N;Paten B;Raney BJ;Smit AF;Speir ML;Zweig AS;Haussler D;Kuhn RM;Kent WJ
通讯作者：
Kent WJ
DOI：
10.1261/rna.047126.114
发表时间：
2014-12
期刊：
RNA (New York, N.Y.)
影响因子：
--
作者：
Lasda E;Parker R
通讯作者：
Parker R
影响因子：
14.9
作者：
Haeussler M;Zweig AS;Tyner C;Speir ML;Rosenbloom KR;Raney BJ;Lee CM;Lee BT;Hinrichs AS;Gonzalez JN;Gibson D;Diekhans M;Clawson H;Casper J;Barber GP;Haussler D;Kuhn RM;Kent WJ
通讯作者：
Kent WJ
circRNADb：具有蛋白质编码注释的人类环状 RNA 综合数据库
影响因子：
4.6
作者：
Chen X;Han P;Zhou T;Guo X;Song X;Li Y
通讯作者：
Li Y