The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations.
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DOI：
10.1093/nar/gku631
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发表时间：
2014
影响因子：
14.9
通讯作者：
Theodorescu D
中科院分区：
文献类型：
--
作者：
Ru Y;Kechris KJ;Tabakoff B;Hoffman P;Radcliffe RA;Bowler R;Mahaffey S;Rossi S;Calin GA;Bemis L;Theodorescu D
microRNA (miRNA) 通过促进目标转录物的降解或抑制翻译来调节表达。基于实验验证和使用各种算法的计算预测，miRNA 靶位点已在数据库中编目。一些在线资源提供了多个数据库的集合，但需要导入到其他软件（例如 R）中进行处理、制表、绘图和计算。目前 R 中可用的 miRNA 靶位点包在数据库数量、数据库类型和灵活性方面受到限制。我们推出了 multiMiR，一种新的 miRNA 靶标相互作用 R 包和数据库，其中包括现有 R 包中不具备的几个新功能：（i）从 14 个不同的数据库中汇编了近 5000 万条人类和小鼠记录，比任何其他数据库都多； (ii) 除了许多实验和计算数据库之外，将数据库扩展到基于疾病注释和药物 microRNA 反应的数据库； (iii) 用户定义的预测结合强度截止值，以提供最可信的选择。报告了各种生物医学应用的案例研究，包括小鼠饮酒模型、人类受试者慢性阻塞性肺疾病的研究以及膀胱癌转移的人类细胞系模型。我们还演示了如何使用 multiMiR 生成可测试的假设并进行实验。
microRNAs (miRNAs) regulate expression by promoting degradation or repressing translation of target transcripts. miRNA target sites have been catalogued in databases based on experimental validation and computational prediction using various algorithms. Several online resources provide collections of multiple databases but need to be imported into other software, such as R, for processing, tabulation, graphing and computation. Currently available miRNA target site packages in R are limited in the number of databases, types of databases and flexibility. We present multiMiR, a new miRNA–target interaction R package and database, which includes several novel features not available in existing R packages: (i) compilation of nearly 50 million records in human and mouse from 14 different databases, more than any other collection; (ii) expansion of databases to those based on disease annotation and drug microRNAresponse, in addition to many experimental and computational databases; and (iii) user-defined cutoffs for predicted binding strength to provide the most confident selection. Case studies are reported on various biomedical applications including mouse models of alcohol consumption, studies of chronic obstructive pulmonary disease in human subjects, and human cell line models of bladder cancer metastasis. We also demonstrate how multiMiR was used to generate testable hypotheses that were pursued experimentally.
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影响因子：
14.9
作者：
Maragkakis M;Vergoulis T;Alexiou P;Reczko M;Plomaritou K;Gousis M;Kourtis K;Koziris N;Dalamagas T;Hatzigeorgiou AG
通讯作者：
Hatzigeorgiou AG
影响因子：
14.9
作者：
Anders G;Mackowiak SD;Jens M;Maaskola J;Kuntzagk A;Rajewsky N;Landthaler M;Dieterich C
通讯作者：
Dieterich C
影响因子：
3.7
作者：
Lu TP;Lee CY;Tsai MH;Chiu YC;Hsiao CK;Lai LC;Chuang EY
通讯作者：
Chuang EY
影响因子：
3
作者：
Gaidatzis D;van Nimwegen E;Hausser J;Zavolan M
通讯作者：
Zavolan M
影响因子：
12.3
作者：
Ruepp A;Kowarsch A;Schmidl D;Buggenthin F;Brauner B;Dunger I;Fobo G;Frishman G;Montrone C;Theis FJ
通讯作者：
Theis FJ