YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.
YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.
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DOI：
10.1093/nar/gku1156
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发表时间：
2015-01
影响因子：
14.9
通讯作者：
Wang HW
中科院分区：
文献类型：
--
作者：
Cheng WC;Chung IF;Tsai CF;Huang TS;Chen CY;Wang SC;Chang TY;Sun HJ;Chao JY;Cheng CC;Wu CW;Wang HW
我们之前提出了 YM500，它是一个集成数据库，用于 miRNA 定量、 isomiR 识别、臂切换发现和来自 468 个人类 smRNA-seq 数据集的新 miRNA 预测。在这个更新的YM500v2数据库（http://ngs.ym.edu.tw/ym500/）中，我们重点关注癌症miRNome，使数据库更加面向疾病。 YM500之后开发的新的miRNA相关算法被纳入YM500v2，更重要的是，超过8000个癌症相关的smRNA-seq数据集（包括原发肿瘤、配对正常组织、PBMC、复发肿瘤和转移肿瘤）被纳入YM500v2。新型 miRNA（未包含在 miRBase R21 中的 miRNA）不仅通过三种独立算法进行预测，还通过新的计算机过滤策略进行清理，并通过交联免疫沉淀测序 (CLIP-seq) 等湿实验室数据进行验证，以降低假阳性率。另外还提供了新功能“Meta分析”，允许用户根据客户定义的样本组和熟练临床医生整理的数十个临床标准来识别实时差异表达的miRNA和换臂事件。鉴定出的癌症 miRNA 具有基础研究和生物技术应用的潜力。
We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function ‘Meta-analysis’ is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications.
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影响因子：
64.8
作者：
Lu, J;Getz, G;Golub, TR
通讯作者：
Golub, TR
影响因子：
11.2
作者：
Bader AG;Brown D;Winkler M
通讯作者：
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影响因子：
12.3
作者：
Chen X;Li Q;Wang J;Guo X;Jiang X;Ren Z;Weng C;Sun G;Wang X;Liu Y;Ma L;Chen JY;Wang J;Zen K;Zhang J;Zhang CY
通讯作者：
Zhang CY
影响因子：
14.9
作者：
Humphreys DT;Suter CM
通讯作者：
Suter CM
对 miRNA 中非模板核苷酸和 isomiR 库的全基因组筛选表明了动态和多功能的 microRNAome
影响因子：
2.8
作者：
Guo, Li;Zhao, Yang;Chen, Feng
通讯作者：
Chen, Feng