miRmine: a database of human miRNA expression profiles
miRmine: a database of human miRNA expression profiles
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DOI：
10.1093/bioinformatics/btx019
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发表时间：
2017-05-15
期刊：
影响因子：
5.8
通讯作者：
Guan, Yuanfang
中科院分区：
文献类型：
--
作者：
Panwar, Bharat;Omenn, Gilbert S.;Guan, Yuanfang
MicroRNAs（miRNAs）是一类参与基因表达转录后调控的非编码小分子RNA。在这个高通量测序时代，大量的RNA-seq数据正在积累，充分利用公共可用的miRNA数据是一个重要的挑战。这些数据是有用的，以确定每个miRNA的表达值，但定量管道是在一个原始的阶段，仍在不断发展，有许多因素影响表达values.Results的显着：我们使用了304高质量的microRNA测序（miRNA-seq）数据集从NCBI-SRA和计算不同组织和细胞系的表达谱。在每个miRNA-seq数据集中，我们发现平均超过500个覆盖率高于5倍的miRNA，并且我们探索了每个组织和细胞系中前五个高表达的miRNA。这个用户友好的miRmine数据库可以选择检索特定组织或细胞系（正常或具有疾病信息）的单个或多个miRNA的表达谱。结果可以以多种交互式、图形和可下载的格式显示。
Motivation: MicroRNAs (miRNAs) are small non-coding RNAs that are involved in post-transcriptional regulation of gene expression. In this high-throughput sequencing era, a tremendous amount of RNA-seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly.Results: We used 304 high-quality microRNA sequencing (miRNA-seq) datasets from NCBI-SRA and calculated expression profiles for different tissues and cell-lines. In each miRNA-seq dataset, we found an average of more than 500 miRNAs with higher than 5x coverage, and we explored the top five highly expressed miRNAs in each tissue and cell-line. This user-friendly miRmine database has options to retrieve expression profiles of single or multiple miRNAs for a specific tissue or cellline, either normal or with disease information. Results can be displayed in multiple interactive, graphical and downloadable formats.