SEAweb: the small RNA Expression Atlas web application
SEAweb: the small RNA Expression Atlas web application
复制标题
DOI：
10.1093/nar/gkz869
复制
发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Bonn, Stefan
中科院分区：
文献类型：
--
作者：
Rahman, Raza-Ur;Liebhoff, Anna-Maria;Bonn, Stefan
我们介绍了小RNA表达图谱（SEAweb），这是一个网络应用程序，允许对10种生物中已知和新的小RNA进行交互式查询，可视化和分析。它包含超过4200个已发表样本的sRNA和病原体表达信息，具有标准化的搜索术语和本体。此外，SEAweb允许交互式可视化和重新分析879个差异表达和514个分类比较。SEAweb的用户模型使sRNA研究人员能够比较和重新分析用户特定的和已发表的数据集，突出显示常见和独特的sRNA表达模式。我们通过(i)在29个组织中生成一组591个组织特异性mirna， （ii）在疾病中发现已知和新的细菌和病毒感染，以及（iii）使用新数据确定帕金森病特异性血液生物标志物签名，为SEAweb的保真度提供证据。我们相信，SEAweb简单的语义搜索界面、灵活的交互式报告和具有丰富分析能力的用户模型，将使研究人员能够更好地了解sRNAs或病原体在组织、疾病和生物体中的潜在功能和诊断价值。
We present the Small RNA Expression Atlas ( SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms. It contains sRNA and pathogen expression information for over 4200 published samples with standardized search terms and ontologies. In addition, SEAweb allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEAweb's user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns. We provide evidence for SEAweb's fidelity by (i) generating a set of 591 tissue specific miRNAs across 29 tissues, (ii) finding known and novel bacterial and viral infections across diseases and (iii) determining a Parkinson's disease-specific blood biomarker signature using novel data. We believe that SEAweb's simple semantic search interface, the flexible interactive reports and the user model with rich analysis capabilities will enable researchers to better understand the potential function and diagnostic value of sRNAs or pathogens across tissues, diseases and organisms.