lncFunTK:一个长链非编码RNA功能注释工具包
动机:从高通量RNA-seq数据中新鉴定了数以千计的长链非编码RNAs(long noncoding RNAs,lncRNAs)。用于进一步实验验证以及功能调查的这些lncRNAs的功能注释和优化是许多非编码RNA研究的瓶颈步骤。结果:这里我们描述了lncFunTK,它能够或者作为单机应用程序或者作为网络服务器用于lncRNA的功能注释和优化。它整合了高通量测序数据(即:ChIP-seq、CLIP-seq和RNA-seq)以构建与lncRNAs相关的调控网络。通过该网络,它计算每个lncRNA的功能信息得分(Functional Information Score,FIS),通过临近基因的基因本体论(Gene Ontology,GO)术语,优化和推断它的功能。此外,它也提供了实用脚本以支持输入数据预处理和参数优化。我们进一步证明lncFunTK能够广泛用于各种生物系统以进行lncRNA优化和功能注释。可用性:lncFunTK单机版是一个开源包,可以在http://sunlab.cpy.cuhk.edu.hk/lncfuntk免费获得,遵循MIT许可证。网络服务器实现也可以在http://sunlab.cpy.cuhk.edu.hk/lncfuntk/runlncfuntk.html使用。联系:haosun@cuhk.edu.hk或huating.wang@cuhk.edu.hk。
lncFunTK: A toolkit for functional annotation of long noncoding RNAs
Motivation: Thousands of long noncoding RNAs (lncRNAs) were newly identified from high throughput RNA-seq data. Functional annotation and prioritization of these lncRNAs for further experimental validation as well as the functional investigation is the bottleneck step for many noncoding RNA studies. Results: Here we describe lncFunTK that can run either as standard application or webserver for this purpose. It integrates high throughput sequencing data (i.e. ChIP-seq, CLIP-seq and RNA-seq) to construct the regulatory network associated with lncRNAs. Through the network, it calculates the Functional Information Score (FIS) of each individual lncRNA for prioritizing and inferring its functions through Gene Ontology (GO) terms of neighboring genes. In addition, it also provides utility scripts to support the input data preprocessing and the parameter optimizing. We further demonstrate that lncFunTK can be widely used in various biological systems for lncRNA prioritization and functional annotation. Availability and implementation: The lncFunTK standalone version is an open source package and freely available at http://sunlab.cpy.cuhk.edu.hk/lncfuntk under the MIT license. A webserver implementation is also available at pmid: 29718162 Bioinformatics 影响因子: 4.531 发表日期: 20181001 官网 免费下载
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