lncFunTK: a toolkit for functional annotation of long noncoding RNAs
lncFunTK: a toolkit for functional annotation of long noncoding RNAs
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DOI：
10.1093/bioinformatics/bty339
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发表时间：
2018-10-01
期刊：
影响因子：
5.8
通讯作者：
Sun, Hao
中科院分区：
文献类型：
--
作者：
Zhou, Jiajian;Huang, Yile;Sun, Hao
动机：从高通量RNA-seq数据中新发现了数千种长链非编码rna （lncrna）。这些lncrna的功能注释和优先级排序以进一步实验验证以及功能研究是许多非编码RNA研究的瓶颈步骤。结果：这里我们描述了lncFunTK，它既可以作为标准应用程序运行，也可以作为web服务器运行。整合高通量测序数据（ChIP-seq、CLIP-seq、RNA-seq），构建lncrna相关调控网络。通过网络计算每个lncRNA的功能信息评分（Functional Information Score， FIS），通过邻近基因的基因本体（Gene Ontology， GO）条件对其功能进行排序和推断。此外，还提供了支持输入数据预处理和参数优化的实用程序脚本。我们进一步证明了lnfuntk可以广泛应用于各种生物系统中，用于lncRNA的优先级排序和功能注释。可用性和实现：lncFunTK独立版本是一个开源包，可以在http://sunlab上免费获得。cpy。中大。edu。MIT授权下的hk/lncfuntk。web服务器的实现也可以在http://sunlab上获得。cpy。中大。edu。香港/ lncfuntk / runlncfuntk。超文本标记语言。
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 http://sunlab. cpy. cuhk. edu. hk/lncfuntk/runlncfuntk. html.