The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China.
Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315000, China.
Nucleic Acids Res. 2021 Jul 2;49(W1):W459-W468. doi: 10.1093/nar/gkab435.
Increasing evidence proves the essential regulatory roles of non-coding RNAs (ncRNAs) in biological processes. However, characterizing the specific functions of ncRNAs remains a challenging task, owing to the intensive consumption of the experimental approaches. Here, we present an online platform ncFANs v2.0 that is a significantly enhanced version of our previous ncFANs to provide multiple computational methods for ncRNA functional annotation. Specifically, ncFANs v2.0 was updated to embed three functional modules, including ncFANs-NET, ncFANs-eLnc and ncFANs-CHIP. ncFANs-NET is a new module designed for data-free functional annotation based on four kinds of pre-built networks, including the co-expression network, co-methylation network, long non-coding RNA (lncRNA)-centric regulatory network and random forest-based network. ncFANs-eLnc enables the one-stop identification of enhancer-derived lncRNAs from the de novo assembled transcriptome based on the user-defined or our pre-annotated enhancers. Moreover, ncFANs-CHIP inherits the original functions for microarray data-based functional annotation and supports more chip types. We believe that our ncFANs v2.0 carries sufficient convenience and practicability for biological researchers and facilitates unraveling the regulatory mechanisms of ncRNAs. The ncFANs v2.0 server is freely available at http://bioinfo.org/ncfans or http://ncfans.gene.ac.
越来越多的证据证明非编码 RNA（ncRNA）在生物过程中具有重要的调节作用。然而，由于实验方法的大量消耗，描述 ncRNA 的特定功能仍然是一项具有挑战性的任务。在这里，我们展示了一个在线平台 ncFANs v2.0，它是我们之前的 ncFANs 的一个显著增强版本，为 ncRNA 功能注释提供了多种计算方法。具体来说，ncFANs v2.0 进行了更新，嵌入了三个功能模块，包括 ncFANs-NET、ncFANs-eLnc 和 ncFANs-CHIP。ncFANs-NET 是一个新模块，用于基于四种预先构建的网络（包括共表达网络、共甲基化网络、长非编码 RNA（lncRNA）中心调控网络和基于随机森林的网络）进行无数据功能注释。ncFANs-eLnc 能够根据用户定义或我们预先注释的增强子，从从头组装的转录组中一次性识别增强子衍生的 lncRNA。此外，ncFANs-CHIP 继承了基于微阵列数据进行功能注释的原始功能，并支持更多的芯片类型。我们相信，我们的 ncFANs v2.0 为生物研究人员提供了足够的便利性和实用性，有助于揭示 ncRNA 的调控机制。ncFANs v2.0 服务器可在 http://bioinfo.org/ncfans 或 http://ncfans.gene.ac 免费获得。
