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Nucleic acids research
07 02, 2021;49 (W1): W459-W468.

ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs.

Yuwei Zhang, Dechao Bu, Peipei Huo, Zhihao Wang, Hao Rong, Yanguo Li, Jingjia Liu, Meng Ye, Yang Wu, Zheng Jiang, Qi Liao, Yi Zhao
Author Information
  1. Yuwei Zhang: The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China. ORCID
  2. Dechao Bu: Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
  3. Peipei Huo: Luoyang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Henan, 471000, China.
  4. Zhihao Wang: Luoyang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Henan, 471000, China.
  5. Hao Rong: The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China.
  6. Yanguo Li: Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315000, China.
  7. Jingjia Liu: Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 315000, China.
  8. Meng Ye: The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China.
  9. Yang Wu: Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
  10. Zheng Jiang: Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
  11. Qi Liao: The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, 315000, China.
  12. Yi Zhao: Pervasive Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China. ORCID
PMID: 34050762 DOI: 10.1093/nar/gkab435

Abstract

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.

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MeSH Term

Enhancer Elements, Genetic
Humans
Methylation
Molecular Sequence Annotation
Oligonucleotide Array Sequence Analysis
RNA, Long Noncoding
RNA, Untranslated
Software

Chemicals

RNA, Long Noncoding
RNA, Untranslated
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 3

Word Cloud

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