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ncFANs: a web server for functional annotation of long non-coding RNAs

Q. Liao, H. Xiao, D. Bu, C. Xie, R. Miao, H. Luo, G. Zhao, K. Yu, H. Zhao, G. Skogerbo, R. Chen, Z. Wu (+2 others)
2011 Nucleic Acids Research  
We have developed a practical and user-friendly web interface called ncFANs (non-coding RNA Function ANnotation server), which is the first web service for functional annotation of human and mouse lncRNAs  ...  Recent interest in the non-coding transcriptome has resulted in the identification of large numbers of long non-coding RNAs (lncRNAs) in mammalian genomes, most of which have not been functionally characterized  ...  The authors wish to thank the executive editor and two anonymous referees for their constructive advice and comments to improve this web server.  ... 
doi:10.1093/nar/gkr432 pmid:21715382 pmcid:PMC3125796 fatcat:tosyotiry5bozidv66rgt36qhu

Noncoder: a web interface for exon array-based detection of long non-coding RNAs

Pascal Gellert, Yuliya Ponomareva, Thomas Braun, Shizuka Uchida
2012 Nucleic Acids Research  
Due to recent technical developments, a high number of long non-coding RNAs (lncRNAs) have been discovered in mammals.  ...  To allow for a general usage to the research community, we developed a user-friendly web interface called 'noncoder'.  ...  ACKNOWLEDGEMENTS The authors thank Dr Jose Clemente for his valuable advice and comments on this article.  ... 
doi:10.1093/nar/gks877 pmid:23012263 pmcid:PMC3592461 fatcat:jnj22774zrelzh5wqwklvskrii

The research strategies for probing the function of long noncoding RNAs

Biao Yan, Zhen-Hua Wang, Jin-Tao Guo
2012 Genomics  
Long noncoding RNAs (lncRNAs) represent a new frontier in molecular genetics and molecular biology.  ...  They have a tremendous potential for advancing our comprehensive understanding of biological processes in huma n health and disease.  ...  ., A-2400-11-0209 to Z.-H.W.).  ... 
doi:10.1016/j.ygeno.2011.12.002 pmid:22210346 fatcat:hfrzf427y5gj5en4db4xtdqynm

Long Noncoding RNAs-Related Diseases, Cancers, and Drugs

Jen-Yang Tang, Jin-Ching Lee, Yung-Ting Chang, Ming-Feng Hou, Hurng-Wern Huang, Chih-Chuang Liaw, Hsueh-Wei Chang
2013 The Scientific World Journal  
Long noncoding RNA (lncRNA) function is described in terms of related gene expressions, diseases, and cancers as well as their polymorphisms.  ...  Potential modulators of lncRNA function, including clinical drugs, natural products, and derivatives, are discussed, and bioinformatic resources are summarized.  ...  The noncoding RNA Function Anotation server (ncFANs) [9] , a web server for functional anotation of lncRNAs, includes ten reannotated human and mouse microarray datasets.  ... 
doi:10.1155/2013/943539 pmid:23843741 pmcid:PMC3690748 fatcat:37kt3piuwbec5c6xlmywvgttvy

Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs) Functional Analysis

Letizia Da Sacco, Antonella Baldassarre, Andrea Masotti
2011 International Journal of Molecular Sciences  
The advent of next generation sequencing revealed that a fraction of transcribed RNAs (short and long RNAs) is non-coding.  ...  Long non-coding RNAs (lncRNAs) have a crucial role in regulating gene expression and in epigenetics (chromatin and histones remodeling).  ...  Another web interface, the non-coding RNA Function ANnotation server (ncFANS) (http://www.ebiomed.org/ncFANs/), recently emerged in the panorama of computational tools dedicated to the analysis of lncRNAs  ... 
doi:10.3390/ijms13010097 pmid:22312241 pmcid:PMC3269675 fatcat:t7vzf3w7l5apjoatnkhqhlwbge

deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data

Ling-Ling Zheng, Jun-Hao Li, Jie Wu, Wen-Ju Sun, Shun Liu, Ze-Lin Wang, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu
2015 Nucleic Acids Research  
Small non-coding RNAs (e.g. miRNAs) and long non-coding RNAs (e.g. lincRNAs and circRNAs) are emerging as key regulators of various cellular processes.  ...  However, only a very small fraction of these enigmatic RNAs have been well functionally characterized.  ...  lncFucntion web-server for the functional annotation of lncR-NAs A web-based tool, lncFunction, was also developed to predict lncRNA functions from coding and non-coding coexpression networks.  ... 
doi:10.1093/nar/gkv1273 pmid:26590255 pmcid:PMC4702900 fatcat:cgqvbhjtenhn3etgpdkcssusxi

LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data

Yanan Ren, Ting-You Wang, Leah C. Anderton, Qi Cao, Rendong Yang
2021 BMC Genomics  
for a majority of the annotated lncRNAs.  ...  Background Long non-coding RNAs (lncRNAs) are a growing focus in cancer research. Deciphering pathways influenced by lncRNAs is important to understand their role in cancer.  ...  Jeffrey McDonald at the Hormel Institute for his technical support for computing facilities. Support from the Minnesota Supercomputer Institute (MSI) is also gratefully acknowledged.  ... 
doi:10.1186/s12864-021-07900-y fatcat:6fk7lmzlnfeidf66cmkxdqs3em

Differential Expression of Long Noncoding RNA in Primary and Recurrent Nasopharyngeal Carcinoma

Wei Gao, Jimmy Yu-Wai Chan, Thian-Sze Wong
2014 BioMed Research International  
Recent studies suggested that non-protein-coding genes are implicated in the tumorigenic process of nasopharyngeal carcinoma (NPC).  ...  In the present study, we aimed to identify the differentially expressed long noncoding RNA (lncRNA) using data available in the public domain.Methods.  ...  Acknowledgments This study was supported by Seed Funding of Basic Research, The University of Hong Kong, and Hong Kong Area of Excellent Scheme, Hong Kong UGC.  ... 
doi:10.1155/2014/404567 pmid:24822202 pmcid:PMC4009106 fatcat:22w42m7cmreffbrazyejxd4ktm

circlncRNAnet: An integrated web-based resource for mapping functional networks of long or circular forms of non-coding RNAs

Shao-Min Wu, Hsuan Liu, Po-Jung Huang, Ian Yi-Feng Chang, Chi-Ching Lee, Chia-Yu Yang, Wen-Sy Tsai, Bertrand Chin-Ming Tan
2017 GigaScience  
These non-coding RNA transcripts are known to affect expression of messenger RNAs (mRNAs) via epigenetic and post-transcriptional regulation.  ...  This web server is implemented with several features representing advances in the bioinformatics of ncRNAs: 1) a flexible framework that accepts and processes userdefined NGS-based expression data; 2)  ...  Liao Q, Xiao H, Bu D, Xie C, Miao R, Luo H, et al. ncFANs: a web server for 35 functional annotation of long non-coding RNAs.  ... 
doi:10.1093/gigascience/gix118 pmid:29194536 pmcid:PMC5765557 fatcat:7e4l2evnfrbgvf4ako5xxilyfi

Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data

Zheng Zhao, Jing Bai, Aiwei Wu, Yuan Wang, Jinwen Zhang, Zishan Wang, Yongsheng Li, Juan Xu, Xia Li
2015 Database: The Journal of Biological Databases and Curation  
Abstract Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases.  ...  Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions.  ...  Conflict of interest. None declared.  ... 
doi:10.1093/database/bav082 pmid:26363020 pmcid:PMC4565967 fatcat:feroagesmrf6vdduczopamz4ba

AnnoLnc: a web server for systematically annotating novel human lncRNAs

Mei Hou, Xing Tang, Feng Tian, Fangyuan Shi, Fenglin Liu, Ge Gao
2016 BMC Genomics  
To the best of our knowledge, AnnoLnc is the first web server to provide on-the-fly and systematic annotation for newly identified human lncRNAs.  ...  AnnoLnc offers a full spectrum of annotations covering genomic location, RNA secondary structure, expression, transcriptional regulation, miRNA interaction, protein interaction, genetic association and  ...  A dedicated web server, ncFAN, was developed to predict lncRNA functions based on enriched functional terms of coding genes in the same co-expression module (Liao et al. 2011a; Liao et al. 2011b) ; the  ... 
doi:10.1186/s12864-016-3287-9 pmid:27852242 pmcid:PMC5112684 fatcat:65ai73ck5zf27dfmg56l3dqkpm

AnnoLnc: a web server for systematically annotating novel human lncRNAs [article]

Mei Hou, Xing Tang, Feng Tian, Fangyuan Shi, Fenglin Liu, Ge Gao
2016 bioRxiv   pre-print
To the best of our knowledge, AnnoLnc is the first web server to provide on-the-fly and systematic annotation for newly identified human lncRNAs.  ...  AnnoLnc offers a full spectrum of annotations covering genomic location, RNA secondary structure, expression, transcriptional regulation, miRNA interaction, protein interaction, genetic association and  ...  A dedicated web server, ncFAN, was developed to predict lncRNA functions based on enriched functional terms of coding genes in the same co-expression module (Liao et al. 2011a; Liao et al. 2011b) ; the  ... 
doi:10.1101/042655 fatcat:ebu2k3mmyzcl5eb343wwuy7vwq

The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases

Haixiu Yang, Desi Shang, Yanjun Xu, Chunlong Zhang, Li Feng, Zeguo Sun, Xinrui Shi, Yunpeng Zhang, Junwei Han, Fei Su, Chunquan Li, Xia Li
2017 Scientific Reports  
Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states.  ...  We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs  ...  The ncFANs proposed by Liao et al. has been widely used for the functional annotation of long non-coding RNAs in various studies [10] [11] [12] [13] , and becomes a popular method to re-annotate microarray  ... 
doi:10.1038/s41598-017-06897-3 pmid:28751672 pmcid:PMC5532316 fatcat:ygakwdlx2zhnfmk2clb5akv6fe

Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studies

Alfred Chun-Shui Luk, Wai-Yee Chan, Owen M Rennert, Tin-Lap Lee
2014 Reproduction  
Importantly, protein-coding genes only account for a small percentage of transcriptome; the majority are noncoding transcripts that do not translate into proteins.  ...  Although small noncoding RNAs (ncRNAs) such as microRNAs, siRNAs, and Piwi-interacting RNAs are extensively investigated in male germ cell development, the role of long ncRNAs (lncRNAs), commonly defined  ...  The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the review. Funding  ... 
doi:10.1530/rep-13-0594 pmid:24713396 fatcat:zieyreaxw5fn3o2kt3woqyisyi

smORFunction: a tool for predicting functions of small open reading frames and microproteins

Xiangwen Ji, Chunmei Cui, Qinghua Cui
2020 BMC Bioinformatics  
Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown.  ...  Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations.  ...  Non-coding RNA function annotation server (ncFANs) used coding-non-coding gene co-expression network to annotate lncRNA functions [35] .  ... 
doi:10.1186/s12859-020-03805-x pmid:33054771 fatcat:52tzjcdfdfdc5icwxcenyanywq
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