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Noncoding RNAs database (ncRNAdb)

M. Szymanski, V. A. Erdmann, J. Barciszewski
2007 Nucleic Acids Research  
The noncoding RNA database (ncRNAdb) was created as a source of information on RNA molecules, which do not possess protein-coding capacity.  ...  Currently, the ncRNAdb contains >30 000 ncRNA sequences from Eukaryotes, Eubacteria and Archaea, but does not include housekeeping transcripts or microRNAs and snoRNAs for which more specialized databases  ...  As of August 2006, the noncoding regulatory RNA database includes over 30 000 sequences from 99 organisms.  ... 
doi:10.1093/nar/gkl994 pmid:17169980 pmcid:PMC1781251 fatcat:reelj7wrq5bbzmqmw67ijhz3uy

Comprehensive Reconstruction and Visualization of Non-Coding Regulatory Networks in Human

Vincenzo Bonnici, Francesco Russo, Nicola Bombieri, Alfredo Pulvirenti, Rosalba Giugno
2014 Frontiers in Bioengineering and Biotechnology  
The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/.  ...  However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing.  ...  This is the case for example of NONCODE v4, the largest collection of ncRNAs available online, where most of the reported ncRNAs can be only mapped to NONCODE.  ... 
doi:10.3389/fbioe.2014.00069 pmid:25540777 pmcid:PMC4261811 fatcat:ez7vwlrifrep5e7uktoo4w52hq

NONCODEv4: exploring the world of long non-coding RNA genes

Chaoyong Xie, Jiao Yuan, Hui Li, Ming Li, Guoguang Zhao, Dechao Bu, Weimin Zhu, Wei Wu, Runsheng Chen, Yi Zhao
2013 Nucleic Acids Research  
NONCODE (http://www.bioinfo.org/noncode/) is an integrated knowledge database dedicated to noncoding RNAs (excluding tRNAs and rRNAs).  ...  Since NONCODE version 3.0 was released 2 years ago, discovery of novel ncRNAs has been promoted by high-throughput RNA sequencing (RNA-Seq).  ...  RNA databases.  ... 
doi:10.1093/nar/gkt1222 pmid:24285305 pmcid:PMC3965073 fatcat:hh44zvq4urefxi43d7xa7c3pv4

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).  ...  Bioinformatics Resources Year Web Link Reference Databases and public repositories NcRNAdb 2003 http://biobases.ibch.poznan.pl/ncRNA [47] Rfam 2003 http://www.sanger.ac.uk/Software/Rfam  ... 
doi:10.3390/ijms13010097 pmid:22312241 pmcid:PMC3269675 fatcat:t7vzf3w7l5apjoatnkhqhlwbge

Prediction of small non-coding RNA in bacterial genomes using support vector machines

Tzu-Hao Chang, Li-Ching Wu, Jun-Hong Lin, Hsien-Da Huang, Baw-Jhiune Liu, Kuang-Fu Cheng, Jorng-Tzong Horng
2010 Expert systems with applications  
Small non-coding RNA genes have been shown to play important regulatory roles in a variety of cellular processes, but prediction of non-coding RNA genes is a great challenge, using either an experimental  ...  Validation with identified sRNAs in the ncRNAdb The non-coding RNA database (ncRNAdb) was created as a source of information on RNA molecules that do not possess protein-coding capacity.  ...  The total number of non-coding RNAs identified from the ncRNAdb database was 437, including sRNA, tRNA, rRNA and these non-coding RNA are present in 43 species across various bacterial genomes (as shown  ... 
doi:10.1016/j.eswa.2010.02.058 fatcat:gfut7togyjazvh43ya24isuf7a

Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing

Rosemarie Weikard, Frieder Hadlich, Christa Kuehn
2013 BMC Genomics  
A large group of UTs (4,848) was predicted to potentially represent long noncoding RNA (lncRNA).  ...  Deep RNA sequencing (RNAseq) has opened a new horizon for understanding global gene expression.  ...  Refseq RNAdb: diverse RNA databases containing known coding RNA sequences. ncRNAdb: diverse RNA databases containing known noncoding RNA sequences.  ... 
doi:10.1186/1471-2164-14-789 pmid:24225384 pmcid:PMC3833843 fatcat:tn3puoozyfabfaltlbatcq5s7q

Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing

Wanfei Liu, Yuhui Zhao, Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Xinyu Tan, Shuhui Song, Jun Yu, Songnian Hu
2011 Frontiers in Genetics  
Here, we report a discovery of thousands of novel transcripts (mostly non-coding RNAs) that are expressed in mouse cerebrum, testis, and embryonic stem (ES) cells, through an in-depth analysis of rmRNA-seq  ...  Fourth, we annotated and removed certain exons by comparing our putative exons with several databases (UCSC, ENSEMBL, NONCODE, RNAdb, fRNAdb, Rfam, miR-Base, tRNAdb, and ncRNAdb).  ...  We also built a custom-designed ncRNA database through integrating several databases that include mouse ncRNA data in ENSEMBL (Flicek et al., 2011) , UCSC (Fujita et al., 2011) , NONCODE (He et al.,  ... 
doi:10.3389/fgene.2011.00093 pmid:22303387 pmcid:PMC3268642 fatcat:j2erdwv44bhvnbc6hjuiavdjyq

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Wei Gong, Lingfang Zhang, Jianing Geng, Bing Zhang, Xiaomin Yu, Jin Yang, Songnian Hu, Jun Yu
2010 Genomics  
To compare the two RNA-sequencing protocols, ribo-minus RNA-sequencing (rmRNA-seq) and polyA-selected RNA-sequencing (mRNA-seq), we acquired transcriptomic data-52 and 32 million alignable reads of 35  ...  Finally, through comparative analyses of gene expression profiles among multiple datasets, we demonstrated that different RNA sample preparations may result in significant variations in gene expression  ...  Defining known ncRNAs and novel transcripts To define known ncRNAs, we collected mouse ncRNA annotation data from publically available ncRNA databases that include ncRNAdb, RNAdb, fRNAdb, FANTOM3, NONCODE  ... 
doi:10.1016/j.ygeno.2010.07.010 pmid:20688152 fatcat:ht6ykchhcrf4ba5xuguk4uz7pq

A comprehensive review of web-based resources of non-coding RNAs for plant science research

Peiran Liao, Shipeng Li, Xiuming Cui, Yun Zheng
2018 International Journal of Biological Sciences  
Noncoding RNAs database (ncRNAdb) collected currently available sequence data on ncRNAs which have regulatory functions in prokaryotic, animal and plant cells, including regulation of chromatin structure  ...  NONCODE is an integrated knowledge database dedicated to non-coding RNAs, including non-coding RNAs of plants [102] .  ... 
doi:10.7150/ijbs.24593 pmid:29989090 pmcid:PMC6036741 fatcat:ega4utdykbap5m4zgavecnprli

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

Pieter-Jan Volders, Kenny Helsens, Xiaowei Wang, Björn Menten, Lennart Martens, Kris Gevaert, Jo Vandesompele, Pieter Mestdagh
2012 Nucleic Acids Research  
Here, we present LNCipedia (http://www.lncipedia .org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes.  ...  The database may serve as a resource to initiate small-and large-scale lncRNA studies.  ...  The NONCODE database (12) contains a larger collection of human long non-coding RNAs (33 829) obtained from different sources and by different experimental procedures (13) .  ... 
doi:10.1093/nar/gks915 pmid:23042674 pmcid:PMC3531107 fatcat:wqhiflur5zgc5mjjt4w7n6nddi

FASTR3D: a fast and accurate search tool for similar RNA 3D structures

C.-E. Lai, M.-Y. Tsai, Y.-C. Liu, C.-W. Wang, K.-T. Chen, C. L. Lu
2009 Nucleic Acids Research  
FASTR3D is a web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs.  ...  In addition, the user can run FASTR3D with specifying additional filtering options: (i) the released date of RNA structures in the PDB database, and (ii) the experimental methods used to determine RNA  ...  For this purpose, several databases of ncRNAs have been proposed, such as NONCODE (5) , RNAdb (6) , miRBase (7) , fRNAdb (8) and ncRNAdb (9) .  ... 
doi:10.1093/nar/gkp330 pmid:19435878 pmcid:PMC2703968 fatcat:bodzirfxwvei7ld4cfq7wqkppa

PNRD: a plant non-coding RNA database

Xin Yi, Zhenhai Zhang, Yi Ling, Wenying Xu, Zhen Su
2014 Nucleic Acids Research  
In 2010, we constructed a plant miRNA database named PMRD to meet the demand for miRNA research in plants.  ...  We also integrated currently prevalent technologies and toolkits to strengthen the capability of the database and provide a one-stop service for scientific users.  ...  ), or more organisms (PNRD 150 organisms and ncRNAdb 99 organisms), which manifest the advantage of data size of our database.  ... 
doi:10.1093/nar/gku1162 pmid:25398903 pmcid:PMC4383960 fatcat:hycquuzacfhunefncckaz7m7ri

Molecular Characterization of Peripheral Extracellular Vesicles in Clinically Isolated Syndrome: Preliminary Suggestions from a Pilot Study

Nicoletta Nuzziello, Maria Blonda, Flavio Licciulli, Sabino Liuni, Antonella Amoruso, Alessio Valletti, Arianna Consiglio, Carlo Avolio, Maria Liguori
2017 Medical Sciences  
This essential role may be due to their proteins and RNAs cargo that possibly modify the phenotypes of the targeted cells.  ...  In line with previous reports, distinct classes of non-coding RNAs have been detected in both the EVs subsets, offering interesting suggestions on their origins and functions.  ...  After pre-processing, read-length distribution is computed and reads >15 nucleotides were aligned against a non-redundant non-coding RNA (ncRNA) reference database (ncRNAdb http://ncRNAdb.ba.itb.cnr.it  ... 
doi:10.3390/medsci5030019 pmid:29099035 pmcid:PMC5635803 fatcat:5wq4gsmdo5ftdmxkrtywdxxypq

An integrative framework to identify cell death-related microRNAs in esophageal squamous cell carcinoma

Bing-Li Wu, Dong Wang, Wen-Jing Bai, Fan Zhang, Xing Zhao, Ying Yi, Ting Zhang, Wen-Jun Shen, En-Min Li, Li-Yan Xu, Jian-Zhen Xu
2016 OncoTarget  
INTRODUCTION MicroRNAs (miRNAs) are a group of ~21 nucleotide long endogenous noncoding RNAs, which play an important role in a broad range of biological processes [1] [2] [3] [4] [5] [6] .  ...  From our manually collection of ncRNADB database, we compiled a list of 221 known human cell death miRNAs. Combining this list of miRNAs with the initial 629 miRNAs resulted in 176 miRNAs.  ... 
doi:10.18632/oncotarget.10779 pmid:27462775 pmcid:PMC5302951 fatcat:xsvdipmihfdrlplpalol2vwpia

NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences

Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. Stadler, Jörg Hackermüller
2008 Genomics  
We demonstrate the practical use of NcDNAlign in three case studies: the search for ncRNAs in gammaproteobacteria and the analysis of conserved noncoding DNA in nematodes and teleost fish, in the latter  ...  Furthermore, 25 NcDNAlign-prepared vs. 24 TBA-prepared RNAz hits align with Noncode entries, and 28 NcDNAlign-prepared vs. 31 TBAprepared RNAz hits align with ncRNAdb sequences.  ...  structured RNAs [7, 8] .  ... 
doi:10.1016/j.ygeno.2008.04.003 pmid:18511233 fatcat:aaerexa4pngyff2mzhhpwqmfvu
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