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Protocols

deepBase specifications

Information


Unique identifier OMICS_02782
Name deepBase
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus
    • Xenopus tropicalis

Maintainers


  • person_outline Jian-Hua Yang
  • person_outline Liang-Hu Qu
  • person_outline Ling-Ling Zheng

Publications for deepBase

deepBase citations

 (18)
library_books

Small RNA profiling for identification of miRNAs involved in regulation of saponins biosynthesis in Chlorophytum borivilianum

2017
BMC Plant Biol
PMCID: 5745966
PMID: 29281971
DOI: 10.1186/s12870-017-1214-0

[…] d and 5′ and 3′ adapter sequences were eliminated using Cutadapt tool (v-1.3) []. Remaining reads were then aligned against a number of databases like GtRNAdb, Rfam, piRNABank, siRNAdb, NCBI Genbank, deepBase to eliminate other non-coding RNAs like tRNA, rRNA, piRNA, siRNA, snRNA, and snoRNA, respectively using Bowtie2 program (version 2.1.0) []. The remaining reads were used to predict known and […]

library_books

Heterogeneous circRNA expression profiles and regulatory functions among HEK293T single cells

2017
Sci Rep
PMCID: 5663837
PMID: 29089539
DOI: 10.1038/s41598-017-14807-w

[…] een identified in many kinds of species and implicated in important functions in physiological and disease process–. Hence, several comprehensive databases such as CircBase, Circ2Traits, circRNABase, deepBase, and circRNADb, have been developed to merge and unify information of published circRNAs and provide a series of online alignment tools to maintain structure and function prediction. To meet […]

call_split

Repertoire of noncoding RNAs in corpus luteum of early pregnancy in buffalo (Bubalus bubalis)

2017
PMCID: 5639113
PMID: 29062204
DOI: 10.14202/vetworld.2017.1129-1134
call_split See protocol

[…] ASE database were aligned against various ncRNA databases, namely, GtRNA (http://gtrnadb.ucsc.edu/) [], piwi-RNA (http://pirnabank.ibab.ac.in/) [], RFAM (http://rfam.xfam.org/) [], deep guide (http://deepbase.sysu.edu.cn/prediction.php) [], and snoRNA (http://lowelab.ucsc.edu/snoRNAdb/) []. Reads lengths varying at both 3’ and 5’ and possessing a single or no mismatch inside of the sequence were a […]

call_split

Circular RNAs: Isolation, characterization and their potential role in diseases

2017
RNA Biol
PMCID: 5731806
PMID: 28820337
DOI: 10.1080/15476286.2017.1367886
call_split See protocol

[…] hich can be accessed freely at http://uroborus.openbioinformatics.org/. The UROBORUS tool can detect lowly expressed circRNAs in total RNA-seq, without RNase R treatment. Zheng et al. developed their deepBase v1.0 to deepBase v2.0 (http://biocenter.sysu.edu.cn/deepBase/), providing more comprehensive expression and evolution profiles of long non-coding RNAs (lncRNAs), circRNAs and small RNAs. […]

library_books

Clinical Significance and Effect of lncRNA HOXA11 AS in NSCLC: A Study Based on Bioinformatics, In Vitro and in Vivo Verification

2017
Sci Rep
PMCID: 5514100
PMID: 28717185
DOI: 10.1038/s41598-017-05856-2

[…] D: 221883. HOXA11-AS is one of the homeobox (HOX) family genes, and the length of HOXA11-AS is 3885 nt. Interestingly, no HOXA11-AS expression was found in normal lung tissues (http://rna.sysu.edu.cn/deepBase/). Previously, we have investigated the expression and the underlying pathways of HOXA11-AS in NSCLC based on the Cancer Genome Atlas (TCGA) database and bioinformatics analyses (gene ontolog […]

library_books

Genome wide profiling of Sus scrofa circular RNAs across nine organs and three developmental stages

2017
PMCID: 5737845
PMID: 28575165
DOI: 10.1093/dnares/dsx022

[…] en the emerging understanding of the biological importance of circRNAs and research efforts to understand them, researchers have constructed several circRNA databases, including Circ2Traits, CircNet, deepBase v2.0, CircInteractome, and SomamiR2.0. At present, these databases include human, mouse, and C. elegans circRNAs, but not S. scrofa circRNAs, because identification of circRNAs in pigs has la […]


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deepBase institution(s)
RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou China
deepBase funding source(s)
Supported by Ministry of Science and Technology of China, National Basic Research Program [2011CB811300]; National Natural Science Foundation of China [30900820, 31230042, 31370791, 31401975, 31471223, 91440110]; Guangdong Province [S2012010010510, S2013010012457]; Theproject of Science and Technology New Star in ZhuJiang Guangzhou city [2012J2200025]; Fundamental Research Funds for the Central Universities [2011330003161070, 14lgjc18]; China Postdoctoral Science Foundation [200902348]; and in part by the Guangdong Province Key Laboratory of Computational Science and the Guangdong Province Computational Science Innovative Research Team.

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