Tag Archives: database
Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor overlaps. The availability of the raw RNA-Seq datasets in public domain encompassing critical developmental time-points and adult tissues provides us with a unique opportunity to understand the spatiotemporal expression patterns of lncRNAs.
Now, researchers from the CSIR-Institute of Genomics and Integrative Biology have created a catalog of lncRNAs in zebrafish, derived largely from the three annotation sets, as well as manual curation of literature to compile a total of 2,267 lncRNA transcripts in zebrafish. The lncRNAs were further classified based on the genomic context and relationship with protein coding gene neighbors into 4 categories. Analysis revealed a total of 86 intronic, 309 promoter associated, 485 overlapping and 1,386 lincRNAs. They have created a comprehensive resource which houses the annotation of lncRNAs as well as associated information including expression levels, promoter epigenetic marks, genomic variants and retroviral insertion mutants. The resource also hosts a genome browser where the datasets could be browsed in the genome context.
Availability – The resource is freely available at URL: http://genome.igib.res.in/zflncRNApedia
- Dhiman H, Kapoor S, Sivadas A, Sivasubbu S, Scaria V. (2015) zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs. PLoS One 10(6):e0129997. [article]
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LNCipedia collects long non-coding RNA sequences and annotation from different sources. In version 3.0, over 90,000 new transcripts were added to the database. 6917 of these transcripts were obtained from RefSeq by filtering for accession prefix (NR_) and size (200bp). This filtering strategy however, does not confine to long non-coding RNAs and also yields transcripts associated with protein coding genes. Transcripts with incomplete open reading frames that are subject to nonsense-mediated mRNA decay for instance are also annotated with accession prefix NR_. These transcripts are generally not considered as true lncRNAs and typically exhibit a high coding potential score when assessed by PhyloCSF. The authors therefore chose to exclude these transcripts from the database and confine their analysis to the RefSeq subset with keyword biomol_ncrna_lncrna as suggested by RefSeq’s Dr. Kimm D. Pruit. This change is reflected in LNCipedia.org update 3.1 and this corrigendum serves to elucidate the discrepancies in the article caused by this update. (read more…)
Long non-coding RNAs (lncRNAs) play key roles in various cellular contexts and diseases by diverse mechanisms. With the rapid growth of identified lncRNAs and disease-associated single nucleotide polymorphisms (SNPs), there is a great demand to study SNPs in lncRNAs. Aiming to provide a useful resource about lncRNA SNPs, researchers from the Huazhong University of Science and Technology systematically identified SNPs in lncRNAs and analyzed their potential impacts on lncRNA structure and function. In total, they identified 495,729 and 777,095 SNPs in more than 30,000 lncRNA transcripts in human and mouse, respectively. A large number of SNPs were predicted with the potential to impact on the miRNA-lncRNA interaction. The experimental evidence and conservation of miRNA-lncRNA interaction, as well as miRNA expressions from TCGA were also integrated to prioritize the miRNA-lncRNA interactions and SNPs on the binding sites. Furthermore, by mapping SNPs to GWAS results, they found that 142 human lncRNA SNPs are GWAS tagSNPs and 197,827 lncRNA SNPs are in the GWAS linkage disequilibrium regions. All these data for human and mouse lncRNAs were imported into lncRNASNP database, which includes two sub-databases lncRNASNP-human and lncRNASNP-mouse. The lncRNASNP database has a user-friendly interface for searching and browsing through the SNP, lncRNA and miRNA sections.
Availability – the lncRNASNP database is available at: http://bioinfo.life.hust.edu.cn/lncRNASNP/
- Gong J, Liu W, Zhang J, Miao X, Guo AY. (2015) lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res 43(Database issue):D181-6. [article]
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- A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Per
- The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3中文版
The domestic-animal lncRNA database (ALDB) is the first comprehensive database with a focus on the domestic-animal lncRNAs. ALDB currently comprises 12,103 pig lincRNAs, 8,923 chicken lincRNAs, and 8,250 cow lincRNAs, which have been identified using computational pipeline in this study. Moreover, ALDB provides related useful data, such as genome-wide expression profile and animal quantitative trait loci (QTLs), that is not available in the existing lncRNA database (lncRNAdb and NONCODE), along with convenient tools, such as BLAST, GBrowse and flexible search functionalities.
- Li, Aimin (2015): ALDB: a domestic-animal long noncoding RNA database. figshare.
LncRNA2Target – a database for differentially expressed genes after lncRNA knockdown or overexpression
Long noncoding RNAs (lncRNAs) have been emerged as critical regulators of gene expression at epigenetic, transcriptional and post-transcriptional level, yet what genes are regulated by lncRNAs remains to be characterized. To assess the effects of a specific lncRNA on gene expression, increasing researchers profiled the genome-wide or individual gene expression level changes after knocking down or overexpressing the lncRNA. However, no online repository is currently available to collect these differentially expressed genes regulated by lncRNAs.
To make it convenient for researchers to know what genes are regulated by a lncRNA or which lncRNAs regulate a given gene of interest, researchers at the Harbin Institute of Technology have developed LncRNA2Target: a comprehensive resource of differentially expressed genes after lncRNA knockdown or overexpression.
In this database system, target genes of a lncRNA are defined as the differentially expressed genes after knocking down or overexpressing the lncRNA. By reviewing all published lncRNA papers, we manually curated the differentially expressed target genes confirmed by qRT-PCR or western blot, and identified all the differential target genes from the microarray or RNA-seq data.
Availability – the LncRNA2Target database is available at: http://www.lncrna2target.org/
- Qinghua Jiang; Jixuan Wang; Xiaoliang Wu; Rui Ma; Tianjiao Zhang; Shuilin Jin; Zhijie Han; Renjie Tan; Jiajie Peng; Guiyou Liu; Yu Li; Yadong Wang. LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression. Nucleic Acids Research 2014; doi: 10.1093/nar/gku1173
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- how to overexpress lincRNA
- lncrna overexpression no effect