List of long non-coding RNA databases

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This is a list of long noncoding RNA databases , which provide information about lncRNAs. [1] [2]

Long non-coding RNA databases

NameDescriptionReferences
deepBase Identification, expression, evolution and function of long non-coding RNAs (LncRNAs), small RNAs and circular RNAs from deep-sequencing data [3]
LNCipedia A comprehensive compendium of human long non-coding RNAs. [4] [5]
lncRNAdb The Reference Database For Functional Long Noncoding RNAs. [6]
LncRNAWiki A wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs) [7]
LncBook A comprehensive collection of 270,044 human lncRNAs and systematic curation of lncRNAs’ annotation by multi-omics data integration, function annotation and disease association [8]
MONOCLdb The MOuse NOnCode Lung database provides the annotations and expression profiles of mouse long non-coding RNAs (lncRNAs) involved in influenza and SARS-CoV infections. [9]
NONCODE An integrated knowledge database dedicated to ncRNAs, especially lncRNAs [10]
lncRNome A comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans.
NRED A database of long noncoding RNA expression. [11]
C-It-Loci A tool to explore and to compare the expression profiles of conserved loci among various tissues in three organisms

[12]

MiTranscriptome A catalog of human long poly-adenylated RNA transcripts derived from computational analysis of high-throughput RNA-Seq data from over 6,500 samples, spanning diverse cancer and tissue types [13]
slncky Evolution Browser This site contains alignments and evolutionary metrics of conserved lncRNAs. [14]
Cancer LncRNA Census (CLC) Database of long-noncoding RNAs causally implicated in cancer through in vivo, in vitro and other evidence. [15]
BIGTranscriptome High-confidence of coding and noncoding transcriptomes assembled with hundreds of pseudo-stranded and stranded RNA-seq datasets. [16]
lncRNAKB A knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA [17]
lncHUB2 Functional predictions of human and mouse long non-coding RNAs based on lncRNA-gene co-expression correlations. [18]

Related Research Articles

<span class="mw-page-title-main">Non-coding RNA</span> Class of ribonucleic acid that is not translated into proteins

A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR.

<span class="mw-page-title-main">Small nucleolar SNORD12/SNORD106</span>

In molecular biology, the small nucleolar RNAs SNORD106 and SNORD12 are two related snoRNAs which belongs to the C/D class of small nucleolar RNAs (snoRNAs). Both contain the conserved C (UGAUGA) and D (CUGA) box sequence motifs

<span class="mw-page-title-main">Telomerase RNA component</span> NcRNA found in eukaryotes

Telomerase RNA component, also known as TR, TER or TERC, is an ncRNA found in eukaryotes that is a component of telomerase, the enzyme used to extend telomeres. TERC serves as a template for telomere replication by telomerase. Telomerase RNAs differ greatly in sequence and structure between vertebrates, ciliates and yeasts, but they share a 5' pseudoknot structure close to the template sequence. The vertebrate telomerase RNAs have a 3' H/ACA snoRNA-like domain.

<span class="mw-page-title-main">Long non-coding RNA</span> Non-protein coding transcripts longer than 200 nucleotides

Long non-coding RNAs are a type of RNA, generally defined as transcripts more than 200 nucleotides that are not translated into protein. This arbitrary limit distinguishes long ncRNAs from small non-coding RNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs. Given that some lncRNAs have been reported to have the potential to encode small proteins or micro-peptides, the latest definition of lncRNA is a class of RNA molecules of over 200 nucleotides that have no or limited coding capacity. Long intervening/intergenic noncoding RNAs (lincRNAs) are sequences of lncRNA which do not overlap protein-coding genes.

<span class="mw-page-title-main">Therapeutic Targets Database</span> Database of protein targets in drug design

Therapeutic Target Database (TTD) is a pharmaceutical and medical repository constructed by the Innovative Drug Research and Bioinformatics Group (IDRB) at Zhejiang University, China and the Bioinformatics and Drug Design Group at the National University of Singapore. It provides information about known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Detailed knowledge about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, and clinical development status. TTD is freely accessible without any login requirement at https://idrblab.org/ttd/.

miRBase

In bioinformatics, miRBase is a biological database that acts as an archive of microRNA sequences and annotations. As of September 2010 it contained information about 15,172 microRNAs. This number has risen to 38,589 by March 2018. The miRBase registry provides a centralised system for assigning new names to microRNA genes.

This microRNA database and microRNA targets databases is a compilation of databases and web portals and servers used for microRNAs and their targets. MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (ncRNAs) that regulate gene expression by targeting messenger RNAs.

<span class="mw-page-title-main">LncRNAdb</span>

In bioinformatics, lncRNAdb is a biological database of Long non-coding RNAs The database focuses on those RNAs which have been experimentally characterised with a biological function. The database currently holds over 290 lncRNAs from around 60 species. Example lncRNAs in the database are HOTAIR and Xist.

<span class="mw-page-title-main">Triple helix</span> Set of three congruent geometrical helices with the same axis

In the fields of geometry and biochemistry, a triple helix is a set of three congruent geometrical helices with the same axis, differing by a translation along the axis. This means that each of the helices keeps the same distance from the central axis. As with a single helix, a triple helix may be characterized by its pitch, diameter, and handedness. Examples of triple helices include triplex DNA, triplex RNA, the collagen helix, and collagen-like proteins.

In molecular biology, Highly Up-regulated in Liver Cancer , also known as HULC, is a long non-coding RNA. It was first identified in hepatocellular carcinoma, and is also expressed in colorectal carcinomas that metastasise to the liver. It may have a role in the post-transcriptional regulation of gene expression. It downregulates the expression of several microRNAs, including miR-372. Expression of HULC is upregulated by CREB, there is a CREB-binding site in the promoter of HULC. miR-372 represses translation of the kinase PRKACB, so downregulation of miR-372 leads to increased levels of PRKACB. PRKACB activates CREB by phosphorylation, therefore leading to increased expression of HULC.

The NONCODE database is a collection of expression and functional lncRNA data obtained from re-annotated microarray studies.

In molecular biology mir-542 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms.

Cancer systems biology encompasses the application of systems biology approaches to cancer research, in order to study the disease as a complex adaptive system with emerging properties at multiple biological scales. Cancer systems biology represents the application of systems biology approaches to the analysis of how the intracellular networks of normal cells are perturbed during carcinogenesis to develop effective predictive models that can assist scientists and clinicians in the validations of new therapies and drugs. Tumours are characterized by genomic and epigenetic instability that alters the functions of many different molecules and networks in a single cell as well as altering the interactions with the local environment. Cancer systems biology approaches, therefore, are based on the use of computational and mathematical methods to decipher the complexity in tumorigenesis as well as cancer heterogeneity.

Competing endogenous RNAs hypothesis: ceRNAs regulate other RNA transcripts by competing for shared microRNAs. They are playing important roles in developmental, physiological and pathological processes, such as cancer. Multiple classes of ncRNAs and protein-coding mRNAs function as key ceRNAs (sponges) and to regulate the expression of mRNAs in plants and mammalian cells.

Single nucleotide polymorphism annotation is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query. SNP functional annotation is typically performed based on the available information on nucleic acid and protein sequences.

Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, efficiently plan experiments, integrate their data with existing knowledge, and formulate new hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.

Transcription factors are proteins that bind genomic regulatory sites. Identification of genomic regulatory elements is essential for understanding the dynamics of developmental, physiological and pathological processes. Recent advances in chromatin immunoprecipitation followed by sequencing (ChIP-seq) have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications. The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.

References

  1. ↑ Rinn, J. L.; Chang, H. Y. (2012). "Genome Regulation by Long Noncoding RNAs". Annual Review of Biochemistry . 81: 145–166. doi:10.1146/annurev-biochem-051410-092902. PMC   3858397 . PMID   22663078.
  2. ↑ Martin, L.; Chang, H. Y. (2012). "Uncovering the role of genomic "dark matter" in human disease". Journal of Clinical Investigation . 122 (5): 1589–1595. doi:10.1172/JCI60020. PMC   3336981 . PMID   22546862.
  3. ↑ Zheng, LL; Li, JH; Wu, J; Sun, WJ; Liu, S; Wang, ZL; Zhou, H; Yang, JH; Qu, LH (4 January 2016). "deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data". Nucleic Acids Research. 44 (D1): D196–202. doi:10.1093/nar/gkv1273. PMC   4702900 . PMID   26590255.
  4. ↑ Volders, P. -J.; Helsens, K.; Wang, X.; Menten, B.; Martens, L.; Gevaert, K.; Vandesompele, J.; Mestdagh, P. (2012). "LNCipedia: A database for annotated human lncRNA transcript sequences and structures". Nucleic Acids Research . 41 (Database issue): D246–D251. doi:10.1093/nar/gks915. PMC   3531107 . PMID   23042674.
  5. ↑ Volders, P. J.; Verheggen, K; Menschaert, G; Vandepoele, K; Martens, L; Vandesompele, J; Mestdagh, P (2015). "An update on LNCipedia: A database for annotated human lncRNA sequences". Nucleic Acids Research. 43 (Database issue): D174–180. doi:10.1093/nar/gku1060. PMC   4383901 . PMID   25378313.
  6. ↑ Amaral, P. P.; Clark, M. B.; Gascoigne, D. K.; Dinger, M. E.; Mattick, J. S. (2010). "LncRNAdb: A reference database for long noncoding RNAs". Nucleic Acids Research. 39 (Database issue): D146–D151. doi:10.1093/nar/gkq1138. PMC   3013714 . PMID   21112873.
  7. ↑ Ma, Lina; Li, Ang; Zou, Dong; Xu, Xingjian; Xia, Lin; Yu, Jun; Bajic, Vladimir B.; Zhang, Zhang (2015). "LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs". Nucleic Acids Research. 43 (Database issue): D187–D92. doi:10.1093/nar/gku1167. PMC   4383965 . PMID   25399417.
  8. ↑ Ma, Lina; Cao, Jiabao; Liu, Lin; Du, Qiang; Li, Zhao; Zou, Dong; Bajic, Vladimir B.; Zhang, Zhang (2019). "LncBook: a curated knowledgebase of human long non-coding RNAs". Nucleic Acids Research. 47 (Database issue): D128–D134. doi:10.1093/nar/gky960. PMC   6323930 . PMID   30329098.
  9. ↑ Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR; et al. (2014). "Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts". RNA Biol. 11 (7): 875–90. doi:10.4161/rna.29442. PMC   4179962 . PMID   24922324.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ↑ Bu, D.; Yu, K.; Sun, S.; Xie, C.; Skogerbø, G.; Miao, R.; Xiao, H.; Liao, Q.; Luo, H.; Zhao, G.; Zhao, H.; Liu, Z.; Liu, C.; Chen, R.; Zhao, Y. (2011). "NONCODE v3.0: Integrative annotation of long noncoding RNAs". Nucleic Acids Research. 40 (Database issue): D210–D215. doi:10.1093/nar/gkr1175. PMC   3245065 . PMID   22135294.
  11. ↑ Dinger, M. E.; Pang, K. C.; Mercer, T. R.; Crowe, M. L.; Grimmond, S. M.; Mattick, J. S. (2009). "NRED: A database of long noncoding RNA expression". Nucleic Acids Research. 37 (Database issue): D122–D126. doi:10.1093/nar/gkn617. PMC   2686506 . PMID   18829717.
  12. ↑ Weirick, T.; David, J.; Stefanie, D.; Uchida, S. (2015). "C-It-Loci: a knowledge database for tissue-enriched loci". Bioinformatics . 31 (21): 3537–3543. doi: 10.1093/bioinformatics/btv410 . PMID   26163692.
  13. ↑ Iyer, Matthew K.; Niknafs, Yashar S.; Malik, Rohit; Singhal, Udit; Sahu, Anirban; Hosono, Yasuyuki; Barrette, Terrence R.; Prensner, John R.; Evans, Joseph R. (March 2015). "The landscape of long noncoding RNAs in the human transcriptome". Nature Genetics . 47 (3): 199–208. doi:10.1038/ng.3192. ISSN   1546-1718. PMC   4417758 . PMID   25599403.
  14. ↑ Chen, Jenny; Shishkin, Alexander A.; Zhu, Xiaopeng; Kadri, Sabah; Maza, Itay; Guttman, Mitchell; Hanna, Jacob H.; Regev, Aviv; Garber, Manuel (2016-02-02). "Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs". Genome Biology. 17: 19. doi: 10.1186/s13059-016-0880-9 . ISSN   1474-760X. PMC   4739325 . PMID   26838501.
  15. ↑ Carlevaro-Fita, Joana; Lanzós, Andrés; Feuerbach, Lars; Hong, Chen; Mas-Ponte, David; Skou Pedersen, Jakob; Johnson, Rory (2020). "Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis". Communications Biology. 3 (1): 56. doi: 10.1038/s42003-019-0741-7 . PMC   7002399 . PMID   32024996.
  16. ↑ You, Bo-Hyun; Yoon, Sang-Ho; Nam, Jin-Wu (2017-06-01). "High-confidence coding and noncoding transcriptome maps". Genome Research. 27 (6): 1050–1062. doi: 10.1101/gr.214288.116 . ISSN   1088-9051. PMC   5453319 . PMID   28396519.
  17. ↑ Seifuddin, Fayaz; Singh, Komudi; Suresh, Abhilash; Judy, Jennifer T.; Chen, Yun-Ching; Chaitankar, Vijender; Tunc, Ilker; Ruan, Xiangbo; Ping, Li; Chen, Yi; Cao, Haiming; Lee, Richard S.; Goes, Fernando S.; Zandi, Peter P.; Jafri, M. Saleet; Pirooznia, Mehdi (2020-10-05). "lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA". Scientific Data . 7 (1) 326: 326. Bibcode:2020NatSD...7..326S. doi: 10.1038/s41597-020-00659-z . PMC   7536183 . PMID   33020484.
  18. ↑ Marino, Giacomo B; Wojciechowicz, Megan L; Clarke, Daniel J B; Kuleshov, Maxim V; Xie, Zhuorui; Jeon, Minji; Lachmann, Alexander; Ma’ayan, Avi (2023-03-04). "lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs". Database. 2023. doi:10.1093/database/baad009. ISSN   1758-0463. PMC   9985331 . PMID   36869839.
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