Databases for LncRNAs: a Comparative Evaluation of Emerging Tools

Overview

Journal RNA

Specialty Molecular Biology

Date 2014 Oct 18

PMID 25323317

Citations 49

Authors

Sabrina Fritah

Simone P Niclou

Francisco Azuaje

Affiliations

Soon will be listed here.

Abstract

The vast majority of the human transcriptome does not code for proteins. Advances in transcriptome arrays and deep sequencing are giving rise to a fast accumulation of large data sets, particularly of long noncoding RNAs (lncRNAs). Although it is clear that individual lncRNAs may play important and diverse biological roles, there is a large gap between the number of existing lncRNAs and their known relation to molecular/cellular function. This and related information have recently been gathered in several databases dedicated to lncRNA research. Here, we review the content of general and more specialized databases on lncRNAs. We evaluate these resources in terms of the quality of annotations, the reporting of validated or predicted molecular associations, and their integration with other resources and computational analysis tools. We illustrate our findings using known and novel cancer-related lncRNAs. Finally, we discuss limitations and highlight potential future directions for these databases to help delineating functions associated with lncRNAs.

Citing Articles

Gene coexpression networks reveal a broad role for lncRNAs in inflammatory bowel disease.

Johnson J, Sargsyan D, Neiman E, Hart A, Stojmirovic A, Kosoy R JCI Insight. 2024; 9(3).

PMID: 38329124 PMC: 10967393. DOI: 10.1172/jci.insight.168988.

Noncoding RNAs in apoptosis: identification and function.

Tuncel O, Kara M, Yaylak B, Erdogan I, Akgul B Turk J Biol. 2023; 46(1):1-40.

PMID: 37533667 PMC: 10393110. DOI: 10.3906/biy-2109-35.

Extracellular vesicles of trypomastigotes of Trypanosoma cruzi induce changes in ubiquitin-related processes, cell-signaling pathways and apoptosis.

Cornet-Gomez A, Retana Moreira L, Kronenberger T, Osuna A Sci Rep. 2023; 13(1):7618.

PMID: 37165081 PMC: 10171165. DOI: 10.1038/s41598-023-34820-6.

Non-Coding RNAs Regulating Mitochondrial Functions and the Oxidative Stress Response as Putative Targets against Age-Related Macular Degeneration (AMD).

Hyttinen J, Blasiak J, Kaarniranta K Int J Mol Sci. 2023; 24(3).

PMID: 36768958 PMC: 9917342. DOI: 10.3390/ijms24032636.

Altered genome-wide hippocampal gene expression profiles following early life lead exposure and their potential for reversal by environmental enrichment.

Singh G, Singh V, Kim T, Ertel A, Fu W, Schneider J Sci Rep. 2022; 12(1):11937.

PMID: 35879375 PMC: 9314447. DOI: 10.1038/s41598-022-15861-9.

References

Cheetham S, Gruhl F, Mattick J, Dinger M . Long noncoding RNAs and the genetics of cancer. Br J Cancer. 2013; 108(12):2419-25. PMC: 3694235. DOI: 10.1038/bjc.2013.233. View

Cabili M, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A . Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011; 25(18):1915-27. PMC: 3185964. DOI: 10.1101/gad.17446611. View

Amaral P, Clark M, Gascoigne D, Dinger M, Mattick J . lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res. 2010; 39(Database issue):D146-51. PMC: 3013714. DOI: 10.1093/nar/gkq1138. View

Liao Q, Liu C, Yuan X, Kang S, Miao R, Xiao H . Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res. 2011; 39(9):3864-78. PMC: 3089475. DOI: 10.1093/nar/gkq1348. View

Paraskevopoulou M, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas T . DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res. 2012; 41(Database issue):D239-45. PMC: 3531175. DOI: 10.1093/nar/gks1246. View

Kong L, Zhang Y, Ye Z, Liu X, Zhao S, Wei L . CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007; 35(Web Server issue):W345-9. PMC: 1933232. DOI: 10.1093/nar/gkm391. View

Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A . The human genome browser at UCSC. Genome Res. 2002; 12(6):996-1006. PMC: 186604. DOI: 10.1101/gr.229102. View

Yin Q, Yang L, Zhang Y, Xiang J, Wu Y, Carmichael G . Long noncoding RNAs with snoRNA ends. Mol Cell. 2012; 48(2):219-30. DOI: 10.1016/j.molcel.2012.07.033. View

Brockdorff N, Ashworth A, Kay G, McCabe V, Norris D, Cooper P . The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell. 1992; 71(3):515-26. DOI: 10.1016/0092-8674(92)90519-i. View

10.

Jiang J, Jing Y, Cost G, Chiang J, Kolpa H, Cotton A . Translating dosage compensation to trisomy 21. Nature. 2013; 500(7462):296-300. PMC: 3848249. DOI: 10.1038/nature12394. View

11.

Bhartiya D, Pal K, Ghosh S, Kapoor S, Jalali S, Panwar B . lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database (Oxford). 2013; 2013:bat034. PMC: 3708617. DOI: 10.1093/database/bat034. View

12.

Jin J, Liu J, Wang H, Wong L, Chua N . PLncDB: plant long non-coding RNA database. Bioinformatics. 2013; 29(8):1068-71. PMC: 3624813. DOI: 10.1093/bioinformatics/btt107. View

13.

Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M . Antisense transcription in the mammalian transcriptome. Science. 2005; 309(5740):1564-6. DOI: 10.1126/science.1112009. View

14.

Foulds C, Tsimelzon A, Long W, Le A, Tsai S, Tsai M . Research resource: expression profiling reveals unexpected targets and functions of the human steroid receptor RNA activator (SRA) gene. Mol Endocrinol. 2010; 24(5):1090-105. PMC: 2870939. DOI: 10.1210/me.2009-0427. View

15.

Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X . LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res. 2012; 41(Database issue):D983-6. PMC: 3531173. DOI: 10.1093/nar/gks1099. View

16.

Place R, Noonan E . Non-coding RNAs turn up the heat: an emerging layer of novel regulators in the mammalian heat shock response. Cell Stress Chaperones. 2013; 19(2):159-72. PMC: 3933615. DOI: 10.1007/s12192-013-0456-5. View

17.

Muniategui A, Pey J, Planes F, Rubio A . Joint analysis of miRNA and mRNA expression data. Brief Bioinform. 2012; 14(3):263-78. DOI: 10.1093/bib/bbs028. View

18.

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S . Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002; 420(6915):563-73. DOI: 10.1038/nature01266. View

19.

Tripathi V, Song D, Zong X, Shevtsov S, Hearn S, Fu X . SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles. Mol Biol Cell. 2012; 23(18):3694-706. PMC: 3442416. DOI: 10.1091/mbc.E12-03-0206. View

20.

Wan G, Hu X, Liu Y, Han C, Sood A, Calin G . A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation. EMBO J. 2013; 32(21):2833-47. PMC: 3817469. DOI: 10.1038/emboj.2013.221. View