MicroRNA and microRNA target database

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.[1]

microRNA target gene databases

Name Description type Link References
StarBase starBase is designed for decoding miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA, protein-lncRNA, protein-sncRNA, protein-mRNA and protein-pseudogene interactions and ceRNA networks from 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets. It also provides Pan-Cancer Analysis for microRNAs, lncRNAs, circRNAs and protein-coding genes from 6000 tumor samples. database website [2][3]
StarScan StarScan is developed for scanning small RNA (miRNA, piRNA, siRNA) mediated RNA cleavage events in lncRNA, circRNA, mRNA and pseudo genes from degradome sequencing data. web-based software website [4]
Cupid Cupid is a method for simultaneous prediction of miRNA-target interactions and their mediated competing endogenous RNA (ceRNA) interactions. It is an integrative approach significantly improves on miRNA-target prediction accuracy as assessed by both mRNA and protein level measurements in breast cancer cell lines. Cupid is implemented in 3 steps: Step 1: re-evaluate candidate miRNA binding sites in 3’ UTRs. Step2: interactions are predicted by integrating information about selected sites and the statistical dependency between the expression profiles of miRNA and putative targets. Step 3: Cupid assesses whether inferred targets compete for predicted miRNA regulators. * Only the source code for step 3 is provided. software (MATLAB) website [5]
TargetScan Predicts biological targets of miRNAs by searching for the presence of sites that match the seed region of each miRNA. In flies and nematodes, predictions are ranked based on the probability of their evolutionary conservation. In zebrafish, predictions are ranked based on site number, site type, and site context, which includes factors that influence target-site accessibility. In mammals, the user can choose whether the predictions should be ranked based on the probability of their conservation or on site number, type, and context. In mammals and nematodes, the user can choose to extend the predictions beyond conserved sites and consider all sites. database, webserver website [6][7][8][9][10]
TarBase A comprehensive database of experimentally supported animal microRNA targets database website [11]
Diana-microT DIANA-microT 3.0 is an algorithm based on several parameters calculated individually for each microRNA and it combines conserved and non-conserved microRNA recognition elements into a final prediction score.webserverwebserver [12]
miRecords an integrated resource for microRNA-target interactions. database website [13]
PicTar PicTar is Combinatorial microRNA target predictions. database, webserver, predictions website [14]
PITA PITA, incorporates the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition.webserver, predictions predictions [15]
RepTar A database of inverse miRNA target predictions, based on the RepTar algorithm that is independent of evolutionary conservation considerations and is not limited to seed pairing sites. database website [16]
RNA22 The first link (predictions) provides RNA22 predictions for all protein coding transcripts in human, mouse, roundworm, and fruit fly. It allows you to visualize the predictions within a cDNA map and also find transcripts where multiple miR's of interest target. The second web-site link (custom) first finds putative microRNA binding sites in the sequence of interest, then identifies the targeted microRNA. webserver, predictions predictions custom [17]
miRTarBase The experimentally validated microRNA-target interactions database. database website [18]
miRwalk Aggregates and compare results from other miRNA-to-mRNA databases database, webserver [19]
MBSTAR Multiple Instance approach for finding out true or functional microRNA binding sites. webserver, predictions predictions [20]
.

microRNA databases

Name Description type Link References
deepBase deepBase is a database for annotating and discovering small and long ncRNAs (microRNAs, siRNAs, piRNAs...) from high-throughput deep sequencing data. database website [21]
miRBase miRBase database is a searchable database of published miRNA sequences and annotation. database website [22]
microRNA.org microRNA.org is a ddatabase for Experimentally observed microRNA expression patterns and predicted microRNA targets & target downregulation scores. database website [23]
miRGen 2.0 miRGen 2.0: a database of microRNA genomic information and regulation database website [24]
miRNAMap miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes database website [25]
PMRD PMRD: plant microRNA database database website [26]
TargetScan TargetScan7.0 classifies microRNAs according to their level of conservation (i.e., species-specific, conserved among mammals, or broadly conserved among vertebrates) and aggregates them into families based upon their seed sequence. It also annotates conserved isomiRs using small RNA sequencing datasets.[10] database website [10]
VIRmiRNA VIRmiRNA is the first dedicated resource on experimental viral miRNA and their targets. This resource also provides inclusive knowledge about anti-viral miRNAs known to play role in antiviral immunity of host. Database website [27]

References

  1. ↑ Bartel, D. P. (2009). "MicroRNAs: Target Recognition and Regulatory Functions". Cell. 136 (2): 215–233. doi:10.1016/j.cell.2009.01.002. PMC 3794896Freely accessible. PMID 19167326.
  2. ↑ Yang, J. -H.; Li, J. -H.; Shao, P.; Zhou, H.; Chen, Y. -Q.; Qu, L. -H. (2010). "StarBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data". Nucleic Acids Research. 39 (Database issue): D202–D209. doi:10.1093/nar/gkq1056. PMC 3013664Freely accessible. PMID 21037263.
  3. ↑ Li, JH; Liu, S; Zhou, H; Qu, LH; Yang, JH (Jan 1, 2014). "starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.". Nucleic Acids Research. 42 (1): D92–7. doi:10.1093/nar/gkt1248. PMID 24297251.
  4. ↑ Liu, S; Li, JH; Wu, J; Zhou, KR; Zhou, H; Yang, JH; Qu, LH (18 May 2015). "StarScan: a web server for scanning small RNA targets from degradome sequencing data.". Nucleic Acids Research. 43: W480–6. doi:10.1093/nar/gkv524. PMID 25990732.
  5. ↑ Chiu, Hua-Sheng; Llobet-Navas, David; Yang, Xuerui; Chung, Wei-Jen; Ambesi-Impiombato, Alberto; Iyer, Archana; Kim, Hyunjae "Ryan"; Seviour, Elena G.; Luo, Zijun; Sehgal, Vasudha; Moss, Tyler; Lu, Yiling; Ram, Prahlad; Silva, José; Mills, Gordon B.; Califano, Andrea; Sumazin, Pavel (February 2015). "Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks". Genome Research. 25 (2): 257–67. doi:10.1101/gr.178194.114. PMID 25378249.
  6. ↑ Lewis, BP; Burge CB; Bartel DP (Jan 14, 2005). "Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets". Cell. 120 (1): 15–20. doi:10.1016/j.cell.2004.12.035. PMID 15652477.
  7. ↑ Grimson, A; Farh, KK; Johnston, WK; Garrett-Engele, P; Lim, LP; Bartel, DP (Jul 6, 2007). "MicroRNA targeting specificity in mammals: determinants beyond seed pairing.". Molecular Cell. 27 (1): 91–105. doi:10.1016/j.molcel.2007.06.017. PMC 3800283Freely accessible. PMID 17612493.
  8. ↑ Friedman, RC; Farh, KK; Burge, CB; Bartel, DP (January 2009). "Most mammalian mRNAs are conserved targets of microRNAs.". Genome Research. 19 (1): 92–105. doi:10.1101/gr.082701.108. PMC 2612969Freely accessible. PMID 18955434.
  9. ↑ Garcia, DM; Baek, D; Shin, C; Bell, GW; Grimson, A; Bartel, DP (Sep 11, 2011). "Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.". Nature Structural & Molecular Biology. 18 (10): 1139–46. doi:10.1038/nsmb.2115. PMC 3190056Freely accessible. PMID 21909094.
  10. 1 2 3 Agarwal, Vikram; Bell, George W.; Nam, Jin-Wu; Bartel, David P. (2015-08-12). "Predicting effective microRNA target sites in mammalian mRNAs". eLife. 4: e05005. doi:10.7554/eLife.05005. ISSN 2050-084X. PMC 4532895Freely accessible. PMID 26267216.
  11. ↑ Sethupathy P, Corda B, Hatzigeorgiou AG (2006). "TarBase: A comprehensive database of experimentally supported animal microRNA targets.". RNA. 12 (2): 192–197. doi:10.1261/rna.2239606. PMC 1370898Freely accessible. PMID 16373484.
  12. ↑ Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (2009). "Accurate microRNA target prediction correlates with protein repression levels.". BMC Bioinformatics. 10: 295. doi:10.1186/1471-2105-10-295. PMC 2752464Freely accessible. PMID 19765283.
  13. ↑ Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T (2009). "miRecords: an integrated resource for microRNA-target interactions.". Nucl. Acids Res. 37 (Database issue): D105–110. doi:10.1093/nar/gkn851. PMC 2686554Freely accessible. PMID 18996891.
  14. ↑ Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N (2005). "Combinatorial microRNA target predictions.". Nat Genet. 37 (5): 495–500. doi:10.1038/ng1536. PMID 15806104.
  15. ↑ Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007). "The role of site accessibility in microRNA target recognition.". Nat Genet. 39 (10): 1278–84. doi:10.1038/ng2135. PMID 17893677.
  16. ↑ Elefant, Naama; Berger Amnon; Shein Harel; Hofree Matan; Margalit Hanah; Altuvia Yael (Jan 2011). "RepTar: a database of predicted cellular targets of host and viral miRNAs". Nucleic Acids Res. England. 39 (Database issue): D188–94. doi:10.1093/nar/gkq1233. PMC 3013742Freely accessible. PMID 21149264.
  17. ↑ Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I (2006). "A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.". Cell. 126 (6): 1203–17. doi:10.1016/j.cell.2006.07.031. PMID 16990141.
  18. ↑ Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, Huang HD (2011). "miRTarBase: a database curates experimentally validated microRNA-target interactions.". Nucleic Acids Research. 39 (Database issue): D163–9. doi:10.1093/nar/gkq1107. PMC 3013699Freely accessible. PMID 21071411.
  19. ↑ Dweep H, Sticht C, Pandey P, Gretz N (2011). "miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes.". JBI. 44 (5): 839–47. doi:10.1016/j.jbi.2011.05.002. PMID 21605702.
  20. ↑ Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z (2015). "MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets.". Sci Rep. 5: 8004. doi:10.1038/srep08004. PMID 25614300.
  21. ↑ Yang JH, Shao P, Zhou H, Chen YQ, Qu LH (2010). "deepBase: a database for deeply annotating and mining deep sequencing data.". Nucl. Acids Res. 38 (Database issue): D123–130. doi:10.1093/nar/gkp943. PMC 2808990Freely accessible. PMID 19966272.
  22. ↑ Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008). "miRBase: tools for microRNA genomics.". Nucl. Acids Res. 36: D154–D158. doi:10.1093/nar/gkm952. PMC 2238936Freely accessible. PMID 17991681.
  23. ↑ Betel D, Wilson M, Gabow A, Marks DS, Sander C (2007). "The microRNA.org resource: targets and expression.". Nucl. Acids Res. 36 (Database issue): D149–153. doi:10.1093/nar/gkm995. PMC 2238905Freely accessible. PMID 18158296.
  24. ↑ Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG (2010). "miRGen 2.0: a database of microRNA genomic information and regulation.". Nucl. Acids Res. 38 (Database issue): D137–41. doi:10.1093/nar/gkp888. PMC 2808909Freely accessible. PMID 19850714.
  25. ↑ Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S, Hofacker IL (2006). "miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.". Nucl. Acids Res. 34 (Database issue): D135–139. doi:10.1093/nar/gkj135. PMC 1347497Freely accessible. PMID 16381831.
  26. ↑ Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z (2010). "PMRD: plant microRNA database.". Nucl. Acids Res. 38 (Database issue): D806–813. doi:10.1093/nar/gkp818. PMC 2808885Freely accessible. PMID 19808935.
  27. ↑ Qureshi, Abid; Thakur, Nishant; Monga, Isha; Thakur, Anamika; Kumar, Manoj (2014-01-01). "VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets". Database: The Journal of Biological Databases and Curation. 2014. doi:10.1093/database/bau103. ISSN 1758-0463. PMC 4224276Freely accessible. PMID 25380780.

Further reading

External links

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