MiRMaid: A unified programming interface for microRNA data resources

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Jacobsen, Anders ^a,b   Krogh, Anders ^a   Kauppinen, Sakari ^c,d   Lindow, Morten ^c  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c Santaris Pharma AS   (Denmark)

^d AALBORG UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICIANS; MODULAR SOFTWARES; ONLINE REPOSITORIES; OPEN SOURCE LICENSE; POST-TRANSCRIPTIONAL REGULATIONS; PROGRAMMING INTERFACE; SOFTWARE FRAMEWORKS; WEB SERVICE INTERFACE;

BIOINFORMATICS; COMPUTER PROGRAMMING; GENE EXPRESSION; OPEN SYSTEMS; WEB SERVICES; WEBSITES;

RNA;

ANIMALIA;

MICRORNA;

ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER LANGUAGE; COMPUTER PROGRAM; GENETIC DATABASE; METHODOLOGY; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; MICRORNAS; PROGRAMMING LANGUAGES; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 77649115847     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-29     Document Type: Article

References (22)

1. Bartel DP. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
2. Chekulaeva M, Filipowicz W. Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells. Current Opinion in Cell Biology 2009, 21:452-460. 10.1016/j.ceb.2009.04.009, 19450959.
3. Medina PP, Slack FJ. microRNAs and cancer: an overview. Cell Cycle 2008, 7:2485-2492.
4. Petri A, Lindow M, Kauppinen S. MicroRNA silencing in primates: towards development of novel therapeutics. Cancer Res 2009, 69:393-395. 10.1158/0008-5472.CAN-08-2749, 19147547.
5. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-158. 10.1093/nar/gkm952, 2238936, 17991681.
6. Ambros V, Bartel B, Bartel DP, et al. A uniform system for microRNA annotation. RNA 2003, 9:277-279. 10.1261/rna.2183803, 1370393, 12592000.
7. Gerlach D, Kriventseva EV, Rahman N, Vejnar CE, Zdobnov EM. miROrtho: computational survey of microRNA genes. Nucleic Acids Res 2009, 37:D111-117. 10.1093/nar/gkn707, 2686488, 18927110.
8. Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG. miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res 2007, 35:D149-155. 10.1093/nar/gkl904, 1669779, 17108354.
9. Taccioli C, Fabbri E, Visone R, et al. UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. Nucleic Acids Res 2009, 37:D41-48. 10.1093/nar/gkn702, 2686429, 18945703.
10. Levy A, Sela N, Ast G. TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res 2008, 36:D47-52. 10.1093/nar/gkm949, 2238949, 17986453.
11. Lewis B, Burge C, Bartel D. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:20. 15..
12. Hsu S, Chu C, Tsou A, et al. miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res 2008, 36:D165-169. 10.1093/nar/gkm1012, 2238982, 18029362.
13. Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, 36:D149-153. 10.1093/nar/gkm995, 2238905, 18158296.
14. Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 2008, 14:1012-1017. 10.1261/rna.965408, 2390791, 18426918.
15. Xiao F, Zuo Z, Cai G, et al. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009, 37:D105-110. 10.1093/nar/gkn851, 2686554, 18996891.
16. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG. The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 2009, 37:D155-8. 10.1093/nar/gkn809, 2686456, 18957447.
17. Jiang Q, Wang Y, Hao Y, et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 2009, 37:D98-104. 10.1093/nar/gkn714, 18927107.
18. Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG. DIANA-mirPath: Integrating human and mouse microRNAs in pathways. Bioinformatics 2009, 25:1991-1993. 10.1093/bioinformatics/btp299, 19435746.
19. Nam S, Li M, Choi K, et al. MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 2009, 37:W356-362. 10.1093/nar/gkp294, 2703907, 19420067.
20. Fielding RT, Taylor RN. Principled design of the modern Web architecture. ACM Trans Internet Technol 2002, 2:115-150.
21. R Development Core Team R: A Language and Environment for Statistical Computing. Version 2.10.1 2009, R Development Core Team.
22. Jiang Q, Wang Y, Hao Y, et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 2009, 37:D98-D104. 10.1093/nar/gkn714, 2686559, 18927107.