MiRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Naeem, Haroon ^a   Küffner, Robert ^a   Csaba, Gergely ^a   Zimmer, Ralf ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED EXTRACTION; BIOMEDICAL LITERATURE; COMPUTATIONAL PREDICTIONS; LARGE SCALE EXPERIMENTS; MIRNA TARGET PREDICTIONS; PREDICTION ALGORITHMS; REGULATORY NETWORK; WEB-BASED INTERFACE;

ALGORITHMS; DATA MINING; DATABASE SYSTEMS; EXTRACTION; GENE EXPRESSION; MULTIMEDIA SYSTEMS; PROTEINS;

RNA;

RATTUS;

MICRORNA;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; DATA MINING; GENETIC DATABASE; GENETICS; INTERNET; MEDLINE; METHODOLOGY; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, GENETIC; INTERNET; MICRORNAS; PUBMED; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 77952304446     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-135     Document Type: Article

References (44)

1. Brodersen P, Voinnet O. Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 2009, 10(2):141-148. 10.1038/nrm2619, 19145236.
2. Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP. The impact of microRNAs on protein output. Nature 2008, 455(7209):64-71. 10.1038/nature07242, 2745094, 18668037.
3. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136(2):215-233. 10.1016/j.cell.2009.01.002, 19167326.
4. Orom UA, Lund AH. Experimental identification of microRNA targets. Gene 2009, 1-5.
5. Li M, Marin-Muller C, Bharadwaj U, Chow KH, Yao Q, Chen C. MicroRNAs: control and loss of control in human physiology and disease. World J Surg 2009, 33(4):667-684. 10.1007/s00268-008-9836-x, 19030926.
6. Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 2009, 37:D98-104. 10.1093/nar/gkn714, 2686559, 18927107.
7. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75(5):843-854. 10.1016/0092-8674(93)90529-Y, 8252621.
8. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-8. 10.1093/nar/gkm952, 2238936, 17991681.
9. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39(10):1278-84. 10.1038/ng2135, 17893677.
10. 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.
11. Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression. Nucleic Acids Res 2008, (36 Database):D149-53. 2238905, 18158296.
12. Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N. Combinatorial microRNA target predictions. Nat Genet 2005, 37:495-500. 10.1038/ng1536, 15806104.
13. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003, 115:787-798. 10.1016/S0092-8674(03)01018-3, 14697198.
14. Ragan C, Cloonan N, Grimmond SM, Zuker M, Ragan MA. Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH. PLoS One 2009, 4(5):e5745. 10.1371/journal.pone.0005745, 2684643, 19478946.
15. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A. A combined computational-experimental approach predicts human microRNA targets. Genes Dev 2004, 18:1165-78. 10.1101/gad.1184704, 415641, 15131085.
16. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009, 37:D105-10. 10.1093/nar/gkn851, 2686554, 18996891.
17. Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 2006, 12:192-197. 10.1261/rna.2239606, 1370898, 16373484.
18. 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.
19. Nam S, Kim B, Shin S, Lee S. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res 2008, 36:159-164.
20. Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG. miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res 2009, 1-5.
21. Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, Birney E. The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res 2008, 36:D445-448. 10.1093/nar/gkm881, 2238870, 17984084.
22. Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA, . Mouse Genome Database Group The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 2008, 36:724-728. Mouse Genome Database Group.
23. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2007, 35:D26-D31. 10.1093/nar/gkl993, 1761442, 17148475.
24. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31:365-70. 10.1093/nar/gkg095, 165542, 12520024.
25. Hsu SD, Chu CH, Tsou AP, Chen SJ, Chen HC, Hsu PW, Wong YH, Chen YH, Chen GH, Huang HD. miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res 2008, 36:165-169.
26. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455(7209):58-63. 10.1038/nature07228, 18668040.
27. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 433(7027):769-73. 10.1038/nature03315, 15685193.
28. Calin GA, Cimmino A, Fabbri M, Ferracin M, Wojcik SE, Shimizu M, Taccioli C, Zanesi N, Garzon R, Aqeilan RI, Alder H, Volinia S, Rassenti L, Liu X, Liu CG, Kipps TJ, Negrini M, Croce CM. MiR-15a and miR-16-1 cluster functions in human leukemia. Proceedings of the National Academy of Sciences of the USA 2008, 105(13):5166-71. 10.1073/pnas.0800121105, 2278188, 18362358.
29. Jeyaseelan K, Lim KY, Armugam A. MicroRNA expression in the blood and brain of rats subjected to transient focal ischemia by middle cerebral artery occlusion. Stroke 2008, 39(3):959-66. 10.1161/STROKEAHA.107.500736, 18258830.
30. Ritchie W, Flamant S, Rasko JE. Predicting microRNA targets and functions: traps for the unwary. Nat 2009, 6(6):397-8.
31. Hanisch D, Fundel K, Mevissen HT, Zimmer R, Fluck J. ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 2005, 6(Suppl 1):S14. 10.1186/1471-2105-6-S1-S14, 1869006, 15960826.
32. Fundel K, Zimmer R. Gene and protein nomenclature in public databases. BMC Bioinformatics 2006, 7:372. 10.1186/1471-2105-7-372, 1560172, 16899134.
33. Fundel K, Güttler D, Zimmer R, Apostolakis J. A simple approach for protein name identification: prospects and limits. BMC Bioinformatics 2005, 6(Suppl 1):S15. 10.1186/1471-2105-6-S1-S15, 1869007, 15960827.
34. Jensen LJ, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 2006, 7:119-129. 10.1038/nrg1768, 16418747.
35. Erhardt RA, Schneider R, Blaschke C. Status of text-mining techniques applied to biomedical text. Drug Discovery Today 2006, 11:315-325. 10.1016/j.drudis.2006.02.011, 16580973.
36. Ananiadou S, Kell DB, Tsujii J. Text mining and its potential applications in systems biology. Trends Biotechnol 2006, 24:571-579. 10.1016/j.tibtech.2006.10.002, 17045684.
37. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T. A uniform system for microRNA annotation. RNA 2003, 9(3):277-279. 10.1261/rna.2183803, 1370393, 12592000.
38. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res 2004, 32:109-111.
39. Csaba G. syngrep - Fast synonym-based named entity recognition, Personal communication. LMU, Munich 2008,
40. Aho VA, Corasick MJ. Efficient string matching: An aid to bibliographic search. Communications of the ACM 1975, 18:333-340.
41. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2009, 37:5-15.
42. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R, . Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32:D258-61. 10.1093/nar/gkh066, 308770, 14681407, Gene Ontology Consortium.
43. Gansner ER, North SC. An open graph visualization system and its applications to software engineering. Software: Practice and Experience 2000, 1203-1233.
44. Xi Y, Shalgi R, Fodstad O, Pilpel Y, Ju J. Differentially regulated micro-RNAs and actively translated messenger RNA transcripts by tumor suppressor p53 in colon cancer. Clin Cancer Res 2006, 12(7 Pt 1):2014-24. 10.1158/1078-0432.CCR-05-1853, 16609010.