ExprTarget: An integrative approach to predicting human microRNA targets

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Gamazon, Eric R ^a   Im, Hae Kyung ^a   Duan, Shiwei ^c   Lussier, Yves A ^a,b   Cox, Nancy J ^a   Dolan, M Eileen ^a   Zhang, Wei ^d  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c AGENCY FOR SCIENCE   (Singapore)

^d UNIVERSITY OF ILLINOIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ALGORITHM; ARTICLE; EXPRTARGET; GENE EXPRESSION PROFILING; GENE TARGETING; GOLD STANDARD; HUMAN; LYMPHOBLASTOID CELL LINE; PREDICTION; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; VALIDATION STUDY; GENETICS; THERMODYNAMICS;

ALGORITHMS; HUMANS; MICRORNAS; THERMODYNAMICS;

EID: 78149459713     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013534     Document Type: Article

References (41)

1. Sotiriou C, Pusztai L (2009) Gene-expression signatures in breast cancer. N Engl J Med 360: 790-800.
2. Nannini M, Pantaleo MA, Maleddu A, Astolfi A, Formica S, et al. (2009) Gene expression profiling in colorectal cancer using microarray technologies: results and perspectives. Cancer Treat Rev 35: 201-209.
3. Bacher U, Kohlmann A, Haferlach T (2009) Perspectives of gene expression profiling for diagnosis and therapy in haematological malignancies. Brief Funct Genomic Proteomic 8: 184-193.
4. Seo D, Ginsburg GS, Goldschmidt-Clermont PJ (2006) Gene expression analysis of cardiovascular diseases: novel insights into biology and clinical applications. J Am Coll Cardiol 48: 227-235.
5. Xu B, Karayiorgou M, Gogos JA MicroRNAs in psychiatric and neuro-developmental disorders. Brain Res 1338: 78-88.
6. The International HapMap Consortium (2003) The International HapMap Project. Nature 426: 789-796.
7. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
8. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747.
9. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
10. Zhang W, Duan S, Kistner EO, Bleibel WK, Huang RS, et al. (2008) Evaluation of genetic variation contributing to differences in gene expression between populations. Am J Hum Genet 82: 631-640.
11. Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, et al. (2007) Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 39: 226-231.
12. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nat Genet 39: 1217-1224.
13. Storey JD, Madeoy J, Strout JL, Wurfel M, Ronald J, et al. (2007) Gene- expression variation within and among human populations. Am J Hum Genet 80: 502-509.
14. Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, et al. (2005) Genome-wide associations of gene expression variation in humans. PLoS Genet 1: e78.
15. Zhang W, Dolan ME (2009) Use of cell lines in the investigation of pharmacogenetic loci. Curr Pharm Des 15: 3782-3795.
16. Welsh M, Mangravite L, Medina MW, Tantisira K, Zhang W, et al. (2009) Pharmacogenomic discovery using cell-based models. Pharmacol Rev 61: 413-429.
17. Gamazon ER, Huang RS, Cox NJ, Dolan ME (2010) Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Proc Natl Acad Sci USA 107: 9287-9292.
18. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5: 522-531.
19. Lim LP (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
20. Bushati N, Cohen SM (2008) MicroRNAs in neurodegeneration. Curr Opin Neurobiol 18: 292-296.
21. Barringhaus KG, Zamore PD (2009) MicroRNAs: regulating a change of heart. Circulation 119: 2217-2224.
22. Medina PP, Slack FJ (2008) microRNAs and cancer: an overview. Cell Cycle 7: 2485-2492.
23. Sethupathy P, Corda B, Hatzigeorgiou AG (2006) TarBase: A comprehensive database of experimentally supported animal microRNA targets. Rna 12: 192-197.
24. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 37: D155-158.
25. Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al. (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1.
26. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) MiRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-158.
27. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
28. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
29. Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
30. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37: 495-500.
31. Bentwich I (2005) Prediction and validation of microRNAs and their targets. FEBS Lett 579: 5904-5910.
32. Sethupathy P, Megraw M, Hatzigeorgiou AG (2006) A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods 3: 881-886.
33. Zhang W, Duan S, Bleibel WK, Wisel SA, Huang RS, et al. (2009) Identification of common genetic variants that account for transcript isoform variation between human populations. Hum Genet 125: 81-93.
34. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, et al. (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6: e1000888.
35. Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, et al. (2009) SCAN: SNP and copy number annotation. Bioinformatics 26: 259-262.
36. Klein TE, Chang JT, Cho MK, Easton KL, Fergerson R, et al. (2001) Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J 1: 167-170.
37. Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, et al. (2007) A comparison of background correction methods for two-colour microarrays. Bioinformatics 23: 2700-2707.
38. R Development Core Team (2005) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
39. Sing T, Sander O, Beerenwinkel N, Lengauer T (2005) ROCR: visualizing classifier performance in R. Bioinformatics 21: 3940-3941.
40. Hanley JA, McNeil BJ (1982) The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143: 29-36.
41. Hanley JA, McNeil BJ (1983) A method of comparing the areas under receiver operating characteristic curves derived from the same cases. Radiology 148: 839-843.