The DIANA-mirExTra web server: From gene expression data to microRNA function

PLoS ONE

Volumn 5, Issue 2, 2010, Pages

  Alexiou, Panagiotis ^a,b   Maragkakis, Manolis ^a,c   Papadopoulos, Giorgio L ^a   Simmosis, Victor A ^a   Zhang, Lin ^d   Hatzigeorgiou, Artemis G ^a,d  

^a Biomedical Sciences Research Center Alexander Fleming Institute of Molecular Oncology   (Greece)

^b ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

^c MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; DIANA MIREXTRA; GENE EXPRESSION; GENE FUNCTION; GENE OVEREXPRESSION; GENETIC DATABASE; HUMAN; INTERNET; NONHUMAN; 3' UNTRANSLATED REGION; ALGORITHM; ANIMAL; BIOLOGY; COMPUTER PROGRAM; DNA MICROARRAY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; OVARY TUMOR; PATHOLOGY;

3' UNTRANSLATED REGIONS; ALGORITHMS; ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; INTERNET; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OVARIAN NEOPLASMS; SOFTWARE;

EID: 77949430343     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009171     Document Type: Article

References (22)

1. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
2. Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
3. Zhang R, Su B (2009) Small but influential: the role of microRNAs on gene regulatory network and 3′UTR evolution. J Genet Genomics 36: 1-6.
4. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
5. Krutzfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, et al. (2005) Silencing of microRNAs in vivo with 'antagomirs'. Nature 438: 685-689.
6. Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34: W369-373.
7. Bussemaker HJ, Li H, Siggia ED (2001) Regulatory element detection using correlation with expression. Nat Genet 27: 167-171.
8. Sood P, Krek A, Zavolan M, Macino G, Rajewsky N (2006) Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A 103: 2746-2751.
9. van Dongen S, Abreu-Goodger C, Enright AJ (2008) Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods 5: 1023-1025.
10. Elkon R, Agami R (2008) Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs. PLoS Comput Biol 4: e1000189.
11. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, et al. (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18: 1165-1178.
12. 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.
13. Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, et al. (2009) DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 37: W273-276.
14. Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, et al. (2009) Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10: 295.
15. Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG (2009) DIANA-mirPath: Integrating human and mouse microRNAs in pathways. Bioinformatics 25: 1991-1993.
16. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
17. Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, et al. (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 36: W423-426.
18. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature.
19. Zhang L, Volinia S, Bonome T, Calin GA, Greshock J, et al. (2008) Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer. Proc Natl Acad Sci U S A 105: 7004-7009.
20. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, et al. (2008) Ensembl 2008. Nucleic Acids Res 36: D707-714.
21. Griffiths-Jones S (2006) miRBase: the microRNA sequence database. Methods Mol Biol 342: 129-138.
22. Karolchik D, Hinrichs AS, Kent WJ (2007) The UCSC Genome Browser. Curr Protoc Bioinformatics Chapter 1: Unit 1 4.