Systematic analysis of regulation and functions of co-expressed microRNAs in humans

Molecular BioSystems

Volumn 6, Issue 10, 2010, Pages 1863-1872

  Liao, Mingzhi ^a   Jiang, Wei ^a   Chen, Xiaowen ^a   Lian, Baofeng ^a   Li, Wei ^a   Lv, Yingli ^a   Wang, Yanqiu ^a   Wang, Shiyuan ^a   Li, Xia ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR;

ARTICLE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HUMAN; HUMAN CHROMOSOME; HUMAN GENOME; METABOLISM;

CHROMOSOMES, HUMAN; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; MICRORNAS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 77956495732     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/b926947a     Document Type: Article

References (56)

1. R. C. Lee R. L. Feinbaum V. Ambros The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 1993 75 843 54
2. D. P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 2004 116 281 97
3. S. Griffiths-Jones H. K. Saini S. van Dongen A. J. Enright miRBase: tools for microRNA genomics Nucleic Acids Res. 2008 36 D154 8
4. B. P. Lewis C. B. Burge D. P. Bartel Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 2005 120 15 20
5. G. A. Calin C. M. Croce MicroRNA signatures in human cancers Nat. Rev. Cancer 2006 6 857 66
6. S. Tsuchiya Y. Okuno G. Tsujimoto MicroRNA: biogenetic and functional mechanisms and involvements in cell differentiation and cancer J. Pharmacol. Sci. 2006 101 267 70
7. B. Yang H. Lin J. Xiao Y. Lu X. Luo B. Li Y. Zhang C. Xu Y. Bai H. Wang G. Chen Z. Wang The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2 Nat. Med. 2007 13 486 91
8. J. P. t. Morris M. T. McManus Slowing down the Ras lane: miRNAs as tumor suppressors? Science's STKE 2005 pe41
9. G. A. Calin C. D. Dumitru M. Shimizu R. Bichi S. Zupo E. Noch H. Aldler S. Rattan M. Keating K. Rai L. Rassenti T. Kipps M. Negrini F. Bullrich C. M. Croce Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia Proc. Natl. Acad. Sci. U. S. A. 2002 99 15524 9
10. J. Yue G. Tigyi MicroRNA trafficking and human cancer Cancer Biol. Ther. 2006 5 573 8
11. S. Pfeffer O. Voinnet Viruses, microRNAs and cancer Oncogene 2006 25 6211 9
12. Z. Ghosh J. Chakrabarti B. Mallick miRNomics-The bioinformatics of microRNA genes Biochem. Biophys. Res. Commun. 2007 363 6 11
13. A. Esquela-Kerscher F. J. Slack The age of high-throughput microRNA profiling Nat. Methods 2004 1 106 7
14. P. T. Nelson D. A. Baldwin L. M. Scearce J. C. Oberholtzer J. W. Tobias Z. Mourelatos Microarray-based, high-throughput gene expression profiling of microRNAs Nat. Methods 2004 1 155 61
15. Y. Gusev D. J. Brackett MicroRNA expression profiling in cancer from a bioinformatics prospective Expert Rev. Mol. Diagn. 2007 7 787 92
16. H. Wang W. H. Li Increasing MicroRNA target prediction confidence by the relative R(2) method J. Theor. Biol. 2009 259 793 8
17. J. Hausser P. Berninger C. Rodak Y. Jantscher S. Wirth M. Zavolan MirZ: an integrated microRNA expression atlas and target prediction resource Nucleic Acids Res. 2009 37 W266 72
18. V. A. Gennarino M. Sardiello R. Avellino N. Meola V. Maselli S. Anand L. Cutillo A. Ballabio S. Banfi MicroRNA target prediction by expression analysis of host genes Genome Res. 2009 19 481 90
19. L. Alves-Junior S. Niemeier A. Hauenschild M. Rehmsmeier T. Merkle Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana Nucleic Acids Res. 2009 37 4010 21
20. J. Ruan H. Chen L. Kurgan K. Chen C. Kang P. Pu HuMiTar: a sequence-based method for prediction of human microRNA targets Algorithms Mol. Biol. 2008 3 16
21. M. Hammell D. Long L. Zhang A. Lee C. S. Carmack M. Han Y. Ding V. Ambros mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts Nat. Methods 2008 5 813 9
22. M. Rehmsmeier Prediction of microRNA targets Methods Mol. Biol. 2006 342 87 99
23. L. Xia D. Zhang R. Du Y. Pan L. Zhao S. Sun L. Hong J. Liu D. Fan miR-15b and miR-16 modulate multidrug resistance by targeting BCL2 in human gastric cancer cells Int. J. Cancer 2008 123 372 9
24. R. Malumbres K. A. Sarosiek E. Cubedo J. W. Ruiz X. Jiang R. D. Gascoyne R. Tibshirani I. S. Lossos Differentiation stage-specific expression of microRNAs in B lymphocytes and diffuse large B-cell lymphomas Blood 2009 113 3754 64
25. T. Katada H. Ishiguro Y. Kuwabara M. Kimura A. Mitui Y. Mori R. Ogawa K. Harata Y. Fujii microRNA expression profile in undifferentiated gastric cancer Int. J. Oncol. 2009 34 537 42
26. J. Guo Y. Miao B. Xiao R. Huan Z. Jiang D. Meng Y. Wang Differential expression of microRNA species in human gastric cancer versus non-tumorous tissues J. Gastroenterol. Hepatol. 2009 24 652 7
27. E. Ferretti E. De Smaele A. Po L. Di Marcotullio E. Tosi M. S. Espinola C. Di Rocco R. Riccardi F. Giangaspero A. Farcomeni I. Nofroni P. Laneve U. Gioia E. Caffarelli I. Bozzoni I. Screpanti A. Gulino MicroRNA profiling in human medulloblastoma Int. J. Cancer 2009 124 568 77
28. S. Baskerville D. P. Bartel Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes RNA 2005 11 241 7
29. S. Bandyopadhyay M. Bhattacharyya Analyzing miRNA co-expression networks to explore TF-miRNA regulation BMC Bioinformatics 2009 10 163
30. R. Shalgi D. Lieber M. Oren Y. Pilpel Global and local architecture of the mammalian microRNA-transcription factor regulatory network PLoS Comput. Biol. 2007 3 e131
31. N. J. Martinez M. C. Ow M. I. Barrasa M. Hammell R. Sequerra L. Doucette-Stamm F. P. Roth V. R. Ambros A. J. Walhout A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity Genes Dev. 2008 22 2535 49
32. L. Ma J. Teruya-Feldstein R. A. Weinberg Tumour invasion and metastasis initiated by microRNA-10b in breast cancer Nature 2007 449 682 8
33. Y. Gusev T. D. Schmittgen M. Lerner R. Postier D. Brackett Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer BMC Bioinformatics 2007 8 suppl 7 S16
34. J. Lu G. Getz E. A. Miska E. Alvarez-Saavedra J. Lamb D. Peck A. Sweet-Cordero B. L. Ebert R. H. Mak A. A. Ferrando J. R. Downing T. Jacks H. R. Horvitz T. R. Golub MicroRNA expression profiles classify human cancers Nature 2005 435 834 8
35. S. Griffiths-Jones R. J. Grocock S. van. Dongen A. Bateman A. J. Enright miRBase: microRNA sequences, targets and gene nomenclature Nucleic Acids Res. 2006 34 D140 4
36. E. Wingender X. Chen R. Hehl H. Karas I. Liebich V. Matys T. Meinhardt M. Pruss I. Reuter F. Schacherer TRANSFAC: an integrated system for gene expression regulation Nucleic Acids Res. 2000 28 316 9
37. A. Krek D. Grun M. N. Poy R. Wolf L. Rosenberg E. J. Epstein P. MacMenamin I. da Piedade K. C. Gunsalus M. Stoffel N. Rajewsky Combinatorial microRNA target predictions Nat. Genet. 2005 37 495 500
38. M. Ashburner C. A. Ball J. A. Blake D. Botstein H. Butler J. M. Cherry A. P. Davis K. Dolinski S. S. Dwight J. T. Eppig M. A. Harris D. P. Hill L. Issel-Tarver A. Kasarskis S. Lewis J. C. Matese J. E. Richardson M. Ringwald G. M. Rubin G. Sherlock Gene ontology: tool for the unification of biology Nat. Genet. 2000 25 25 9
39. D. Yang Y. Li H. Xiao Q. Liu M. Zhang J. Zhu W. Ma C. Yao J. Wang D. Wang Z. Guo B. Yang Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories Bioinformatics 2008 24 265 71
40. U. Burk J. Schubert U. Wellner O. Schmalhofer E. Vincan S. Spaderna T. A. Brabletz reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells EMBO Rep. 2008 9 582 9
41. S. M. Park A. B. Gaur E. Lengyel M. E. Peter The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2 Genes Dev. 2008 22 894 907
42. M. Korpal E. S. Lee G. Hu Y. Kang The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2 J. Biol. Chem. 2008 283 14910 4
43. P. A. Gregory A. G. Bert E. L. Paterson S. C. Barry A. Tsykin G. Farshid M. A. Vadas Y. Khew-Goodall G. J. Goodall The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1 Nat. Cell Biol. 2008 10 593 601
44. C. P. Bracken P. A. Gregory N. Kolesnikoff A. G. Bert J. Wang M. F. Shannon G. J. Goodall A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition Cancer Res. 2008 68 7846 54
45. Y. Katoh M. Katoh Hedgehog signaling, epithelial-to-mesenchymal transition and miRNA (review) Int. J. Mol. Med. 2008 22 271 5
46. M. V. Iorio R. Visone G. Di Leva V. Donati F. Petrocca P. Casalini C. Taccioli S. Volinia C. G. Liu H. Alder G. A. Calin S. Menard C. M. Croce MicroRNA signatures in human ovarian cancer Cancer Res. 2007 67 8699 707
47. D. D. Taylor C. Gercel-Taylor MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer Gynecol. Oncol. 2008 110 13 21
48. S. Guil J. F. Caceres The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a Nat. Struct. Mol. Biol. 2007 14 591 6
49. A. Tanzer P. F. Stadler Molecular evolution of a microRNA cluster J. Mol. Biol. 2004 339 327 35
50. C. J. Braun X. Zhang I. Savelyeva S. Wolff U. M. Moll T. Schepeler T. F. Orntoft C. L. Andersen M. Dobbelstein p53-Responsive micrornas 192 and 215 are capable of inducing cell cycle arrest Cancer Res. 2008 68 10094 104
51. G. A. Calin et al. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia N. Engl. J. Med. 2005 353 1793 801
52. M. Mraz S. Pospisilova K. Malinova I. Slapak J. Mayer MicroRNAs in chronic lymphocytic leukemia pathogenesis and disease subtypes Leuk. Lymphoma 2009 50 506 9
53. T. Hubbard et al. The Ensembl genome database project Nucleic Acids Res. 2002 30 38 41
54. M. Q. Zhang A discrimination study of human core-promoters Pac Symp. Biocomput. 1998 240 51
55. T. J. Storey JD D. Siegmund Strong control, conservative point estimation, and simultaneous conservative consistency of false discovery rates: A unified approach J. R. Stat. Soc., Ser. B: Stat. Methodol. 2004 66 187 205
56. D. Lin An information-theoretic definition of similarity Proceedings of the 15th International Conference on Machine Learning 1998 1 296 304