Profiling of molecular pathways regulated by microRNA 601

Computational Biology and Chemistry

Volumn 33, Issue 6, 2009, Pages 429-433

  Ohdaira, Hiroaki ^a   Nakagawa, Hiroki ^a   Yoshida, Kenichi ^a  

^a MEIJI UNIVERSITY   (Japan)

Author keywords

Bioinformatics; GenMAPP; miRNA; NF kappaB

Indexed keywords

A549 CELLS; ACTIN CYTOSKELETON; BIOLOGICAL PROCESS; CELLULAR SIGNALING; COMPLEX REGULATION; DNA MICRO-ARRAY; DOWN-REGULATION; GENE ONTOLOGY; GENMAPP; HUMAN LUNG CANCER CELLS; INDUCED APOPTOSIS; KEY COMPONENT; LUCIFERASE REPORTER ASSAYS; MICRORNAS; MOLECULAR FRAMEWORKS; MOLECULAR PATHWAYS; NF-KAPPAB; NUCLEAR FACTORS; ONCOGENESIS; PATHWAY ANALYSIS; SIGNALING PATHWAYS; SOMATIC CELLS; UP-REGULATION;

BIOACTIVITY; BIOLOGICAL ORGANS; CELL DEATH; DRUG PRODUCTS; NUCLEIC ACIDS; ONTOLOGY; RNA; SIGNALING; TRANSCRIPTION; TRANSCRIPTION FACTORS;

BIOINFORMATICS;

LUCIFERASE; MICRORNA;

ARTICLE; BIOLOGY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; HUMAN; LUNG TUMOR; METABOLISM; REPORTER GENE; SIGNAL TRANSDUCTION; TUMOR CELL LINE;

CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENES, REPORTER; HUMANS; LUCIFERASES; LUNG NEOPLASMS; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

VERTEBRATA;

EID: 70449713252     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2009.09.003     Document Type: Article

References (31)

1. Ambros V. The functions of animal microRNAs. Nature 431 (2004) 350-355
2. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., and Sherlock G. Gene ontology: tool for the unification of biology, The Gene Ontology Consortium. Nat. Genet. 25 (2000) 25-29
3. Baltimore D., Boldin M.P., O'Connell R.M., Rao D.S., and Taganov K.D. MicroRNAs: new regulators of immune cell development and function. Nat. Immunol. 9 (2008) 839-845
4. Basak S., and Hoffmann A. Crosstalk via the NF-kappaB signaling system. Cytokine Growth Factor Rev. 19 (2008) 187-197
5. Blakaj A., and Lin H. Piecing together the mosaic of early mammalian development through microRNAs. J. Biol. Chem. 283 (2008) 9505-9508
6. Carrington J.C., and Ambros V. Role of microRNAs in plant and animal development. Science 301 (2003) 336-338
7. Cho W.C. OncomiRs: the discovery and progress of microRNAs in cancers. Mol. Cancer 6 (2007) 60
8. Cummins J.M., He Y., Leary R.J., Pagliarini R., Diaz L.A.J., Sjoblom T., Barad O., Bentwich Z., Szafranska A.E., Labourier E., Raymond C.K., Roberts B.S., Juhl H., Kinzler K.W., Vogelstein B., and Velculescu V.E. The colorectal microRNAome. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 3687-3692
9. Dahlquist K.D. Using GenMAPP and MAPPFinder to view microarray data on biological pathways and identify global trends in the data. Curr. Protoc. Bioinformatics (2004) 5 (Chapter 7, Unit 7)
10. Dahlquist K.D., Salomonis N., Vranizan K., Lawlor S.C., and Conklin B.R. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet. 31 (2002) 19-20
11. Doniger S.W., Salomonis N., Dahlquist K.D., Vranizan K., Lawlor S.C., and Conklin B.R. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 4 (2003) R7
12. Esquela-Kerscher A., and Slack F.J. Oncomirs-microRNAs with a role in cancer. Nat. Rev. Cancer 6 (2006) 259-269
13. Karin M. Nuclear factor-kappaB in cancer development and progression. Nature 441 (2006) 431-436
14. Lindsay M.A. microRNAs and the immune response. Trends Immunol. 29 (2008) 343-351
15. Makunin I.V., Pheasant M., Simons C., and Mattick J.S. Orthologous microRNA genes are located in cancer-associated genomic regions in human and mouse. PLoS ONE 2 (2007) e1133
16. Medina P.P., and Slack F.J. microRNAs and cancer: an overview. Cell Cycle 7 (2008) 2485-2492
17. Nam S., Kim B., Shin S., and Lee S. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res. 36 (2008) D159-D164
18. Naugler W.E., and Karin M. NF-kappaB and cancer-identifying targets and mechanisms. Curr. Opin. Genet. Dev. 18 (2008) 19-26
19. Pahl H.L. Activators and target genes of Rel/NF-kappaB transcription factors. Oncogene 18 (1999) 6853-6866
20. Rajewsky N. microRNA target predictions in animals. Nat. Genet. 38 (2006) S8-13
21. Salomonis N., Hanspers K., Zambon A.C., Vranizan K., Lawlor S.C., Dahlquist K.D., Doniger S.W., Stuart J., Conklin B.R., and Pico A.R. GenMAPP 2 new features and resources for pathway analysis. BMC Bioinformatics 8 (2007) 217
22. Schickel R., Boyerinas B., Park S.M., and Peter M.E. MicroRNAs: key players in the immune system, differentiation, tumorigenesis and cell death. Oncogene 27 (2008) 5959-5974
23. Schottelius A.J., and Dinter H. Cytokines, NF-kappaB, microenvironment, intestinal inflammation and cancer. Cancer Treat Res. 130 (2006) 67-87
24. Shi X.B., Tepper C.G., and deVere White R.W. Cancerous miRNAs and their regulation. Cell Cycle 7 (2008) 1529-1538
25. Sonkoly E., Ståhle M., and Pivarcsi A. MicroRNAs and immunity: novel players in the regulation of normal immune function and inflammation. Semin. Cancer Biol. 18 (2008) 131-140
26. Stefani G. Roles of microRNAs and their targets in cancer. Expert. Opin. Biol. Ther. 7 (2007) 1833-1840
27. Tategu M., Nakagawa H., Hayashi R., and Yoshida K. Transcriptional co-factor CDCA4 participates in the regulation of JUN oncogene expression. Biochimie 90 (2008) 1515-1522
28. Volinia S., Calin G.A., Liu C.G., Ambs S., Cimmino A., Petrocca F., Visone R., Iorio M., Roldo C., Ferracin M., Prueitt R.L., Yanaihara N., Lanza G., Scarpa A., Vecchione A., Negrini M., Harris C.C., and Croce C.M. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 2257-2261
29. Wada T., Berggren P., Steineck G., Adolfsson J., Wijkström H., Norming U., Hansson J., Hemminki K., and Larsson P. Bladder neoplasms-regions at chromosome 9 with putative tumour suppressor genes. Scand. J. Urol. Nephrol. 37 (2003) 106-111
30. Watanabe Y., Tomita M., and Kanai A. Computational methods for microRNA target prediction. Methods Enzymol. 427 (2007) 65-86
31. Zhang B., Pan X., Cobb G.P., and Anderson T.A. microRNAs as oncogenes and tumor suppressors. Dev. Biol. 302 (2007) 1-12