[2] Analyzing Micro-RNA Expression Using Microarrays

Methods in Enzymology

Volumn 411, Issue , 2006, Pages 14-34

  Davison, Timothy S ^a   Johnson, Charles D ^a   Andruss, Bernard F ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA;

CANCER; GENE EXPRESSION; HUMAN; MICROARRAY ANALYSIS; PRIORITY JOURNAL; REVIEW; RNA ANALYSIS; RNA ISOLATION; RNA PURIFICATION; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; ANIMAL; BIOSYNTHESIS; DNA MICROARRAY; GENETICS; METHODOLOGY;

ANIMALS; HUMANS; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 33747887038     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(06)11002-2     Document Type: Review

References (65)

1. Allison D.B., Cui X., Page G.P., and Sabripour M. Microarray data analysis: From disarray to consolidation and consensus. Nature Rev. Genet. 7 1 (2006) 55-65
2. Alvarez-Garcia I., and Miska E.A. MicroRNA functions in animal development and human disease. Development 132 (2005) 4653-4662
3. Ambros V., Bartel B., Bartel D.P., Burge C.B., Carrington J.C., Chen X., Dreyfuss G., Eddy S.R., Griffiths-Jones S., Marshall M., Matzke M., Ruvkun G., and Tuschl T. A uniform system for microRNA annotation. RNA 9 (2003) 277-279
4. Argyropoulos C., Chatziioannou A.A., Nikiforidis G., Moustakas A., Kollias G., and Aidinis V. Operational criteria for selecting a cDNA microarray data normalization algorithm. Oncol. Rep. 15 4 (2006) 983-996
5. Babak T., Zhang W., Morris Q., Blencowe B.J., and Hughes T.R. Probing microRNAs with microarrays: Tissue specificity and functional inference. RNA 10 (2004) 1813-1819
6. Barad O., Meiri E., Avniel A., Aharonov R., Barzilai A., Bentwich I., Einav U., Gilad S., Hurban P., Karov Y., Lobenhofer E.K., Sharon E., Shiboleth Y.M., Shtutman M., Bentwich Z., and Einat P. MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues. Genome Res. 14 (2004) 2486-2494
7. Bartel D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281
8. Baskerville S., and Bartel D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11 (2005) 241-247
9. Benjamini Y., and Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57 (1995) 289-300
10. Berezikov E., Guryev V., van de Belt J., Wienholds E., Plasterk R.H.A., and Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 (2005) 21
11. Bolstad B.M., Irizarry R.A., Astrand M., and Speed T.P. A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19 2 (2003) 185-193
12. Brennecke J., Hipfner D.R., Stark A., Russell R.B., and Cohen S.M. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113 (2003) 25-36
13. Calin G.A., Dumitru C.D., Shimizu M., Bichi R., Zupo S., Noch E., Aldler H., Rattan S., Keating M., Rai K., Rassenti L., Kipps T., Negrini M., Bullrich F., and Croce C.M. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl. Acad. Sci. USA 99 (2002) 15524-15529
14. Calin G.A., Ferracin M., Cimmino A., Di Leva G., Shimizu M., Wojcik S.E., Iorio M.V., Visone R., Sever N.I., Fabbri M., Iuliano R., Palumbo T., Pichiorri F., Roldo C., Garzon R., Sevignani C., Rassenti L., Alder H., Volinia S., Liu C.G., Kipps T.J., Negrini M., and Croce C.M. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N. Engl. J. Med. 353 (2005) 1793-1801
15. Calin G.A., Liu C.G., Sevignani C., Ferracin M., Felli N., Dumitru C.D., Shimizu M., Cimmino A., Zupo S., Dono M., Dell'Aquila M.L., Alder H., Rassenti L., Kipps T.J., Bullrich F., Negrini M., and Croce C.M. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl. Acad. Sci. USA 101 (2004) 11755-11760
16. Chan J.A., Krichevsky A.M., and Kosik K.S. MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res. 65 (2005) 6029-6033
17. Chang S., Johnston Jr. R.J., Frokjaer-Jensen C., Lockery S., and Hobert O. MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430 (2004) 785-789
18. Cheng A.M., Byrom M.W., Shelton J., and Ford L.P. Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res. 33 (2005) 1290-1297
19. Ciafre S.A., Galardi S., Mangiola A., Ferracin M., Liu C.G., Sabatino G., Negrini M., Maira G., Croce C.M., and Farace M.G. Extensive modulation of a set of microRNAs in primary glioblastoma. Biochem. Biophys. Res. Commun. 334 (2005) 1351-1358
20. Cimmino A., Calin G.A., Fabbri M., Iorio M.V., Ferracin M., Shimizu M., Wojcik S.E., Aqeilan R.I., Zupo S., Dono M., Rassenti L., Alder H., Volinia S., Liu C.G., Kipps T.J., Negrini M., and Croce C.M. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc. Natl. Acad. Sci. USA 102 (2005) 13944-13949
21. Croce C.M., and Calin G.A. miRNAs, cancer, and stem cell division. Cell 122 (2005) 6-7
22. Cummins J.M., He Y., Leary R.J., Pagliarini R., Diaz Jr. L.A., 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. USA 103 10 (2006) 3687-3692
23. Dostie J., Mourelatos Z., Yang M., Sharma A., and Dreyfuss G. Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9 (2003) 180-186
24. Elbashir S.M., Lendeckel W., and Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15 (2001) 188-200
25. Esquela-Kerscher A., and Slack F.J. Oncomirs: MicroRNAs with a role in cancer. Nature Rev. Cancer 6 (2006) 259-269
26. Garzon R., Pichiorri F., Palumbo T., Iuliano R., Cimmino A., Aqeilan R., Volinia S., Bhatt D., Alder H., Marcucci G., Calin G.A., Liu C.G., Bloomfield C.D., Andreeff M., and Croce C.M. MiRNA fingerprints during human megakaryocytopoiesis. Proc. Natl. Acad. Sci. USA 101 (2006) 5078-5083
27. Gregory R.I., and Shiekhattar R. MicroRNA biogenesis and cancer. Cancer Res. 65 (2005) 3509-3512
28. Griffiths-Jones S., Grocock R.J., van Dongen S., Bateman A., and Enright A.J. miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34 (2006) D140-D144
29. Hammond S.M. MicroRNAs as oncogenes. Curr. Opin. Genet. Dev. 16 (2006) 4-9
30. Harfe B.D. MicroRNAs in vertebrate development. Curr. Opin. Genet. Dev. 15 (2005) 410-415
31. Hornstein E., Mansfield J.H., Yekta S., Hu J.K., Harfe B.D., McManus M.T., Baskerville S., Bartel D.P., and Tabin C.J. The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development. Nature 438 (2005) 671-674
32. Huber W., Von Heydebreck A., Sultmann H., Poustka A., and Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 Suppl. 1 (2002) S96-S104
33. Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B., and Speed T.P. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31 4 (2003) e15
34. Johnson S.M., Grosshans H., Shingara J., Byrom M., Jarvis R., Cheng A., Labourier E., Reinert K.L., Brown D., and Slack F.J. RAS is Regulated by the let-7 microRNA Family. Cell 120 (2005) 635
35. Karube Y., Tanaka H., Osada H., Tomida S., Tatematsu Y., Yanagisawa K., Yatabe Y., Takamizawa J., Miyoshi S., Mitsudomi T., and Takahashi T. Reduced expression of Dicer associated with poor prognosis in lung cancer patients. Cancer Sci. 96 (2005) 111-115
36. Klein M.E., Impey S., and Goodman R.H. Role reversal: The regulation of neuronal gene expression by microRNAs. Curr. Opin. Neurobiol. 15 (2005) 507-513
37. Krichevsky A.M., King K.S., Donahue C.P., Khrapko K., and Kosik K.S. A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9 (2003) 1274-1281
38. Lee R.C., Feinbaum R.L., and Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 (1993) 843-854
39. Lim L.P., Glasner M.E., Yekta S., Burge C.B., and Bartel D.P. Vertebrate microRNA genes. Science 299 (2003) 1540
40. Liu C.G., Calin G.A., Meloon B., Gamliel N., Sevignani C., Ferracin M., Dumitru C.D., Shimizu M., Zupo S., Dono M., Alder H., Bullrich F., Negrini M., and Croce C.M. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc. Natl. Acad. Sci. USA 101 (2004) 9740-9744
41. Lu J., Getz G., Miska E.A., Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert B.L., Mak R.H., Ferrando A.A., Downing J.R., Jacks T., Horvitz H.R., and Golub T.R. MicroRNA expression profiles classify human cancers. Nature 435 (2005) 834
42. Lu J., Qian J., Chen F., Tang X., Li C., and Cardoso W.V. Differential expression of components of the microRNA machinery during mouse organogenesis. Biochem. Biophys. Res. Commun. 334 (2005) 319-323
43. Metzler M., Wilda M., Busch K., Viehmann S., and Borkhardt A. High expression of precursor microRNA-155/BIC RNA in children with Burkitt lymphoma. Genes Chromosomes Cancer 39 (2004) 167-169
44. Michael M.Z., O'Connor S.M., van Holst Pellekaan N.G., Young G.P., and James R.J. Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol. Cancer Res. 1 (2003) 882-891
45. Miska E.A., Alvarez-Saavedra E., Townsend M., Yoshii A., Sestan N., Rakic P., Constantine-Paton M., and Horvitz H.R. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 5 (2004) R68
46. Pasquinelli A.E., Hunter S., and Bracht J. MicroRNAs: A developing story. Curr. Opin. Genet. Dev. 15 (2005) 200-205
47. Quackenbush J. Microarray data normalization and transformation. Nature Genet. 32 Suppl. (2002) 496-501
48. Reinhart B.J., Slack F.J., Basson M., Pasquinelli A.E., Bettinger J.C., Rougvie A.E., Horvitz H.R., and Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403 (2000) 901-906
49. Rogaev E.I. Small RNAs in human brain development and disorders. Biochemistry 70 (2005) 1404-1407
50. Schulman B.R., Esquela-Kerscher A., and Slack F.J. Reciprocal expression of lin-41 and the microRNAs let-7 and mir-125 during mouse embryogenesis. Dev. Dyn. 234 (2005) 1046-1054
51. Shai O., Morris Q., and Frey B.J. Spatial bias removal in microarray images (2003), University of Toronto Technical Report PSI-2003-21
52. Shingara J., Keiger K., Shelton J., Laosinchai-Wolf W., Powers P., Conrad R., Brown D., and Labourier E. An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 11 (2005) 1461-1470
53. Slack F.J., and Weidhaas J.B. MicroRNAs as a potential magic bullet in cancer. Fut. Oncol. 2 (2006) 73-82
54. Smirnova L., Grafe A., Seiler A., Schumacher S., Nitsch R., and Wulczyn F.G. Regulation of miRNA expression during neural cell specification. Eur. J. Neurosci. 21 (2005) 1469-1477
55. Sun Y., Koo S., White N., Peralta E., Esau C., Dean N.M., and Perera R.J. Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acids Res. 32 (2004) e188
56. Takamizawa J., Konishi H., Yanagisawa K., Tomida S., Osada H., Endoh H., Harano T., Yatabe Y., Nagino M., Nimura Y., Mitsudomi T., and Takahashi T. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res. 64 (2004) 3753-3756
57. Tang F., Hajkova P., Barton S.C., Lao K., and Surani M.A. MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res. 34 (2006) e9
58. Thomson J.M., Parker J., Perou C.M., and Hammond S.M. A custom microarray platform for analysis of microRNA gene expression. Nature Methods 1 (2004) 47-53
59. 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. USA 103 7 (2006) 2257-2261
60. Wienholds E., and Plasterk R.H. MicroRNA function in animal development. FEBS Lett. 579 (2005) 5911-5922
61. Wightman B., Ha I., and Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75 (1993) 855-862
62. Xu P., Vernooy S.Y., Guo M., and Hay B.A. The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13 (2003) 790-795
63. Yanaihara N., Caplen N., Bowman E., Seike M., Kumamoto K., Yi M., Stephens R.M., Okamoto A., Yokota J., Tanaka T., Calin G.A., Liu C.G., Croce C.M., and Harris C.C. Unique miRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9 3 (2006) 189-198
64. Yi R., O'Carroll D., Pasolli H.A., Zhang Z., Dietrich F.S., Tarakhovsky A., and Fuchs E. Morphogenesis in skin is governed by discrete sets of differentially expressed microRNAs. Nature Genet. 38 (2006) 356-362
65. Zamore P.D., and Haley B. Ribo-gnome: The big world of small RNAs. Science 309 (2005) 1519-1524