RNA profiling in circadian biology

Methods in Enzymology

Volumn 393, Issue , 2005, Pages 366-376

  Walker, John R ^a   Hogenesch, John B ^a,b  

^a GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; CIRCADIAN RHYTHM; DNA MICROARRAY; GENE AMPLIFICATION; GENE EXPRESSION; GENE TARGETING; GENETIC TRANSCRIPTION; HUMAN; MEDICAL LITERATURE; POLYMERIZATION; PRIORITY JOURNAL; RNA ANALYSIS;

EID: 16844363738     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)93016-4     Document Type: Article

References (38)

1. Akhtar R.A., Reddy A.B., Maywood E.S., Clayton J.D., King V.M., Smith A.G., Gant T.W., Hastings M.H., Kyriacou C.P. Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus. Curr. Biol. 12:2002;540-550
2. Antoch M.P., Song E.J., Chang A.M., Vitaterna M.H., Zhao Y., Wilsbacher L.D., Sangoram A.M., King D.P., Pinto L.H., Takahashi J.S. Functional identification of the mouse circadian Clock gene by transgenic BAC rescue. Cell. 89:1997;655-667
3. Balasubramaniam J., Del Bigio M.R. Analysis of age-dependent alteration in the brain gene expression profile following induction of hydrocephalus in rats. Exp. Neurol. 173:2002;105-113
4. Britton R.A. DNA microarrays and bacterial gene expression. Methods Enzymol. 370:2003;264-278
5. Bunger M.K., Wilsbacher L.D., Moran S.M., Clendenin C., Radcliffe L.A., Hogenesch J.B., Simon M.C., Takahashi J.S., Bradfield C.A. Mop3 is an essential component of the master circadian pacemaker in mammals. Cell. 103:2000;1009-1017
6. Burgess J.K., McParland B.E. Analysis of gene expression. Methods Enzymol. 356:2002;259-270
7. Cho R.J., Campbell M.J., Winzeler E.A., Steinmetz L., Conway A., Wodicka L., Wolfsberg T.G., Gabrielian A.E., Landsman D., Lockhart D.J., Davis R.W. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 2:1998;65-73
8. Claridge-Chang A., Wijnen H., Naef F., Boothroyd C., Rajewsky N., Young M.W. Circadian regulation of gene expression systems in the Drosophila head. Neuron. 32:2001;657-671
9. Duffield G.E., Best J.D., Meurers B.H., Bittner A., Loros J.J., Dunlap J.C. Circadian programs of transcriptional activation, signaling, and protein turnover revealed by microarray analysis of mammalian cells. Curr. Biol. 12:2002;551-557
10. Dunlap J.C. Molecular bases for circadian clocks. Cell. 96:1999;271-290
11. Edgar R., Domrachev M., Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30:2002;207-210
12. Green C.B., Besharse J.C. Identification of a novel vertebrate circadian clock-regulated gene encoding the protein nocturnin. Proc. Natl. Acad. Sci. USA. 93:1996;14884-14888
13. Harmer S.L., Hogenesch J.B., Straume M., Chang H.S., Han B., Zhu T., Wang X., Kreps J.A., Kay S.A. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science. 290:2000;2110-2113
14. Ihaka R., Gentlemen R. R: A language for data analysis and graphics. J. Comput. Graph. Stat. 5:1996;299-314
15. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 4:2003;249-264
16. King D.P., Zhao Y., Sangoram A.M., Wilsbacher L.D., Tanaka M., Antoch M.P., Steeves T.D., Vitaterna M.H., Kornhauser J.M., Lowrey P.L., Turek F.W., Takahashi J.S. Positional cloning of the mouse circadian clock gene. Cell. 89:1997;641-653
17. Kornmann B., Preitner N., Rifat D., Fleury-Olela F., Schibler U. Analysis of circadian liver gene expression by ADDER, a highly sensitive method for the display of differentially expressed mRNAs. Nucleic Acids Res. 29:2001;E51
18. Li C., Hung Wong W. Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application. Genome Biol. 2,:2001;. RESEARCH0032. Epub, August 2003.
19. Lin Y., Han M., Shimada B., Wang L., Gibler T.M., Amarakone A., Awad T.A., Stormo G.D., Van Gelder R.N., Taghert P.H. Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA. 99:2002;9562-9567
20. Martin R.G., Rosner J.L. Analysis of microarray data for the marA, soxS, and rob regulons of Escherichia coli. Methods Enzymol. 370:2003;278-280
21. McDonald M.J., Rosbash M. Microarray analysis and organization of circadian gene expression in Drosophila. Cell. 107:2001;567-578
22. Panda S., Antoch M.P., Miller B.H., Su A.I., Schook A.B., Straume M., Schultz P.G., Kay S.A., Takahashi J.S., Hogenesch J.B. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell. 109:2002;307-320
23. Panda S., Hogenesch J.B., Kay S.A. Circadian rhythms from flies to human. Nature. 417:2002;329-335
24. Reppert S.M., Weaver D.R. Coordination of circadian timing in mammals. Nature. 418:2002;935-941
25. Roy S., Khanna S., Bentley K., Beffrey P., Sen C.K. Functional genomics: High-density oligonucleotide arrays. Methods Enzymol. 353:2002;487-497
26. Sandberg R., Yasuda R., Pankratz D.G., Carter T.A., Del Rio J.A., Wodicka L., Mayford M., Lockhart D.J., Barlow C. Regional and strain-specific gene expression mapping in the adult mouse brain. Proc. Natl. Acad. Sci. USA. 97:2000;11038-11043
27. Sato T.K., Panda S., Miraglia L.J., Reyes T.M., Rudic R.D., McNamara P., Naik K.A., FitzGerald G.A., Kay S.A., Hogenesch J.B. A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron. 43:2004;527-537
28. Scherer A., Krause A., Walker J.R., Sutton S.E., Seron D., Raulf F., Cooke M.P. Optimized protocol for linear RNA amplification and application to gene expression profiling of human renal biopsies. Biotechniques. 34:2003;546-556
29. Storch K.F., Lipan O., Leykin I., Viswanathan N., Davis F.C., Wong W.H., Weitz C.J. Extensive and divergent circadian gene expression in liver and heart. Nature. 417:2002;78-83
30. Straume M. DNA microarray time series analysis: Automated statistical assessment of circadian rhythms in gene expression patterning. Methods Enzymol. 383:2004;149-166
31. Thomas R.P., Guigneaux M., Wood T., Evers B.M. Age-associated changes in gene expression patterns in the liver. J. Gastrointest. Surg. 6:2002;445-453. ; discussion 454.
32. Thomas R.S., Rank D.R., Penn S.G., Craven M.W., Drinkwater N.R., Bradfield C.A. Developing toxicologically predictive gene sets using cDNA microarrays and Bayesian classification. Methods Enzymol. 357:2002;198-205
33. Ueda H.R., Chen W., Adachi A., Wakamatsu H., Hayashi S., Takasugi T., Nagano M., Nakahama K., Suzuki Y., Sugano S., Iino M., Shigeyoshi Y., Hashimoto S. A transcription factor response element for gene expression during circadian night. Nature. 418:2002;534-539
34. Van Gelder R.N., von Zastrow M.E., Yool A., Dement W.C., Barchas J.D., Eberwine J.H. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. USA. 87:1990;1663-1667
35. Wittliff J.L., Erlander M.G. Laser capture microdissection and its applications in genomics and proteomics. Methods Enzymol. 356:2002;12-25
36. Wu Z., Irizarry R.A., Gentlemen R., Murillo F.M., Spencer F. A model based background adjustment for oligonucleotide expression arrays. 2003;. Johns Hopkins University Dept. of Biostatistics Working Papers, 1-29.
37. Zhang L., Miles M.F., Aldape K.D. A model of molecular interactions on short oligonucleotide microarrays. Nature Biotechnol. 21:2003;818-821
38. Zinke I., Schutz C.S., Katzenberger J.D., Bauer M., Pankratz M.J. Nutrient control of gene expression in Drosophila: Microarray analysis of starvation and sugar-dependent response. Embo J. 21:2002;6162-6173