Molecular and statistical tools for circadian transcript profiling

Methods in Enzymology

Volumn 393, Issue , 2005, Pages 341-365

  Wijnen, Herman ^a   Naef, Felix ^b   Young, Michael W ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b SWISS INST FOR EXP CANCER RESEARCH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ARTICLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; DATA ANALYSIS; DNA MICROARRAY; DROSOPHILA; GENE DUPLICATION; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENOTYPE; MEDICAL LITERATURE; MOLECULAR DYNAMICS; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL;

EID: 16844362269     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)93015-2     Document Type: Article

References (31)

1. Allada R., White N.E., So W.V., Hall J.C., Rosbash M. A mutant Drosophila homolog of mammalian Clock disrupts circadian rhythms and transcription of period and timeless. Cell. 93:1998;791-804
2. Ausubel F.M. "Current Protocols in Molecular Biology." 2001;Wiley, New York
3. Blau J., Young M.W. Cycling vrille expression is required for a functional Drosophila clock. Cell. 99:1999;661-671
4. Bowtell D., Sambrook J. "DNA Microarrays: A Molecular Cloning Manual." 2003;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
5. Brownstein M.J., Khodursky A.B. "Functional Genomics: Methods and Protocols." 2003;Humana Press, Totowa, NJ
6. Bustin S.A. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25:2000;169-193
7. Ceriani M.F., Hogenesch J.B., Yanovsky M., Panda S., Straume M., Kay S.A. Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior. J. Neurosci. 22:2002;9305-9319
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. Hardin P.E., Hall J.C., Rosbash M. Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. Nature. 343:1990;536-540
11. 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
12. Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B., Speed T.P. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31:2003;e15
13. Kerr K. Experimental design to make the most of microarray studies. Brownstein M.J., Khodursky A.B. "Functional Genomics: Methods and Protocols" 2003a;137-148 Humana Press, Totowa, NJ
14. Kerr R. Quantitation of multiple RNA species. Bartlett J.M.S., Stirling D. "PCR Protocols" 2nd Ed. :2003b;211-216 Humana Press, Totowa, NJ
15. 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
16. McDonald M.J., Rosbash M. Microarray analysis and organization of circadian gene expression in Drosophila. Cell. 107:2001;567-578
17. Naef F., Magnasco M.O. Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 011906:2003;1-4
18. 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
19. Plautz J.D., Kaneko M., Hall J.C., Kay S.A. Independent photoreceptive circadian clocks throughout Drosophila. Science. 278:1997;1632-1635
20. Press W.H., Teukolsky S.A., Vetterling W.T., Flannery B.P. "Numerical Recipes in C," 2nd Ed. :1994;Cambridge Univ. Press, Cambridge
21. Sambrook J., Russell D.W. "Molecular Cloning: A Laboratory Manual." 2001;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
22. Schena M. "Microarray Analysis." 2003;Wiley-Liss, Hoboken, NJ
23. Sehgal A., Price J.L., Man B., Young M.W. Loss of circadian behavioral rhythms and per RNA oscillations in the Drosophila mutant timeless. Science. 263:1994;1603-1606
24. Sehgal A., Rothenfluh-Hilfiker A., Hunter-Ensor M., Chen Y., Myers M.P., Young M.W. Rhythmic expression of timeless: A basis for promoting circadian cycles in period gene autoregulation. Science. 270:1995;808-810
25. Stirling D. Qualitative and quantitative PCR: A technical overview. Bartlett J.M.S., Stirling D. "PCR Protocols" 2nd Ed. :2003;181-183 Humana Press, Totowa, NJ
26. 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
27. 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. 418:2002a;534-539
28. Ueda H.R., Matsumoto A., Kawamura M., Iino M., Tanimura T., Hashimoto S. Genome-wide transcriptional orchestration of circadian rhythms in Drosophila. J. Biol. Chem. 277:2002b;14048-14052
29. Wilhelm J., Pingoud A. Real-time polymerase chain reaction. Chembiochemical. 4:2003;1120-1128
30. Wu Z., Irizarry R.A. Stochastic models inspired by hybridization theory for short oligonucleotide arrays. Proceedings of RECOMB. 2004;98-106
31. Yang Y.H., Speed T.P. Design and analysis of comparative microarray experiments. Speed T.P. "Statistical Analysis of Gene Expression Microarray Data" 2003;35-91 CRC, Boca Raton, FL