References
- Akhtar RA, Reddy AB, Maywood ES, Clayton JD, King VM, Smith AG, … Kyriacou CP. (2002). Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus. Curr Biol : CB. 12:540–50.
- Balsalobre A, Damiola F, Schibler U. (1998). A serum shock induces circadian gene expression in mammalian tissue culture cells. Cell. 93:929–37. http://doi.org/10.1016/S0092-8674(00)81199-X
- Cadenas C, van de Sandt L, Edlund K, Lohr M, Hellwig B, Marchan R, … Hengstler JG. (2014). Loss of circadian clock gene expression is associated with tumor progression in breast cancer. Cell Cycle (Georgetown, TX). 13:3282–91. http://doi.org/10.4161/15384101.2014.954454
- Chen S-T, Choo K-B, Hou M-F, Yeh K-T, Kuo S-J, Chang J-G. (2005). Deregulated expression of the PER1, PER2 and PER3 genes in breast cancers. Carcinogenesis. 26:1241–6. http://doi.org/10.1093/carcin/bgi075
- Edgar R, Domrachev M, Lash AE. (2002). Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30:207–10.
- Filipski E, Li XM, Levi F. (2006). Disruption of circadian coordination and malignant growth. Cancer Causes Control : CCC. 17:509–14. http://doi.org/10.1007/s10552-005-9007-4
- Foulkes WD, Smith IE, Reis-Filho JS. (2010). Triple-negative breast cancer. New Engl J Med. 363:1938–48. http://doi.org/10.1056/NEJMra1001389
- Gekakis N, Staknis D, Nguyen HB, Davis FC, Wilsbacher LD, King DP, … Weitz CJ. (1998). Role of the CLOCK protein in the mammalian circadian mechanism. Science (New York, NY). 280:1564–9.
- Griffin EA. J., Staknis D, Weitz CJ. (1999). Light-independent role of CRY1 and CRY2 in the mammalian circadian clock. Science (New York, NY). 286:768–71.
- Hennessy BT, Gonzalez-Angulo A-M, Stemke-Hale K, Gilcrease MZ, Krishnamurthy S, Lee J-S, … Mills GB. (2009). Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics. Cancer Res. 69:4116–24. http://doi.org/10.1158/0008-5472.CAN-08-3441
- Kuo S-J, Chen S-T, Yeh K-T, Hou M-F, Chang Y-S, Hsu NC, Chang J-G. (2009). Disturbance of circadian gene expression in breast cancer. Virchows Archiv: Int J Pathol. 454:467–74. http://doi.org/10.1007/s00428-009-0761-7
- Livak KJ, Schmittgen TD. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. 408:402–8. http://doi.org/10.1006/meth.2001.1262
- McCarthy JJ, Andrews JL, McDearmon EL, Campbell KS, Barber BK, Miller BH, … Esser KA. (2007). Identification of the circadian transcriptome in adult mouse skeletal muscle. Physiol Genom. 31:86–95. http://doi.org/10.1152/physiolgenomics.00066.2007
- Miller BH, McDearmon EL, Panda S, Hayes KR, Zhang J, Andrews JL, … Takahashi JS. (2007). Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation. Proc Natl Acad Sci USA. 104:3342–7. http://doi.org/10.1073/pnas.0611724104
- Oishi K, Miyazaki K, Kadota K, Kikuno R, Nagase T, Atsumi G, … Ishida N. (2003). Genome-wide expression analysis of mouse liver reveals CLOCK-regulated circadian output genes. J Biol Chem. 278:41519–27. http://doi.org/10.1074/jbc.M304564200
- Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, … Botstein D. (2000). Molecular portraits of human breast tumours. Nature. 406:747–52. http://doi.org/10.1038/35021093
- Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK. (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics (Oxford, England). 23:2700–7. http://doi.org/10.1093/bioinformatics/btm412
- Rossetti S, Esposito J, Corlazzoli F, Gregorski A, Sacchi N. (2012). Entrainment of breast (cancer) epithelial cells detects distinct circadian oscillation patterns for clock and hormone receptor genes. Cell Cycle (Georgetown, TX). 11:350–60. http://doi.org/10.4161/cc.11.2.18792
- Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, … Velculescu VE. (2006). The consensus coding sequences of human breast and colorectal cancers. Science (New York, NY) 314: 268–74. http://doi.org/10.1126/science.1133427
- Smyth GK, Speed T. (2003). Normalization of cDNA microarray data. Methods (San Diego, CA) 31:265–73.
- Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, … Børresen-Dale AL. (2001). Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA. 98:10869–74. http://doi.org/10.1073/pnas.191367098
- Soule HD, Maloney TM, Wolman SR, Line EC, Peterson WD, Brenz R, … Brooks SC. (1990). Isolation and characterization of a spontaneously immortalized isolation and characterization of a spontaneously immortalized human breast. Cancer Res. 50:6075–86.
- Takahashi JS, Hong H-K, Ko CH, McDearmon EL. (2008). The genetics of mammalian circadian order and disorder: Implications for physiology and disease. Nat Rev Genet. 9:764–75. http://doi.org/10.1038/nrg2430
- Trevino V, Falciani F, Barrera-Saldana HA. (2007). DNA microarrays: A powerful genomic tool for biomedical and clinical research. Molecular Medicine (Cambridge, MA). 13:527–41. http://doi.org/10.2119/2006-00107.Trevino
- Vandesompele J, Preter K De, Poppe B, Roy N Van, Paepe A De. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3:1–12.
- Winter SL, Bosnoyan-Collins L, Pinnaduwage D, Andrulis IL. (2007). Expression of the circadian clock genes Per1 and Per2 in sporadic and familial breast tumors. Neoplasia (New York, NY). 9:797–800.
- Xiang S, Mao L, Duplessis T, Yuan L, Dauchy R, Dauchy E, … Hill SM. (2012). Oscillation of clock and clock controlled genes induced by serum shock in human breast epithelial and breast cancer cells: Regulation by melatonin. Breast Cancer : Basic Clin Res. 6:137–50. http://doi.org/10.4137/BCBCR.S9673
- Yamada R, Ueda HR. (2007). Microarrays: Statistical methods for circadian rhythms. Methods Mol Biol. (Clifton, NJ). 362:245–64. http://doi.org/10.1007/978-1-59745-257-1_17
- Yang R, Zhang C, Su Z. (2011). LSPR: An integrated periodicity detection algorithm for unevenly sampled temporal microarray data. Bioinformatics (Oxford, England). 27:1023–5. http://doi.org/10.1093/bioinformatics/btr041
- Yang X, Wood PA, Ansell CM, Quiton DFT, Oh E-Y, Du-Quiton J, Hrushesky WJM. (2009). The circadian clock gene Per1 suppresses cancer cell proliferation and tumor growth at specific times of day. Chronobiol Int. 26:1323–39. http://doi.org/10.3109/07420520903431301
- Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB. (2014). A circadian gene expression atlas in mammals: Implications for biology and medicine. Proc Natl Acad Sci USA. 111:16219–24. http://doi.org/10.1073/pnas.1408886111