Complexity of Stress Signaling

Handbook of Cell Signaling, Second Edition

Volumn 3, Issue , 2009, Pages 2107-2125

  Hyduke, Daniel R ^a,b   Amundson, Sally A ^c   Fornace, Albert J ^b,d  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c NewYork Presbyterian Hospital   (United States)

^d GEORGETOWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77949772972     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-374145-5.00257-6     Document Type: Chapter

References (264)

1. HH Li, J Aubrecht and AJ Fornace Jr (2007) Toxicogenomics: overview and potential applications for the study of non-covalent DNA interacting chemicals. Mutat Res 623(1–2), 98-108.
2. LE Dietrich, A Price-Whelan, A Petersen, M Whiteley and DK Newman (2006) The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa. Mol Microbiol 61(5), 1308-1321.
3. LEP Dietrich, TK Teal, A Price-Whelan and DK Newman (2008) Redox-active antibiotics control gene expression and community behavior in divergent bacteria. Science 321(5893), 1203-1206.
4. AM Lazdunski, I Ventre and JN Sturgis (2004) Regulatory circuits and communication in Gram-negative bacteria. Nat Rev Microbiol 2(7), 581-592.
5. DM Bodenmiller and S Spiro (2006) The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator. J Bacteriol 188(3), 874-881.
6. KW Kohn (1999) Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol Biol Cell 10(8), 2703-2734.
7. KW Kohn, MI Aladjem, S Kim, JN Weinstein and Y Pommier (2006) Depicting combinatorial complexity with the molecular interaction map notation. Mol Syst Biol 2 51.
8. KW Kohn, MI Aladjem, JN Weinstein and Y Pommier (2006) Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell 17(1), 1-13.
9. AH Singh, DM Wolf, P Wang and AP Arkin (2008) Modularity of stress response evolution. Proc Natl Acad Sci USA 105(21), 7500-7505.
10. H Nagasawa and JB Little (1992) Induction of sister chromatid exchanges by extremely low doses of alpha-particles. Cancer Res 52(22), 6394-6396.
11. TK Hei, H Zhou, VN Ivanov, M Hong, HB Lieberman, DJ Brenner, SA Amundson and CR Geard (2008) Mechanism of radiation-induced bystander effects: a unifying model. J Pharm Pharmacol 60(8), 943-950.
12. M Mancuso, E Pasquali, S Leonardi, M Tanori, S Rebessi, V Di Majo, S Pazzaglia, MP Toni, M Pimpinella, V Covelli and A Saran (2008) Oncogenic bystander radiation effects in Patched heterozygous mouse cerebellum. Proc Natl Acad Sci USA 105(34), 12,445-12,450.
13. H Zhou, VN Ivanov, YC Lien, M Davidson and TK Hei (2008) Mitochondrial function and nuclear factor-kappaB-mediated signaling in radiation-induced bystander effects. Cancer Res 68(7), 2233-2240.
14. A Barzilai, G Rotman and Y Shiloh (2002) ATM deficiency and oxidative stress: a new dimension of defective response to DNA damage. DNA Repair (Amst) 1(1), 3-25.
15. G Rotman and Y Shiloh (1999) ATM: a mediator of multiple responses to genotoxic stress. Oncogene 18(45), 6135-6144.
16. N Weizman, Y Shiloh and A Barzilai (2003) Contribution of the Atm protein to maintaining cellular homeostasis evidenced by continuous activation of the AP-1 pathway in Atm-deficient brains. J Biol Chem 278(9), 6741-6747.
17. JH Lee, MW Jeong, W Kim, YH Choi and KT Kim (2008) Cooperative Roles of c-Abl and Cdk5 in Regulation of p53 in Response to Oxidative Stress. J Biol Chem 283(28), 19,826-19,835.
18. T Morio and H Kim (2008) Ku, Artemis, and ataxia-telangiectasia-mutated: signalling networks in DNA damage. Int J Biochem Cell Biol 40(4), 598-603.
19. M Shrivastav, LP De Haro and JA Nickoloff (2008) Regulation of DNA double-strand break repair pathway choice. Cell Res 18(1), 134-147.
20. R Shroff, A Arbel-Eden, D Pilch, G Ira, WM Bonner, JH Petrini, JE Haber and M Lichten (2004) Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break. Curr Biol 14(19), 1703-1711.
21. CJ Bakkenist and MB Kastan (2003) DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421(6922), 499-506.
22. CT Carson, RA Schwartz, TH Stracker, CE Lilley, DV Lee and MD Weitzman (2003) The Mre11 complex is required for ATM activation and the G2/M checkpoint. EMBO J 22(24), 6610-6620.
23. S Banin, L Moyal, S Shieh, Y Taya, CW Anderson, L Chessa, NI Smorodinsky, C Prives, Y Reiss, Y Shiloh and Y Ziv (1998) Enhanced phosphorylation of p53 by ATM in response to DNA damage. Science 281(5383), 1674-1677.
24. CE Canman, DS Lim, KA Cimprich, Y Taya, K Tamai, K Sakaguchi, E Appella, MB Kastan and JD Siliciano (1998) Activation of the ATM kinase by ionizing radiation and phosphorylation of p53. Science 281(5383), 1677-1679.
25. D Cortez, Y Wang, J Qin and SJ Elledge (1999) Requirement of ATM-dependent phosphorylation of brca1 in the DNA damage response to double-strand breaks. Science 286(5442), 1162-1166.
26. R Khosravi, R Maya, T Gottlieb, M Oren, Y Shiloh and D Shkedy (1999) Rapid ATM-dependent phosphorylation of MDM2 precedes p53 accumulation in response to DNA damage. Proc Natl Acad Sci USA 96(26), 14,973-14,977.
27. B Piret, S Schoonbroodt and J Piette (1999) The ATM protein is required for sustained activation of NF-kappaB following DNA damage. Oncogene 18(13), 2261-2271.
28. T Stiff, M O’Driscoll, N Rief, K Iwabuchi, M Lobrich and PA Jeggo (2004) ATM and DNA-PK function redundantly to phosphorylate H2AX after exposure to ionizing radiation. Cancer Res 64(7), 2390-2396.
29. AM Vines, FM Lyng, B McClean, C Seymour and CE Mothersill (2008) Bystander signal production and response are independent processes which are cell line dependent. Int J Radiat Biol 84(2), 83-90.
30. S Wang, M Guo, H Ouyang, X Li, C Cordon-Cardo, A Kurimasa, DJ Chen, Z Fuks, CC Ling and GC Li (2000) The catalytic subunit of DNA-dependent protein kinase selectively regulates p53-dependent apoptosis but not cell-cycle arrest. Proc Natl Acad Sci USA 97(4), 1584-1588.
31. S Burma, A Kurimasa, G Xie, Y Taya, R Araki, M Abe, HA Crissman, H Ouyang, GC Li and DJ Chen (1999) DNA-dependent protein kinase-independent activation of p53 in response to DNA damage. J Biol Chem 274(24), 17,139-17,143.
32. R Dip and H Naegeli (2005) More than just strand breaks: the recognition of structural DNA discontinuities by DNA-dependent protein kinase catalytic subunit. FASEB J 19(7), 704-715.
33. N Tomimatsu, CG Tahimic, A Otsuki, S Burma, A Fukuhara, K Sato, G Shiota, M Oshimura, DJ Chen and A Kurimasa (2007) Ku70/80 modulates ATM and ATR signaling pathways in response to DNA double strand breaks. J Biol Chem 282(14), 10,138-10,145.
34. S Burma, BP Chen, M Murphy, A Kurimasa and DJ Chen (2001) ATM phosphorylates histone H2AX in response to DNA double-strand breaks. J Biol Chem 276(45), 42,462-42,467.
35. B Mukherjee, C Kessinger, J Kobayashi, BP Chen, DJ Chen, A Chatterjee and S Burma (2006) DNA-PK phosphorylates histone H2AX during apoptotic DNA fragmentation in mammalian cells. DNA Repair (Amst) 5(5), 575-590.
36. O Fernandez-Capetillo, A Lee, M Nussenzweig and A Nussenzweig (2004) H2AX: the histone guardian of the genome. DNA Repair (Amst) 3(8–9), 959-967.
37. A Celeste, S Petersen, PJ Romanienko, O Fernandez-Capetillo, HT Chen, OA Sedelnikova, B Reina-San-Martin, V Coppola, E Meffre, MJ Difilippantonio, C Redon, DR Pilch, A Olaru, M Eckhaus, RD Camerini-Otero, L Tessarollo, F Livak, K Manova, WM Bonner, MC Nussenzweig and A Nussenzweig (2002) Genomic instability in mice lacking histone H2AX. Science 296(5569), 922-927.
38. S Franco, M Gostissa, S Zha, DB Lombard, MM Murphy, AA Zarrin, C Yan, S Tepsuporn, JC Morales, MM Adams, Z Lou, CH Bassing, JP Manis, J Chen, PB Carpenter and FW Alt (2006) H2AX prevents DNA breaks from progressing to chromosome breaks and translocations. Mol Cell 21(2), 201-214.
39. S Zha, J Sekiguchi, JW Brush, CH Bassing and FW Alt (2008) Complementary functions of ATM and H2AX in development and suppression of genomic instability. Proc Natl Acad Sci USA 105(27), 9302-9306.
40. KA Cimprich and D Cortez (2008) ATR: an essential regulator of genome integrity. Nat Rev Mol Cell Biol 9(8), 616-627.
41. E Fanning, V Klimovich and AR Nager (2006) A dynamic model for replication protein A (RPA) function in DNA processing pathways. Nucleic Acids Res 34(15), 4126-4137.
42. J Falck, J Coates and SP Jackson (2005) Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage. Nature 434(7033), 605-611.
43. XQ Wang, JL Redpath, ST Fan and EJ Stanbridge (2006) ATR dependent activation of Chk2. J Cell Physiol 208(3), 613-619.
44. D Batty, V Rapic'-Otrin, AS Levine and RD Wood (2000) Stable binding of human XPC complex to irradiated DNA confers strong discrimination for damaged sites. J Mol Biol 300(2), 275-290.
45. S Jones, WD Chen, G Parmigiani, F Diehl, N Beerenwinkel, T Antal, A Traulsen, MA Nowak, C Siegel, VE Velculescu, KW Kinzler, B Vogelstein, J Willis and SD Markowitz (2008) Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci USA 105(11), 4283-4288.
46. P Kakkar and BK Singh (2007) Mitochondria: a hub of redox activities and cellular distress control. Mol Cell Biochem 305(1–2), 235-253.
47. JE Chipuk, T Kuwana, L Bouchier-Hayes, NM Droin, DD Newmeyer, M Schuler and DR Green (2004) Direct activation of Bax by p53 mediates mitochondrial membrane permeabilization and apoptosis. Science 303(5660), 1010-1014.
48. JI Leu, P Dumont, M Hafey, ME Murphy and DL George (2004) Mitochondrial p53 activates Bak and causes disruption of a Bak-Mcl1 complex. Nat Cell Biol 6(5), 443-450.
49. ME Murphy, JI Leu and DL George (2004) p53 moves to mitochondria: a turn on the path to apoptosis. Cell Cycle 3(7), 836-839.
50. C Giorgi, A Romagnoli, P Pinton and R Rizzuto (2008) Ca2+ signaling, mitochondria and cell death. Curr Mol Med 8(2), 119-130.
51. Y Lao and DC Chang (2008) Mobilization of Ca2+ from endoplasmic reticulum to mitochondria plays a positive role in the early stage of UV- or TNFalpha-induced apoptosis. Biochem Biophys Res Commun 373(1), 42-47.
52. SW Ballinger, C Patterson, CN Yan, R Doan, DL Burow, CG Young, FM Yakes, B Van Houten, CA Ballinger, BA Freeman and MS Runge (2000) Hydrogen peroxide- and peroxynitrite-induced mitochondrial DNA damage and dysfunction in vascular endothelial and smooth muscle cells. Circ Res 86(9), 960-966.
53. FM Yakes and B Van Houten (1997) Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. Proc Natl Acad Sci USA 94(2), 514-519.
54. JH Santos, L Hunakova, Y Chen, C Bortner and B Van Houten (2003) Cell sorting experiments link persistent mitochondrial DNA damage with loss of mitochondrial membrane potential and apoptotic cell death. J Biol Chem 278(3), 1728-1734.
55. JK Leach, G Van Tuyle, PS Lin, R Schmidt-Ullrich and RB Mikkelsen (2001) Ionizing radiation-induced, mitochondria-dependent generation of reactive oxygen/nitrogen. Cancer Res 61(10), 3894-3901.
56. ML Paz, DH Gonzalez Maglio, FS Weill, J Bustamante and J Leoni (2008) Mitochondrial dysfunction and cellular stress progression after ultraviolet B irradiation in human keratinocytes. Photodermatol Photoimmunol Photomed 24(3), 115-122.
57. S Drose and U Brandt (2008) The mechanism of mitochondrial superoxide production by the cytochrome bc1 complex. J Biol Chem 283(31), 21,649-21,654.
58. R Gredilla, A Sanz, M Lopez-Torres and G Barja (2001) Caloric restriction decreases mitochondrial free radical generation at complex I and lowers oxidative damage to mitochondrial DNA in the rat heart. FASEB J 15(9), 1589-1591.
59. RE Huie and S Padmaja (1993) The reaction of no with superoxide. Free Radic Res Commun 18(4), 195-199.
60. F Yamakura, H Taka, T Fujimura and K Murayama (1998) Inactivation of human manganese-superoxide dismutase by peroxynitrite is caused by exclusive nitration of tyrosine 34 to 3-nitrotyrosine. J Biol Chem 273(23), 14,085-14,089.
61. M Ott, V Gogvadze, S Orrenius and B Zhivotovsky (2007) Mitochondria, oxidative stress and cell death. Apoptosis 12(5), 913-922.
62. JA Stuart and MF Brown (2006) Mitochondrial DNA maintenance and bioenergetics. Biochim Biophys Acta 1757(2), 79-89.
63. PA Mason, EC Matheson, AG Hall and RN Lightowlers (2003) Mismatch repair activity in mammalian mitochondria. Nucleic Acids Res 31(3), 1052-1058.
64. D Chen, Z Yu, Z Zhu and CD Lopez (2006) The p53 pathway promotes efficient mitochondrial DNA base excision repair in colorectal cancer cells. Cancer Res 66(7), 3485-3494.
65. Y Yoshida, H Izumi, T Torigoe, H Ishiguchi, H Itoh, D Kang and K Kohno (2003) P53 physically interacts with mitochondrial transcription factor A and differentially regulates binding to damaged DNA. Cancer Res 63(13), 3729-3734.
66. S Pervin, AH Tran, S Zekavati, JM Fukuto, R Singh and G Chaudhuri (2008) Increased susceptibility of breast cancer cells to stress mediated inhibition of protein synthesis. Cancer Res 68(12), 4862-4874.
67. MR Hara, N Agrawal, SF Kim, MB Cascio, M Fujimuro, Y Ozeki, M Takahashi, JH Cheah, SK Tankou, LD Hester, CD Ferris, SD Hayward, SH Snyder and A Sawa (2005) S-nitrosylated GAPDH initiates apoptotic cell death by nuclear translocation following Siah1 binding. Nat Cell Biol 7(7), 665-674.
68. O Takeuchi and S Akira (2007) Recognition of viruses by innate immunity. Immunol Rev 220 214-224.
69. Ishikawa, H. & Barber, G. N. STING is an endoplasmic reticulum adaptor that facilitates innate immune signaling. Nature, 455 (7213), 674–678.
70. DM Townsend (2007) S-glutathionylation: indicator of cell stress and regulator of the unfolded protein response. Mol Interv 7(6), 313-324.
71. JE Chipuk, L Bouchier-Hayes, T Kuwana, DD Newmeyer and DR Green (2005) PUMA couples the nuclear and cytoplasmic proapoptotic function of p53. Science 309(5741), 1732-1735.
72. M Holcik and N Sonenberg (2005) Translational control in stress and apoptosis. Nat Rev Mol Cell Biol 6(4), 318-327.
73. S Yamasaki and P Anderson (2008) Reprogramming mRNA translation during stress. Curr Opin Cell Biol 20(2), 222-226.
74. RC Wek, HY Jiang and TG Anthony (2006) Coping with stress: eIF2 kinases and translational control. Biochem Soc Trans 34(Pt 1), 7-11.
75. HP Harding, I Novoa, Y Zhang, H Zeng, R Wek, M Schapira and D Ron (2000) Regulated translation initiation controls stress-induced gene expression in mammalian cells. Mol Cell 6(5), 1099-1108.
76. E McEwen, N Kedersha, B Song, D Scheuner, N Gilks, A Han, JJ Chen, P Anderson and RJ Kaufman (2005) Heme-regulated inhibitor kinase-mediated phosphorylation of eukaryotic translation initiation factor 2 inhibits translation, induces stress granule formation, and mediates survival upon arsenite exposure. J Biol Chem 280(17), 16,925-16,933.
77. TE Dever (2002) Gene-specific regulation by general translation factors. Cell 108(4), 545-556.
78. RC Wek and DR Cavener (2007) Translational control and the unfolded protein response. Antioxid Redox Signal 9(12), 2357-2371.
79. BC Mak, Q Wang, C Laschinger, W Lee, D Ron, HP Harding, RJ Kaufman, D Scheuner, RC Austin and CA McCulloch (2008) Novel function of perk as a mediator of force-induced apoptosis. J Biol Chem 283(34), 23,462-23,472.
80. L Zhang, Z Smit-McBride, X Pan, J Rheinhardt and JW Hershey (2008) An oncogenic role for the phosphorylated h-subunit of human translation initiation factor eIF3. J Biol Chem 283(35), 24,047-24,060.
81. R Santucci, F Sinibaldi and L Fiorucci (2008) Protein folding, unfolding and misfolding: role played by intermediate States. Mini Rev Med Chem 8(1), 57-62.
82. T Nakamura and SA Lipton (2008) Emerging roles of S-nitrosylation in protein misfolding and neurodegenerative diseases. Antioxid Redox Signal 10(1), 87-101.
83. T Uehara, T Nakamura, D Yao, ZQ Shi, Z Gu, Y Ma, E Masliah, Y Nomura and SA Lipton (2006) S-nitrosylated protein-disulphide isomerase links protein misfolding to neurodegeneration. Nature 441(7092), 513-517.
84. J Ananthan, AL Goldberg and R Voellmy (1986) Abnormal proteins serve as eukaryotic stress signals and trigger the activation of heat shock genes. Science 232(4749), 522-524.
85. MY Sherman and AL Goldberg (2001) Cellular defenses against unfolded proteins: a cell biologist thinks about neurodegenerative diseases. Neuron 29(1), 15-32.
86. M Ilbert, J Horst, S Ahrens, J Winter, PC Graf, H Lilie and U Jakob (2007) The redox-switch domain of Hsp33 functions as dual stress sensor. Nat Struct Mol Biol 14(6), 556-563.
87. M Schroder (2008) Endoplasmic reticulum stress responses. Cell Mol Life Sci 65(6), 862-894.
88. MA Brostrom and CO Brostrom (2003) Calcium dynamics and endoplasmic reticular function in the regulation of protein synthesis: implications for cell growth and adaptability. Cell Calcium 34(4–5), 345-363.
89. JS Schutzbach and WT Forsee (1990) Calcium ion activation of rabbit liver alpha 1,2-mannosidase. J Biol Chem 265(5), 2546-2549.
90. SC Taylor, AD Ferguson, JJ Bergeron and DY Thomas (2004) The ER protein folding sensor UDP-glucose glycoprotein-glucosyltransferase modifies substrates distant to local changes in glycoprotein conformation. Nat Struct Mol Biol 11(2), 128-134.
91. C Hwang, AJ Sinskey and HF Lodish (1992) Oxidized redox state of glutathione in the endoplasmic reticulum. Science 257(5076), 1496-1502.
92. K Kohno (2007) How transmembrane proteins sense endoplasmic reticulum stress. Antioxid Redox Signal 9(12), 2295-2303.
93. A Bertolotti, Y Zhang, LM Hendershot, HP Harding and D Ron (2000) Dynamic interaction of BiP and ER stress transducers in the unfolded-protein response. Nat Cell Biol 2(6), 326-332.
94. JB DuRose, AB Tam and M Niwa (2006) Intrinsic capacities of molecular sensors of the unfolded protein response to sense alternate forms of endoplasmic reticulum stress. Mol Biol Cell 17(7), 3095-3107.
95. DT Rutkowski, SM Arnold, CN Miller, J Wu, J Li, KM Gunnison, K Mori, AA Sadighi Akha, D Raden and RJ Kaufman (2006) Adaptation to ER stress is mediated by differential stabilities of pro-survival and pro-apoptotic mRNAs and proteins. PLoS Biol 4(11), e374.
96. KM Vattem and RC Wek (2004) Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc Natl Acad Sci USA 101(31), 11,269-11,274.
97. HP Harding, Y Zhang, H Zeng, I Novoa, PD Lu, M Calfon, N Sadri, C Yun, B Popko, R Paules, DF Stojdl, JC Bell, T Hettmann, JM Leiden and D Ron (2003) An integrated stress response regulates amino acid metabolism and resistance to oxidative stress. Mol Cell 11(3), 619-633.
98. E Kojima, A Takeuchi, M Haneda, A Yagi, T Hasegawa, K Yamaki, K Takeda, S Akira, K Shimokata and K Isobe (2003) The function of GADD34 is a recovery from a shutoff of protein synthesis induced by ER stress: elucidation by GADD34-deficient mice. FASEB J 17(11), 1573-1575.
99. H Yoshida, T Matsui, A Yamamoto, T Okada and K Mori (2001) XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor. Cell 107(7), 881-891.
100. H Yoshida, S Nadanaka, R Sato and K Mori (2006) XBP1 is critical to protect cells from endoplasmic reticulum stress: evidence from Site-2 protease-deficient Chinese hamster ovary cells. Cell Struct Funct 31(2), 117-125.
101. M Niwa, CK Patil, J DeRisi and P Walter (2005) Genome-scale approaches for discovering novel nonconventional splicing substrates of the Ire1 nuclease. Genome Biol 6(1), R3.
102. T Namba, T Ishihara, K Tanaka, T Hoshino and T Mizushima (2007) Transcriptional activation of ATF6 by endoplasmic reticulum stressors. Biochem Biophys Res Commun 355(2), 543-548.
103. J Ye, RB Rawson, R Komuro, X Chen, UP Dave, R Prywes, MS Brown and JL Goldstein (2000) ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs. Mol Cell 6(6), 1355-1364.
104. K Haze, H Yoshida, H Yanagi, T Yura and K Mori (1999) Mammalian transcription factor ATF6 is synthesized as a transmembrane protein and activated by proteolysis in response to endoplasmic reticulum stress. Mol Biol Cell 10(11), 3787-3799.
105. Y Wang, J Shen, N Arenzana, W Tirasophon, RJ Kaufman and R Prywes (2000) Activation of ATF6 and an ATF6 DNA binding site by the endoplasmic reticulum stress response. J Biol Chem 275(35), 27,013-27,020.
106. A Bowie and LA O’Neill (2000) Oxidative stress and nuclear factor-kappaB activation: a reassessment of the evidence in the light of recent discoveries. Biochem Pharmacol 59(1), 13-23.
107. A Haimovitz-Friedman, CC Kan, D Ehleiter, RS Persaud, M McLoughlin, Z Fuks and RN Kolesnick (1994) Ionizing radiation acts on cellular membranes to generate ceramide and initiate apoptosis. J Exp Med 180(2), 525-535.
108. HZ Ozsoy, N Sivasubramanian, ED Wieder, S Pedersen and DL Mann (2008) Oxidative stress promotes ligand-independent and enhanced ligand-dependent tumor necrosis factor receptor signaling. J Biol Chem 283(34), 23,419-23,428.
109. F Courtois, EG Seidman, E Delvin, C Asselin, S Bernotti, M Ledoux and E Levy (2003) Membrane peroxidation by lipopolysaccharide and iron-ascorbate adversely affects Caco-2 cell function: beneficial role of butyric acid. Am J Clin Nutr 77(3), 744-750.
110. E Lien, TK Means, H Heine, A Yoshimura, S Kusumoto, K Fukase, MJ Fenton, M Oikawa, N Qureshi, B Monks, RW Finberg, RR Ingalls and DT Golenbock (2000) Toll-like receptor 4 imparts ligand-specific recognition of bacterial lipopolysaccharide. J Clin Invest 105(4), 497-504.
111. C Sachsenmaier, A Radler-Pohl, R Zinck, A Nordheim, P Herrlich and HJ Rahmsdorf (1994) Involvement of growth factor receptors in the mammalian UVC response. Cell 78(6), 963-972.
112. C Rosette and M Karin (1996) Ultraviolet light and osmotic stress: activation of the JNK cascade through multiple growth factor and cytokine receptors. Science 274(5290), 1194-1197.
113. D Tobin, M van Hogerlinden and R Toftgard (1998) UVB-induced association of tumor necrosis factor (TNF) receptor 1/TNF receptor-associated factor-2 mediates activation of Rel proteins. Proc Natl Acad Sci USA 95(2), 565-569.
114. R Iyer, BE Lehnert and R Svensson (2000) Factors underlying the cell growth-related bystander responses to alpha particles. Cancer Res 60(5), 1290-1298.
115. C Mothersill and C Seymour (2001) Radiation-induced bystander effects: past history and future directions. Radiat Res 155(6), 759-767.
116. H Zhou, G Randers-Pehrson, CA Waldren, D Vannais, EJ Hall and TK Hei (2000) Induction of a bystander mutagenic effect of alpha particles in mammalian cells. Proc Natl Acad Sci USA 97(5), 2099-2104.
117. EI Azzam, SM de Toledo and JB Little (2001) Direct evidence for the participation of gap junction-mediated intercellular communication in the transmission of damage signals from alpha-particle irradiated to nonirradiated cells. Proc Natl Acad Sci USA 98(2), 473-478.
118. H Yang, V Anzenberg and KD Held (2007) The time dependence of bystander responses induced by iron-ion radiation in normal human skin fibroblasts. Radiat Res 168(3), 292-298.
119. H Yang, N Asaad and KD Held (2005) Medium-mediated intercellular communication is involved in bystander responses of X-ray-irradiated normal human fibroblasts. Oncogene 24(12), 2096-2103.
120. FM Lyng, P Maguire, B McClean, C Seymour and C Mothersill (2006) The involvement of calcium and MAP kinase signaling pathways in the production of radiation-induced bystander effects. Radiat Res 165(4), 400-409.
121. PL Olive and PJ Johnston (1997) DNA damage from oxidants: influence of lesion complexity and chromatin organization. Oncol Res 9(6–7), 287-294.
122. DA Wink and JB Mitchell (1998) Chemical biology of nitric oxide: Insights into regulatory, cytotoxic, and cytoprotective mechanisms of nitric oxide. Free Radic Biol Med 25(4–5), 434-456.
123. K Tasken and EM Aandahl (2004) Localized effects of cAMP mediated by distinct routes of protein kinase A. Physiol Rev 84(1), 137-167.
124. KA Lucas, GM Pitari, S Kazerounian, I Ruiz-Stewart, J Park, S Schulz, KP Chepenik and SA Waldman (2000) Guanylyl cyclases and signaling by cyclic GMP. Pharmacol Rev 52(3), 375-414.
125. AM Shah and H Sauer (2006) Transmitting biological information using oxygen: reactive oxygen species as signalling molecules in cardiovascular pathophysiology. Cardiovasc Res 71(2), 191-194.
126. JRJ Lancaster (1996) Diffusion of free nitric oxide. Methods Enzymol 268 31-50.
127. TA Farazi, SA Juranek and T Tuschl (2008) The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135(7), 1201-1214.
128. JC Liao, TW Hein, MW Vaughn, KT Huang and L Kuo (1999) Intravascular flow decreases erythrocyte consumption of nitric oxide. Proc Natl Acad Sci USA 96(15), 8757-8761.
129. DR Hyduke and JC Liao (2005) Analysis of nitric oxide donor effectiveness in resistance vessels. Am J Physiol Heart Circ Physiol 288(5), H2390-H2399.
130. DD Thomas, LA Ridnour, MG Espey, S Donzelli, S Ambs, SP Hussain, CC Harris, W DeGraff, DD Roberts, JB Mitchell and DA Wink (2006) Superoxide fluxes limit nitric oxide-induced signaling. J Biol Chem 281(36), 25,984-25,993.
131. M Zaccolo and MA Movsesian (2007) cAMP and cGMP signaling cross-talk: role of phosphodiesterases and implications for cardiac pathophysiology. Circ Res 100(11), 1569-1578.
132. DA Mitchell and MA Marletta (2005) Thioredoxin catalyzes the S-nitrosation of the caspase-3 active site cysteine. Nat Chem Biol 1(3), 154-158.
133. M Benhar, MT Forrester, DT Hess and JS Stamler (2008) Regulated protein denitrosylation by cytosolic and mitochondrial thioredoxins. Science 320(5879), 1050-1054.
134. I Rahman, J Marwick and P Kirkham (2004) Redox modulation of chromatin remodeling: impact on histone acetylation and deacetylation, NF-kappaB and pro-inflammatory gene expression. Biochem Pharmacol 68(6), 1255-1267.
135. EL Greer and A Brunet (2008) FOXO transcription factors in ageing and cancer. Acta Physiol (Oxf) 192(1), 19-28.
136. YG Chang, XZ Yan, YY Xie, XC Gao, AX Song, DE Zhang and HY Hu (2008) Different roles for two ubiquitin-like domains of ISG15 in protein modification. J Biol Chem 283(19), 13,370-13,377.
137. J Sun, C Steenbergen and E Murphy (2006) S-nitrosylation: NO-related redox signaling to protect against oxidative stress. Antioxid Redox Signal 8(9–10), 1693-1705.
138. K Chen, MT Kirber, H Xiao, Y Yang and JFJ Keaney (2008) Regulation of ROS signal transduction by NADPH oxidase 4 localization. J Cell Biol 181(7), 1129-1139.
139. JJ Perry, JA Tainer and MN Boddy (2008) A SIM-ultaneous role for SUMO and ubiquitin. Trends Biochem Sci 33(5), 201-208.
140. DV Bulavin, ON Demidov, S Saito, P Kauraniemi, C Phillips, SA Amundson, C Ambrosino, G Sauter, AR Nebreda, CW Anderson, A Kallioniemi, AJ Fornace Jr and E Appella (2002) Amplification of PPM1D in human tumors abrogates p53 tumor-suppressor activity. Nat Genet 31(2), 210-215.
141. K Webley, JA Bond, CJ Jones, JP Blaydes, A Craig, T Hupp and D Wynford-Thomas (2000) Posttranslational modifications of p53 in replicative senescence overlapping but distinct from those induced by DNA damage. Mol Cell Biol 20(8), 2803-2808.
142. S Saito, H Yamaguchi, Y Higashimoto, C Chao, Y Xu, AJ Fornace Jr, E Appella and CW Anderson (2003) Phosphorylation site interdependence of human p53 post-translational modifications in response to stress. J Biol Chem 278(39), 37,536-37,544.
143. S Saito, AA Goodarzi, Y Higashimoto, Y Noda, SP Lees-Miller, E Appella and CW Anderson (2002) ATM mediates phosphorylation at multiple p53 sites, including Ser(46), in response to ionizing radiation. J Biol Chem 277(15), 12,491-12,494.
144. RS Tibbetts, KM Brumbaugh, JM Williams, JN Sarkaria, WA Cliby, SY Shieh, Y Taya, C Prives and RT Abraham (1999) A role for ATR in the DNA damage-induced phosphorylation of p53. Genes Dev 13(2), 152-157.
145. DV Bulavin, S Saito, MC Hollander, K Sakaguchi, CW Anderson, E Appella and AJ Fornace Jr (1999) Phosphorylation of human p53 by p38 kinase coordinates N-terminal phosphorylation and apoptosis in response to UV radiation. EMBO J 18(23), 6845-6854.
146. T Buschmann, O Potapova, A Bar-Shira, VN Ivanov, SY Fuchs, S Henderson, VA Fried, T Minamoto, D Alarcon-Vargas, MR Pincus, WA Gaarde, NJ Holbrook, Y Shiloh and Z Ronai (2001) Jun NH2-terminal kinase phosphorylation of p53 on Thr-81 is important for p53 stabilization and transcriptional activities in response to stress. Mol Cell Biol 21(8), 2743-2754.
147. SW Lowe, HE Ruley, T Jacks and DE Housman (1993) p53-dependent apoptosis modulates the cytotoxicity of anticancer agents. Cell 74(6), 957-967.
148. E Yonish-Rouach, D Resnitzky, J Lotem, L Sachs, A Kimchi and M Oren (1991) Wild-type p53 induces apoptosis of myeloid leukaemic cells that is inhibited by interleukin-6. Nature 352(6333), 345-347.
149. ML Agarwal, A Agarwal, WR Taylor and GR Stark (1995) p53 controls both the G2/M and the G1 cell cycle checkpoints and mediates reversible growth arrest in human fibroblasts. Proc Natl Acad Sci USA 92(18), 8493-8497.
150. KB Spurgers, DL Gold, KR Coombes, NL Bohnenstiehl, B Mullins, RE Meyn, CJ Logothetis and TJ McDonnell (2006) Identification of cell cycle regulatory genes as principal targets of p53-mediated transcriptional repression. J Biol Chem 281(35), 25,134-25,142.
151. JA Bond, FS Wyllie and D Wynford-Thomas (1994) Escape from senescence in human diploid fibroblasts induced directly by mutant p53. Oncogene 9(7), 1885-1889.
152. V Gire and D Wynford-Thomas (1998) Reinitiation of DNA synthesis and cell division in senescent human fibroblasts by microinjection of anti-p53 antibodies. Mol Cell Biol 18(3), 1611-1621.
153. S Weg-Remers, H Ponta, P Herrlich and H Konig (2001) Regulation of alternative pre-mRNA splicing by the ERK MAP-kinase pathway. EMBO J 20(15), 4194-4203.
154. LJ Ignarro (2000) Nitric oxide : biology and pathobiology. 1st ed San Diego: Academic Press
155. JS Stamler, I Simon, JA Osborne, ME Mullins, O Jaraki, T Michel, DJ Singel and J Loscalzo (1992) S-nitrosylation of proteins with nitric oxide: synthesis and characterization of biologically active compounds. Proc Natl Acad Sci USA 89(1), 444-448.
156. DT Hess, A Matsumoto, SO Kim, HE Marshall and JS Stamler (2005) Protein S-nitrosylation: purview and parameters. Nat Rev Mol Cell Biol 6(2), 150-166.
157. A Nott, PM Watson, JD Robinson, L Crepaldi and A Riccio (2008) S-nitrosylation of histone deacetylase 2 induces chromatin remodelling in neurons. Nature 455(7211), 411-415.
158. F Okumura, DJ Lenschow and DE Zhang (2008) Nitrosylation of ISG15 prevents the disulfide bond mediated dimerization of ISG15 and contributes to effective ISGylation. J Biol Chem 283(36), 24,484-24,488.
159. J Fan, X Yang, W Wang, WHR Wood, KG Becker and M Gorospe (2002) Global analysis of stress-regulated mRNA turnover by using cDNA arrays. Proc Natl Acad Sci USA 99(16), 10,611-10,616.
160. DP Bartel (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2), 281-297.
161. K Abdelmohsen, Y Kuwano, HH Kim and M Gorospe (2008) Posttranscriptional gene regulation by RNA-binding proteins during oxidative stress: implications for cellular senescence. Biol Chem 389(3), 243-255.
162. M Selbach, B Schwanhausser, N Thierfelder, Z Fang, R Khanin and N Rajewsky (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455(7209), 58-63.
163. D Baek, J Villen, C Shin, FD Camargo, SP Gygi and DP Bartel (2008) The impact of microRNAs on protein output. Nature 455(7209), 64-71.
164. KV Prasanth and DL Spector (2007) Eukaryotic regulatory RNAs: an answer to the “genome complexity” conundrum. Genes Dev 21(1), 11-42.
165. G Meister and T Tuschl (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431(7006), 343-349.
166. DE Golden, VR Gerbasi and EJ Sontheimer (2008) An inside job for siRNAs. Mol Cell 31(3), 309-312.
167. BP Lewis, IH Shih, MW Jones-Rhoades, DP Bartel and CB Burge (2003) Prediction of mammalian microRNA targets. Cell 115(7), 787-798.
168. A Grimson, KK Farh, WK Johnston, P Garrett-Engele, LP Lim and DP Bartel (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27(1), 91-105.
169. L He, X He, LP Lim, E de Stanchina, Z Xuan, Y Liang, W Xue, L Zender, J Magnus, D Ridzon, AL Jackson, PS Linsley, C Chen, SW Lowe, MA Cleary and GJ Hannon (2007) A microRNA component of the p53 tumour suppressor network. Nature 447(7148), 1130-1134.
170. M Yamakuchi, M Ferlito and CJ Lowenstein (2008) miR-34a repression of SIRT1 regulates apoptosis. Proc Natl Acad Sci USA 105(36), 13,421-13,426.
171. CJ Marsit, K Eddy and KT Kelsey (2006) MicroRNA responses to cellular stress. Cancer Res 66(22), 10,843-10,848.
172. R Kulshreshtha, M Ferracin, SE Wojcik, R Garzon, H Alder, FJ Agosto-Perez, R Davuluri, CG Liu, CM Croce, M Negrini, GA Calin and M Ivan (2007) A microRNA signature of hypoxia. Mol Cell Biol 27(5), 1859-1867.
173. H Ishii and T Saito (2006) Radiation-induced response of micro RNA expression in murine embryonic stem cells. Med Chem 2(6), 555-563.
174. OC Maes, J An, H Sarojini, H Wu and E Wang (2008) Changes in MicroRNA expression patterns in human fibroblasts after low-LET radiation. J Cell Biochem 105(3), 824-834.
175. J Lu, G Getz, EA Miska, E Alvarez-Saavedra, J Lamb, D Peck, A Sweet-Cordero, BL Ebert, RH Mak, AA Ferrando, JR Downing, T Jacks, HR Horvitz and TR Golub (2005) MicroRNA expression profiles classify human cancers. Nature 435(7043), 834-838.
176. W Yu, D Gius, P Onyango, K Muldoon-Jacobs, J Karp, AP Feinberg and H Cui (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451(7175), 202-206.
177. S Hellwig and BL Bass (2008) A starvation-induced noncoding RNA modulates expression of Dicer-regulated genes. Proc Natl Acad Sci USA 105(35), 12,897-12,902.
178. PJ Westfall, JC Patterson, RE Chen and J Thorner (2008) Stress resistance and signal fidelity independent of nuclear MAPK function. Proc Natl Acad Sci USA 105(34), 12,212-12,217.
179. JC Venter, MD Adams, GG Sutton, AR Kerlavage, HO Smith and M Hunkapiller (1998) Shotgun sequencing of the human genome. Science 280(5369), 1540-1542.
180. Shendure JA, Porreca GJ, Church GM. Overview of DNA sequencing strategies. Curr Protoc Mol Biol 2008. Chapter 7, Unit 7.1.
181. M Schena, D Shalon, RW Davis and PO Brown (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235), 467-470.
182. M Walles, C Gauvin, PE Morin, R Panetta and J Ducharme (2007) Comparison of sub-2-microm particle columns for fast metabolite ID. J Sep Sci 30(8), 1191-1199.
183. AD Patterson, H Li, GS Eichler, KW Krausz, JN Weinstein, AJ Fornace Jr, FJ Gonzalez and JR Idle (2008) UPLC-ESI-TOFMS-based metabolomics and gene expression dynamics inspector self-organizing metabolomic maps as tools for understanding the cellular response to ionizing radiation. Anal Chem 80(3), 665-674.
184. DC Dominguez, R Lopes and ML Torres (2007) Proteomics technology. Clin Lab Sci 20(4), 239-244.
185. J Schneider-Mergener (2001) Synthetic Peptide and Protein Domain Arrays Prepared by the SPOT Technology. Comp Funct Genomics 2(5), 307-309.
186. JC Liao, R Boscolo, YL Yang, LM Tran, C Sabatti and VP Roychowdhury (2003) Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci USA 100(26), 15,522-15,527.
187. JK Lee, DM Havaleshko, H Cho, JN Weinstein, EP Kaldjian, J Karpovich, A Grimshaw and D Theodorescu (2007) A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery. Proc Natl Acad Sci USA 104(32), 13,086-13,091.
188. FP Roth, JD Hughes, PW Estep and GM Church (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16(10), 939-945.
189. G Getz, H Gal, I Kela, DA Notterman and E Domany (2003) Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data. Bioinformatics 19(9), 1079-1089.
190. DR Hyduke, L Rohlin, KC Kao and JC Liao (2003) A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3), 227-234.
191. A Subramanian, P Tamayo, VK Mootha, S Mukherjee, BL Ebert, MA Gillette, A Paulovich, SL Pomeroy, TR Golub, ES Lander and JP Mesirov (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102(43), 15,545-15,550.
192. K Baetz, L McHardy, K Gable, T Tarling, D Reberioux, J Bryan, RJ Andersen, T Dunn, P Hieter and M Roberge (2004) Yeast genome-wide drug-induced haploinsufficiency screen to determine drug mode of action. Proc Natl Acad Sci USA 101(13), 4525-4530.
193. M Ronen, R Rosenberg, BI Shraiman and U Alon (2002) Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci USA 99(16), 10,555-10,560.
194. EA Winzeler, DD Shoemaker, A Astromoff, H Liang, K Anderson, B Andre, R Bangham, R Benito, JD Boeke, H Bussey, AM Chu, C Connelly, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285(5429), 901-906.
195. DR Hyduke, LR Jarboe, LM Tran, KJ Chou and JC Liao (2007) Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli. Proc Natl Acad Sci USA 104(20), 8484-8489.
196. LR Jarboe, DR Hyduke, LM Tran, KJ Chou and JC Liao (2008) Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis. J Biol Chem 283(8), 5148-5157.
197. JC Liao (1993) Modelling and analysis of metabolic pathways. Curr Opin Biotechnol 4(2), 211-216.
198. JM Savinell and BO Palsson (1992) Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods. J Theor Biol 155(2), 201-214.
199. MA Savageau (1969) Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. J Theor Biol 25(3), 370-379.
200. A Sorribas and MA Savageau (1989) Strategies for representing metabolic pathways within biochemical systems theory: reversible pathways. Math Biosci 94(2), 239-269.
201. G Stephanopoulos (1994) Metabolic engineering. Curr Opin Biotechnol 5(2), 196-200.
202. J Pramanik and JD Keasling (1998) Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model. Biotechnol Bioeng 60(2), 230-238.
203. T Ideker, V Thorsson, JA Ranish, R Christmas, J Buhler, JK Eng, R Bumgarner, DR Goodlett, R Aebersold and L Hood (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292(5518), 929-934.
204. CT Workman, HC Mak, S McCuine, JB Tagne, M Agarwal, O Ozier, TJ Begley, LD Samson and T Ideker (2006) A systems approach to mapping DNA damage response pathways. Science 312(5776), 1054-1059.
205. GW Birrell, G Giaever, AM Chu, RW Davis and JM Brown (2001) A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity. Proc Natl Acad Sci USA 98(22), 12,608-12,613.
206. JC Game, GW Birrell, JA Brown, T Shibata, C Baccari, AM Chu, MS Williamson and JM Brown (2003) Use of a genome-wide approach to identify new genes that control resistance of Saccharomyces cerevisiae to ionizing radiation. Radiat Res 160(1), 14-24.
207. W Lee, RP St Onge, M Proctor, P Flaherty, MI Jordan, AP Arkin, RW Davis, C Nislow and G Giaever (2005) Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet 1(2), e24.
208. GW Birrell, JA Brown, HI Wu, G Giaever, AM Chu, RW Davis and JM Brown (2002) Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc Natl Acad Sci USA 99(13), 8778-8783.
209. MR Said, TJ Begley, AV Oppenheim, DA Lauffenburger and LD Samson (2004) Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 101(52), 18,006-18,011.
210. S Mousses, NJ Caplen, R Cornelison, D Weaver, M Basik, S Hautaniemi, AG Elkahloun, RA Lotufo, A Choudary, ER Dougherty, E Suh and O Kallioniemi (2003) RNAi microarray analysis in cultured mammalian cells. Genome Res 13(10), 2341-2347.
211. ES Lander, LM Linton, B Birren, C Nusbaum, MC Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh, R Funke, D Gage, K Harris, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409(6822), 860-921.
212. JC Venter, MD Adams, EW Myers, PW Li, RJ Mural, GG Sutton, HO Smith, M Yandell, CA Evans, RA Holt, JD Gocayne, P Amanatides, et al. (2001) The sequence of the human genome. Science 291(5507), 1304-1351.
213. MC Frith, M Pheasant and JS Mattick (2005) The amazing complexity of the human transcriptome. Eur J Hum Genet 13(8), 894-897.
214. E Birney, JA Stamatoyannopoulos, A Dutta, R Guigo, TR Gingeras, EH Margulies, Z Weng, M Snyder, ET Dermitzakis, RE Thurman, MS Kuehn, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146), 799-816.
215. Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA, Stratton MR. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet 2008. Chapter 10, Unit 10.11.
216. GM Euskirchen, JS Rozowsky, CL Wei, WH Lee, ZD Zhang, S Hartman, O Emanuelsson, V Stolc, S Weissman, MB Gerstein, Y Ruan and M Snyder (2007) Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res 17(6), 898-909.
217. YL Yang and JC Liao (2004) Network component analysis of Saccharamyces cerevisiae stress response. Conf Proc IEEE Eng Med Biol Soc 4 2937-2940.
218. A Sweet-Cordero, S Mukherjee, A Subramanian, H You, JJ Roix, C Ladd-Acosta, J Mesirov, TR Golub and T Jacks (2005) An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet 37(1), 48-55.
219. H Hieronymus, J Lamb, KN Ross, XP Peng, C Clement, A Rodina, M Nieto, J Du, K Stegmaier, SM Raj, KN Maloney, J Clardy, WC Hahn, G Chiosis and TR Golub (2006) Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell 10(4), 321-330.
220. J Lamb, ED Crawford, D Peck, JW Modell, IC Blat, MJ Wrobel, J Lerner, JP Brunet, A Subramanian, KN Ross, M Reich, H Hieronymus, G Wei, et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313(5795), 1929-1935.
221. G Wei, D Twomey, J Lamb, K Schlis, J Agarwal, RW Stam, JT Opferman, SE Sallan, ML den Boer, R Pieters, TR Golub and SA Armstrong (2006) Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell 10(4), 331-342.
222. CL Wei, Q Wu, VB Vega, KP Chiu, P Ng, T Zhang, A Shahab, HC Yong, Y Fu, Z Weng, J Liu, XD Zhao, JL Chew, YL Lee, VA Kuznetsov, et al. (2006) A global map of p53 transcription-factor binding sites in the human genome. Cell 124(1), 207-219.
223. K Basso, AA Margolin, G Stolovitzky, U Klein, R Dalla-Favera and A Califano (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 37(4), 382-390.
224. AA Margolin, K Wang, WK Lim, M Kustagi, I Nemenman and A Califano (2006) Reverse engineering cellular networks. Nat Protoc 1(2), 662-671.
225. AA Margolin, I Nemenman, K Basso, C Wiggins, G Stolovitzky, R Dalla Favera and A Califano (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7(Suppl. 1), S7.
226. KM Mani, C Lefebvre, K Wang, WK Lim, K Basso, R Dalla-Favera and A Califano (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol 4 169.
227. SA Amundson, M Bittner, YD Chen, J Trent, P Meltzer and AJ Fornace Jr (1999) Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses. Oncogene 18 3666-3672.
228. SA Amundson, KT Do, S Shahab, M Bittner, P Meltzer, J Trent and AJ Fornace Jr (2000) Identification of potential mRNA biomarkers in peripheral blood lymphocytes for human exposure to ionizing radiation. Radiat Res 154(3), 342-346.
229. SA Amundson, MB Grace, CB McLeland, MW Epperly, A Yeager, Q Zhan, JS Greenberger and AJ Fornace Jr (2004) Human in vivo radiation-induced biomarkers: gene expression changes in radiotherapy patients. Cancer Res 64(18), 6368-6371.
230. SA Amundson, KT Do, LC Vinikoor, RA Lee, CA Koch-Paiz, J Ahn, M Reimers, Y Chen, DA Scudiero, JN Weinstein, JM Trent, ML Bittner, PS Meltzer and AJ Fornace Jr (2008) Integrating global gene expression and radiation survival parameters across the 60 cell lines of the national cancer institute anticancer drug screen. Cancer Res 68(2), 415-424.
231. T Murakami, M Fujimoto, M Ohtsuki and H Nakagawa (2001) Expression profiling of cancer-related genes in human keratinocytes following non-lethal ultraviolet B irradiation. J Dermatol Sci 27(2), 121-129.
232. C Koch-Paiz, SA Amundson, ML Bittner, P Meltzer and AJ Fornace Jr (2004) Functional genomics of UV radiation responses in human cells. Mutat Res 549(1–2), 65-78.
233. AB Scandurro, CW Weldon, YG Figueroa, J Alam and BS Beckman (2001) Gene microarray analysis reveals a novel hypoxia signal transduction pathway in human hepatocellular carcinoma cells. Int J Oncol 19(1), 129-135.
234. SA Jelinsky, P Estep, GM Church and LD Samson (2000) Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: rpn4 links base excision repair with proteasomes. Mol Cell Biol 20 8157-8167.
235. CM Bouton, MA Hossain, LP Frelin, J Laterra and J Pevsner (2001) Microarray analysis of differential gene expression in lead-exposed astrocytes. Toxicol Appl Pharmacol 176(1), 34-53.
236. H Chen, J Liu, BA Merrick and MP Waalkes (2001) Genetic events associated with arsenic-induced malignant transformation: applications of cDNA microarray technology. Mol Carcinog 30(2), 79-87.
237. Y Momose and H Iwahashi (2001) Bioassay of cadmium using a DNA microarray: genome-wide expression patterns of Saccharomyces cerevisiae response to cadmium. Environ Toxicol Chem 20(10), 2353-2360.
238. A Monks, D Scudiero, P Skehan, R Shoemaker, K Paull, D Vistica, C Hose, J Langley, P Cronise, A Vaigro-Wolff, et al. (1991) Feasibility of a high-flux anticancer drug screen using a diverse panel of cultured human tumor cell lines. J Natl Cancer Inst 83(11), 757-766.
239. SA Amundson, TG Myers, D Scudiero, S Kitada, JC Reed and AJ Fornace Jr (2000) An informatics approach identifying markers of chemosensitivity in human cancer cell lines. Cancer Res 60 6101-6110.
240. DT Ross, U Scherf, MB Eisen, CM Perou, C Rees, P Spellman, V Iyer, SS Jeffrey, R.M. Van dRM, M Waltham, A Pergamenschikov, et al. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24(3), 227-235.
241. U Scherf, DT Ross, M Waltham, LH Smith, JK Lee, L Tanabe, KW Kohn, WC Reinhold, TG Myers, DT Andrews, DA Scudiero, MB Eisen, et al. (2000) A gene expression database for the molecular pharmacology of cancer. Nat Genet 24(3), 236-244.
242. JE Staunton, DK Slonim, HA Coller, P Tamayo, MJ Angelo, J Park, U Scherf, JK Lee, WO Reinhold, JN Weinstein, JP Mesirov, ES Lander and TR Golub (2001) Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci USA 98(19), 10,787-10,792.
243. AV Roschke, G Tonon, KS Gehlhaus, N McTyre, KJ Bussey, S Lababidi, DA Scudiero, JN Weinstein and IR Kirsch (2003) Karyotypic complexity of the NCI-60 drug-screening panel. Cancer Res 63(24), 8634-8647.
244. KJ Bussey, K Chin, S Lababidi, M Reimers, WC Reinhold, WL Kuo, F Gwadry, Ajay, H Kouros-Mehr, J Fridlyand, A Jain, C Collins, et al. (2006) Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther 5(4), 853-867.
245. JN Weinstein (2006) Spotlight on molecular profiling: “Integromic” analysis of the NCI-60 cancer cell lines. Mol Cancer Ther 5(11), 2601-2605.
246. UT Shankavaram, WC Reinhold, S Nishizuka, S Major, D Morita, KK Chary, MA Reimers, U Scherf, A Kahn, D Dolginow, J Cossman, et al. (2007) Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol Cancer Ther 6(3), 820-832.
247. RH Shoemaker (2006) The NCI60 human tumour cell line anticancer drug screen. Nat Rev Cancer 6(10), 813-823.
248. C Alfarano, CE Andrade, K Anthony, N Bahroos, M Bajec, K Bantoft, D Betel, B Bobechko, K Boutilier, E Burgess, K Buzadzija, R Cavero, et al. (2005) The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res 33(Database issue), D418-D424.
249. C Jiang, Z Xuan, F Zhao and MQ Zhang (2007) TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res 35(Database issue), D137-D140.
250. B Ren, H Cam, Y Takahashi, T Volkert, J Terragni, RA Young and BD Dynlacht (2002) E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev 16(2), 245-256.
251. S Ishida, E Huang, H Zuzan, R Spang, G Leone, M West and JR Nevins (2001) Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol Cell Biol 21(14), 4684-4699.
252. SA Amundson Jr, KT Do, L Vinikoor, CA Koch-Paiz, ML Bittner, JM Trent, P Meltzer and AJ Fornace (2005) Stress-specific signatures: expression profiling of p53 wild-type and -null human cells. Oncogene 24(28), 4572-4579.
253. V Detours, L Delys, F Libert, D Weiss Solis, T Bogdanova, JE Dumont, B Franc, G Thomas and C Maenhaut (2007) Genome-wide gene expression profiling suggests distinct radiation susceptibilities in sporadic and post-Chernobyl papillary thyroid cancers. Br J Cancer 97(6), 818-825.
254. SE Wang, B Xiang, M Guix, MG Olivares, J Parker, CH Chung, A Pandiella and CL Arteaga (2008) Transforming Growth Factor beta Engages TACE and ErbB3 To Activate Phosphatidylinositol-3 Kinase/Akt in ErbB2-Overexpressing Breast Cancer and Desensitizes Cells to Trastuzumab. Mol Cell Biol 28(18), 5605-5620.
255. CJ Creighton, A Casa, Z Lazard, S Huang, A Tsimelzon, SG Hilsenbeck, CK Osborne and AV Lee (2008) Insulin-like growth factor-I activates gene transcription programs strongly associated with poor breast cancer prognosis. J Clin Oncol 26(25), 4078-4085.
256. I Tirosh and N Barkai (2008) Two strategies for gene regulation by promoter nucleosomes. Genome Res 18(7), 1084-1091.
257. JN Weinstein (2004) Integromic analysis of the NCI-60 cancer cell lines. Breast Dis 19 11-22.
258. IM Stylianou, JP Affourtit, KR Shockley, RY Wilpan, FA Abdi, S Bhardwaj, J Rollins, GA Churchill and B Paigen (2008) Applying gene expression, proteomics and single-nucleotide polymorphism analysis for complex trait gene identification. Genetics 178(3), 1795-1805.
259. MY Hirai, M Yano, DB Goodenowe, S Kanaya, T Kimura, M Awazuhara, M Arita, T Fujiwara and K Saito (2004) Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci USA 101(27), 10,205-10,210.
260. PE Blower, JH Chung, JS Verducci, S Lin, JK Park, Z Dai, CG Liu, TD Schmittgen, WC Reinhold, CM Croce, JN Weinstein and W Sadee (2008) MicroRNAs modulate the chemosensitivity of tumor cells. Mol Cancer Ther 7(1), 1-9.
261. PE Blower, JS Verducci, S Lin, J Zhou, JH Chung, Z Dai, CG Liu, W Reinhold, PL Lorenzi, EP Kaldjian, CM Croce, JN Weinstein and W Sadee (2007) MicroRNA expression profiles for the NCI-60 cancer cell panel. Mol Cancer Ther 6(5), 1483-1491.
262. WC Reinhold, MA Reimers, AK Maunakea, S Kim, S Lababidi, U Scherf, UT Shankavaram, MS Ziegler, C Stewart, H Kouros-Mehr, H Cui, et al. (2007) Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells. Mol Cancer Ther 6(2), 391-403.
263. EV Stevens, S Nishizuka, S Antony, M Reimers, S Varma, L Young, PJ Munson, JN Weinstein, EC Kohn and Y Pommier (2008) Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers. Mol Cancer Ther 7(1), 10-18.
264. JN Weinstein and Y Pommier (2003) Transcriptomic analysis of the NCI-60 cancer cell lines. C R Biol 326(10–11), 909-920.