Skip to main content
SpringerLink
Log in

Cancer Systems Biology

  • Chapter
  • First Online:
Handbook of Statistical Bioinformatics

Part of the book series: Springer Handbooks of Computational Statistics ((SHCS))

Abstract

Cancer is a complex disease, resulting from system-wide interactions of biological processes rather than from any single underlying cause. The processes that drive all cancer development and progression have been termed the ‘hallmarks of cancer’. With the growth of large-scale measurements of numerous molecular and cellular properties, a new approach, cancer systems biology, to understanding the interrelationship between the hallmarks is presently being developed. Cancer systems biology focuses on systems-level analysis and presently strives to develop novel data integration and analysis techniques to model and infer cancer biology and treatment response.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Ach, R. A., Wang, H., & Curry, B. (2008). Measuring micrornas: Comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC Biotechnology, 8, 69.

    Article  Google Scholar 

  2. Ahmed, F., Steele, J. C., Herbert, J. M. J., Steven, N. M., & Bicknell, R. (2008, September). Tumor stroma as a target in cancer. Current Cancer Drug Targets, 8(6), 447–453.

    Google Scholar 

  3. Al-Hajj, M., Wicha, M. S., Benito-Hernandez, A., Morrison, S. J., & Clarke, M. F. (2003, April 1). Prospective identification of tumorigenic breast cancer cells. Proceedings of the National Academy of Sciences of the United States of America, 100(7), 3983–3988.

    Google Scholar 

  4. Alberts, B. (2008). Molecular biology of the cell (5th ed.). New York: Garland Science.

    Google Scholar 

  5. Albini, A., & Sporn, M. B. (2007, February). The tumour microenvironment as a target for chemoprevention. Nature Reviews. Cancer, 7(2), 139–147.

    Google Scholar 

  6. Ali, S., & Ali, S. (2007, October 15). Role of c-KIT/SCF in cause and treatment of gastrointestinal stromal tumors (GIST). Gene, 401(1–2), 38–45.

    Google Scholar 

  7. Allison, D. B., Cui, X., Page, G. P., & Sabripour, M. (2006, January). Microarray data analysis: From disarray to consolidation and consensus. Nature Reviews. Genetics, 7(1), 55–65.

    Google Scholar 

  8. Alter, O., Brown, P. O., & Botstein, D. (2000, August 29). Singular value decomposition for genome-wide expression data processing and modeling. Proceedings of the National Academy of Sciences of the United States of America, 97(18), 10101–10106.

    Google Scholar 

  9. Anderson, A. R. A., & Quaranta, V. (2008, March). Integrative mathematical oncology. Nature Reviews. Cancer, 8(3), 227–234.

    Google Scholar 

  10. Anderson, A. R. A., Weaver, A. M., Cummings, P. T., & Quaranta, V. (2006, December 1). Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment. Cell, 127(5), 905–915.

    Google Scholar 

  11. Bacac, M., Provero, P., Mayran, N., Stehle, J.-C., Fusco, C., & Stamenkovic, I. (2006). A mouse stromal response to tumor invasion predicts prostate and breast cancer patient survival. PLoS ONE, 1, e32.

    Article  Google Scholar 

  12. Baggerly, K. A., Morris, J. S., Edmonson, S. R., & Coombes, K. R. (2005, February). Signal in noise: Evaluating reported reproducibility of serum proteomic tests for ovarian cancer. Journal of the National Cancer Institute, 97(4), 307–309.

    Google Scholar 

  13. Baker, S. G.,& Kramer, B. S. (2008, October). Using microarrays to study the microenvironment in tumor biology: The crucial role of statistics. Seminars in Cancer Biology, 18(5), 305–310.

    Google Scholar 

  14. Barrett, T., Troup, D. B., Wilhite, S. E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I. F., Soboleva, A., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., Muertter, R. N., & Edgar, R. (2009, January). NCBI GEO: Archive for high-throughput functional genomic data. Nucleic Acids Research, 37(Database issue), D885–D890.

    Google Scholar 

  15. Bauch, A., & Superti-Furga, G. (2006, April). Charting protein complexes, signaling pathways, and networks in the immune system. Immunological Reviews, 210, 187–207.

    Google Scholar 

  16. Baylin, S. B., & Ohm, J. E. (2006, February). Epigenetic gene silencing in cancer – a mechanism for early oncogenic pathway addiction? Nature Reviews. Cancer, 6(2), 107–116.

    Google Scholar 

  17. Beerenwinkel, N., Antal, T., Dingli, D., Traulsen, A., Kinzler, K. W., Velculescu, V. E., Vogelstein, B., & Nowak, M. A. (2007). Genetic progression and the waiting time to cancer. PLoS Computational Biology, 3(11), e225.

    Article  MathSciNet  Google Scholar 

  18. Behmoaram, E., Bijian, K., Bismar, T. A., & Alaoui-Jamali, M. A. (2008). Early stage cancer cell invasion: Signaling, biomarkers and therapeutic targeting. Frontiers in Bioscience, 13, 6314–6325.

    Article  Google Scholar 

  19. Bernard, A., & Hartemink, A. J. (2005). Informative structure priors: Joint learning of dynamic regulatory networks from multiple types of data. Pacific Symposium on Biocomputing, 10, 459–470.

    Article  Google Scholar 

  20. Bibikova, M., Lin, Z., Zhou, L., Chudin, E., Garcia, E. W., Wu, B., Doucet, D., Thomas, N. J., Wang, Y., Vollmer, E., Goldmann, T., Seifart, C., Jiang, W., Barker, D. L., Chee, M. S., Floros, J., & Fan, J.-B. (2006, March). High-throughput DNA methylation profiling using universal bead arrays. Genome Research, 16(3), 383–393.

    Google Scholar 

  21. Bidaut, G., Suhre, K., Claverie, J.-M., & Ochs, M. F. (2006). Determination of strongly overlapping signaling activity from microarray data. BMC Bioinformatics, 7, 99.

    Article  Google Scholar 

  22. Bleyer, A., Barr, R., Hayes-Lattin, B., Thomas, D., Ellis, C., & Anderson, B. (2008, April). The distinctive biology of cancer in adolescents and young adults. Nature Reviews. Cancer, 8(4), 288–298.

    Google Scholar 

  23. Blow, J. J., & Gillespie, P. J. (2008, October). Replication licensing and cancer–a fatal entanglement? Nature Reviews. Cancer, 8(10), 799–806.

    Google Scholar 

  24. Bock, C., & Lengauer, T. (2008, January 1). Computational epigenetics. Bioinformatics, 24(1), 1–10.

    Google Scholar 

  25. Bodenreider, O., & Stevens, R. (2006, September). Bio-ontologies: Current trends and future directions. Brief Bioinformatics, 7(3), 256–274.

    Google Scholar 

  26. Brazhnik, P., de la Fuente, A., & Mendes, P. (2002). Gene networks: How to put the function in genomics. Trends Biotechnology, 20(11), 467–472.

    Article  Google Scholar 

  27. Brown, M. P., Grundy, W. N., Lin, D., Cristianini, N., Sugnet, C. W., Furey, T. S., Ares, M., Jr., & Haussler, D. (2000, January 4). Knowledge-based analysis of microarray gene expression data by using support vector machines. Proceedings of the National Academy of Sciences of the United States of America, 97(1), 262–267.

    Google Scholar 

  28. Cai, L., Dalal, C. K., & Elowitz, M. B. (2008, September 25). Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature, 455(7212), 485–490.

    Google Scholar 

  29. Cairns, R. A., Khokha, R., & Hill, R. P. (2003, November). Molecular mechanisms of tumor invasion and metastasis: An integrated view. Current Molecular Medicine, 3(7), 659–671.

    Google Scholar 

  30. Camacho, D., Vera Licona, P., Mendes, P., & Laubenbacher, R. (2007, December). Comparison of reverse-engineering methods using an in silico network. Annals of the New York Academy of Sciences, 1115, 73–89,.

    Google Scholar 

  31. Carvalho, C. M., Chang, J., Lucas, J., Nevins, J. R., Wang, Q., & West, M. (2008). High-dimensional sparse factor modelling: Applications in gene expression genomics. Journal of the American Statistical Association, 103, 1438–1456.

    Article  MathSciNet  Google Scholar 

  32. Chiang, A. C., & Massague, J. (2008, December 25). Molecular basis of metastasis. The New England Journal of Medicine, 359(26), 2814–2823.

    Google Scholar 

  33. Clasper, S., Royston, D., Baban, D., Cao, Y., Ewers, S., Butz, S., Vestweber, D., & Jackson, D. G. (2008, September 15). A novel gene expression profile in lymphatics associated with tumor growth and nodal metastasis. Cancer Research, 68(18), 7293–7303.

    Google Scholar 

  34. Claverie, J. M. (1999). Computational methods for the identification of differential and coordinated gene expression. Human Molecular Genetics, 8(10), 1821–1832.

    Article  Google Scholar 

  35. Croce, C. M. (2008, January 31). Oncogenes and cancer. The New England Journal of Medicine, 358(5), 502–511.

    Google Scholar 

  36. Crosby, M. E., Kulshreshtha, R., Ivan, M., & Glazer, P. M. (2009, February 1). MicroRNA regulation of DNA repair gene expression in hypoxic stress. Cancer Research, 69(3), 1221–1229.

    Google Scholar 

  37. De Wever, O., Demetter, P., Mareel, M., & Bracke, M. (2008, November 15). Stromal myofibroblasts are drivers of invasive cancer growth. International Journal of Cancer, 123(10), 2229–2238.

    Google Scholar 

  38. Dick, J. E. (2008, December 15). Stem cell concepts renew cancer research. Blood, 112(13), 4793–4807.

    Google Scholar 

  39. Draghici, S., Khatri, P., Bhavsar, P., Shah, A., Krawetz, S. A., & Tainsky, M. A. (2003, July). Onto-tools, the toolkit of the modern biologist: Onto-express, onto-compare, onto-design and onto-translate. Nucleic Acids Research, 31(13), 3775–3781.

    Google Scholar 

  40. Duesberg, P., & Li, R. (2003, May-June). Multistep carcinogenesis: A chain reaction of aneuploidizations. Cell Cycle, 2(3), 202–210.

    Google Scholar 

  41. Dupuy, A., & Simon, R. M. (2007, January 17). Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. Journal of the National Cancer Institute, 99(2), 147–157.

    Google Scholar 

  42. Dvorak, H. F. (1986, December 25). Tumors: Wounds that do not heal. similarities between tumor stroma generation and wound healing. The New England Journal of Medicine, 315(26), 1650–1659.

    Google Scholar 

  43. Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998, December 8). Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America, 95(25), 14863–14868.

    Google Scholar 

  44. Eklund, A. C., & Szallasi, Z. (2008). Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biology, 9(2), R26.

    Article  Google Scholar 

  45. Eyler, C. E., & Rich, J. N. (2008, June 10). Survival of the fittest: Cancer stem cells in therapeutic resistance and angiogenesis. Journal of Clinical Oncology, 26(17), 2839–2845.

    Google Scholar 

  46. Fearon, E. R., & Vogelstein, B. (1990, June 1). A genetic model for colorectal tumorigenesis. Cell, 61(5), 759–767.

    Google Scholar 

  47. Feinberg, A. P., Ohlsson, R., & Henikoff, S. (2006, January). The epigenetic progenitor origin of human cancer. Nature Reviews. Genetics, 7(1), 21–33.

    Google Scholar 

  48. Feinberg, A. P., & Tycko, B. (2004, February). The history of cancer epigenetics. Nature Reviews. Cancer, 4(2), 143–153.

    Google Scholar 

  49. Finak, G., Bertos, N., Pepin, F., Sadekova, S., Souleimanova, M., Zhao, H., Chen, H., Omeroglu, G., Meterissian, S., Omeroglu, A., Hallett, M., & Park, M. (2008, May). Stromal gene expression predicts clinical outcome in breast cancer. Nature Medicine, 14(5), 518–527.

    Google Scholar 

  50. Finkel, T., Serrano, M., & Blasco, M. A. (2007, August 16). The common biology of cancer and ageing. Nature, 448(7155), 767–774.

    Google Scholar 

  51. Folkman, J. (2006). Angiogenesis. Annual Review of Medicine, 57, 1–18.

    Article  Google Scholar 

  52. Frisk, T., Foukakis, T., Dwight, T., Lundberg, J., Hoog, A., Wallin, G., Eng, C., Zedenius, J., & Larsson, C. (2002, September). Silencing of the pten tumor-suppressor gene in anaplastic thyroid cancer. Genes Chromosomes Cancer, 35(1), 74–80.

    Google Scholar 

  53. Gao, P., Honkela, A., Rattray, M., & Lawrence, N. D. (2008, August 15). Gaussian process modelling of latent chemical species: Applications to inferring transcription factor activities. Bioinformatics, 24(16), i70–i75.

    Google Scholar 

  54. Gargiulo, G., & Minucci, S. (2009). Epigenomic profiling of cancer cells. International Journal of Biochemistry and Cell Biology, 41(1), 127–135.

    Article  Google Scholar 

  55. Gatenby, R. A., & Vincent, T. L. (2003, October 1). An evolutionary model of carcinogenesis. Cancer Research, 63(19), 6212–6220.

    Google Scholar 

  56. Ge, H., Walhout, A. J. M., & Vidal, M. (2003, October). Integrating ‘omic’ information: A bridge between genomics and systems biology. Trends in Genetics, 19(10), 551–560.

    Google Scholar 

  57. Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A. J., Sawitzki, G., Smith, C., Smyth, G., Tierney, L., Yang, J. Y., & Zhang, J. (2004). Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology, 5(10), R80.

    Article  Google Scholar 

  58. Gevertz, J. L., & Torquato, S., (2006, December 21). Modeling the effects of vasculature evolution on early brain tumor growth. Journal of Theoretical Biology, 243(4), 517–531.

    Google Scholar 

  59. Ghosh, D., & Chinnaiyan, A. M. (2009, January). Genomic outlier profile analysis: Mixture models, null hypotheses, and nonparametric estimation. Biostatistics, 10(1), 60–69.

    Google Scholar 

  60. Giehl, K., & Menke, A. (2008). Microenvironmental regulation of E-Cadherin-mediated adherens junctions. Frontiers in Bioscience, 13, 3975–3985.

    Article  Google Scholar 

  61. Gillespie, D. T. (1976). A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics, 22, 403–434.

    Article  MathSciNet  Google Scholar 

  62. Gius, D., & Spitz, D. R. (2006, July-August). Redox signaling in cancer biology. Antioxid Redox Signal, 8(7–8), 1249–1252.

    Google Scholar 

  63. Greenman, C., Stephens, P., Smith, R., Dalgliesh, G. L., Hunter, C., Bignell, G., Davies, H., Teague, J., Butler, A., Stevens, C., Edkins, S., O’Meara, S., Vastrik, I., Schmidt, E. E., Avis, T., Barthorpe, S., Bhamra, G., Buck, G., Choudhury, B., Clements, J., Cole, J., Dicks, E., Forbes, S., Gray, K., Halliday, K., Harrison, R., Hills, K., Hinton, J., Jenkinson, A., Jones, D., Menzies, A., Mironenko, T., Perry, J., Raine, K., Richardson, D., Shepherd, R., Small, A., Tofts, C., Varian, J., Webb, T., West, S., Widaa, S., Yates, A., Cahill, D. P., Louis, D. N., Goldstraw, P., Nicholson, A. G., Brasseur, F., Looijenga, L., Weber, B. L., Chiew, Y.-E., DeFazio, A., Greaves, M. F., Green, A. R., Campbell, P., Birney, E., Easton, D. F., Chenevix-Trench, G., Tan, M.-H., Khoo, S. K., Teh, B. T., Yuen, S. T., Leung, S. Y., Wooster, R., Futreal, P. A., & Stratton, M. R. (2007, March 8). Patterns of somatic mutation in human cancer genomes. Nature, 446(7132), 153–158.

    Google Scholar 

  64. Griffin, T. J., Gygi, S. P., Ideker, T., Rist, B., Eng, J., Hood, L., & Aebersold, R. (2002, April). Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Molecular & Cellular Proteomics, 1(4), 323–333.

    Google Scholar 

  65. Hahn, W. C., & Weinberg, R. A. (2002, November 14). Rules for making human tumor cells. The New England Journal of Medicine, 347(20), 1593–1603.

    Google Scholar 

  66. Hanahan, D., & Weinberg, R. A. (2000). The hallmarks of cancer. Cell, 100(1), 57–70.

    Article  Google Scholar 

  67. Hanawalt, P. C., & Spivak, G. (2008, December). Transcription-coupled DNA repair: Two decades of progress and surprises. Nature Reviews. Molecular Cell Biology, 9(12), 958–970.

    Google Scholar 

  68. Harley, C. B. (2008, March). Telomerase and cancer therapeutics. Nature Reviews. Cancer, 8(3), 167–179.

    Google Scholar 

  69. Hartemink, A. J., Gifford, D. K., Jaakkola, T. S., & Young, R. A. (2001). Maximum likelihood estimate of optimal scaling factors for expression array normalization. SPIE BiOS. Proc SPIE 4266, 132–140.

    Google Scholar 

  70. Hartemink, A. J., Gifford, D. K., Jaakkola, T. S., & Young, R. A. (2001). Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pacific Symposium on Biocomputing, 6, 422–433.

    Google Scholar 

  71. Herbert, J. M. J., Stekel, D., Sanderson, S., Heath, V. L., & Bicknell, R. (2008). A novel method of differential gene expression analysis using multiple cdna libraries applied to the identification of tumour endothelial genes. BMC Genomics, 9, 153.

    Article  Google Scholar 

  72. Herman, J. G., & Baylin, S. B. (2003, November 20). Gene silencing in cancer in association with promoter hypermethylation. The New England Journal of Medicine, 349(21), 2042–2054.

    Google Scholar 

  73. Hornberg, J. J., Bruggeman, F. J., Westerhoff, H. V., & Lankelma, J. (2006, February-March). Cancer: A systems biology disease. Biosystems, 83(2–3), 81–90.

    Google Scholar 

  74. Hua, F., Hautaniemi, S., Yokoo, R., & Lauffenburger, D. A. (2006, August 22). Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways. Journal of The Royal Society Interface, 3(9), 515–526.

    Google Scholar 

  75. Hunter, D. J., Kraft, P., Jacobs, K. B., Cox, D. G., Yeager, M., Hankinson, S. E., Wacholder, S., Wang, Z., Welch, R., Hutchinson, A., Wang, J., Yu, K., Chatterjee, N., Orr, N., Willett, W. C., Colditz, G. A., Ziegler, R. G., Berg, C. D., Buys, S. S., McCarty, C. A., Feigelson, H. S., Calle, E. E., Thun, M. J., Hayes, R. B., Tucker, M., Gerhard, D. S., Fraumeni, J. F., Jr., Hoover, R. N., Thomas, G., & Chanock, S. J. (2007, July). A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nature Genetics, 39(7), 870–874.

    Google Scholar 

  76. Hwang, D., Rust, A. G., Ramsey, S., Smith, J. J., Leslie, D. M., Weston, A. D., de Atauri, P., Aitchison, J. D., Hood, L., Siegel, A. F., & Bolouri, H. (2005, November 29). A data integration methodology for systems biology. Proceedings of the National Academy of Sciences of the United States of America, 102(48), 17296–17301.

    Google Scholar 

  77. Iacobuzio-Donahue, C. A., Ryu, B., Hruban, R. H., & Kern, S. E. (2002, January). Exploring the host desmoplastic response to pancreatic carcinoma: Gene expression of stromal and neoplastic cells at the site of primary invasion. The American Journal of Pathology, 160(1), 91–99.

    Google Scholar 

  78. Irizarry, R. A., Hobbs, B., Collin, F., Beazer-Barclay, Y. D., Antonellis, K. J., Scherf, U., & Speed, T. P. (2003, April). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4(2), 249–264.

    Google Scholar 

  79. Irizarry, R. A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M., Ji, H., Potash, J. B., Sabunciyan, S., & Feinberg, A. P. (2009, February). The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific cpg island shores. Nature Genetics, 41(2), 178–186.

    Google Scholar 

  80. Irmer, D., Funk, J. O., & Blaukat, A. (2007, August 23). EGFR kinase domain mutations – functional impact and relevance for lung cancer therapy. Oncogene, 26(39), 5693–5701.

    Google Scholar 

  81. Jacks, T., & Weinberg, R. A. (2002, December 27). Taking the study of cancer cell survival to a new dimension. Cell, 111(7), 923–925.

    Google Scholar 

  82. Jemal, A., Siegel, R., Ward, E., Hao, Y., Xu, J., Murray, T., & Thun, M. J. (2008, March-April). Cancer statistics. CA: A Cancer Journal for Clinicians, 58(2), 71–96.

    Google Scholar 

  83. Johnson, W. E., Li, C., & Rabinovic, A. (2007, January). Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics, 8(1), 118–127.

    Google Scholar 

  84. Jones, S., Zhang, X., Parsons, D. W., Lin, J. C.-H., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Kamiyama, H., Jimeno, A., Hong, S.-M., Fu, B., Lin, M.-T., Calhoun, E. S., Kamiyama, M., Walter, K., Nikolskaya, T., Nikolsky, Y., Hartigan, J., Smith, D. R., Hidalgo, M., Leach, S. D., Klein, A. P., Jaffee, E. M., Goggins, M., Maitra, A., Iacobuzio-Donahue, C., Eshleman, J. R., Kern, S. E., Hruban, R. H., Karchin, R., Papadopoulos, N., Parmigiani, G., Vogelstein, B., Velculescu, V. E., & Kinzler, K. W. (2008, September 26). Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science, 321(5897), 1801–1806.

    Google Scholar 

  85. Jordan, J. D., Landau, E. M., & Iyengar, R. (2000, October). Signaling networks: The origins of cellular multitasking. Cell, 103, 193–200.

    Google Scholar 

  86. Keniry, M., & Parsons, R. (2008, September 18). The role of PTEN signaling perturbations in cancer and in targeted therapy. Oncogene, 27(41), 5477–5485.

    Google Scholar 

  87. Khalil, I. G., & Hill, C. (2005, January). Systems biology for cancer. Current Opinion in Oncology, 17(1), 44–48.

    Google Scholar 

  88. Khan, J., Wei, J. S., Ringner, M., Saal, L. H., Ladanyi, M., Westermann, F., Berthold, F., Schwab, M., Antonescu, C. R., Peterson, C., & Meltzer, P. S. (2001, June). Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nature Medicine, 7(6), 673–679.

    Google Scholar 

  89. Kholodenko, B. N., Kiyatkin, A., Bruggeman, F. J., Sontag, E., Westerhoff, H. V., & Hoek, J. B. (2002, October 1). Untangling the wires: A strategy to trace functional interactions in signaling and gene networks. Proceedings of the National Academy of Sciences of the United States of America, 99(20), 12841–12846.

    Google Scholar 

  90. Kiberstis, P. A., & Travis, J. (2006). Celebrating a glass half-full. Science, 312, 1157.

    Article  Google Scholar 

  91. Kim, P. M., & Tidor, B. (2003, July). Subsystem identification through dimensionality reduction of large-scale gene expression data. Genome Research, 13(7), 1706–1718.

    Google Scholar 

  92. Kinzler, K. W., & Vogelstein, B. (1996, October 18). Lessons from hereditary colorectal cancer. Cell, 87(2), 159–170.

    Google Scholar 

  93. Knudson, A. G. (1993, December 1). Antioncogenes and human cancer. Proceedings of the National Academy of Sciences of the United States of America, 90(23), 10914–10921.

    Google Scholar 

  94. Kolch, W. (2000). Meaningful relationships: The regulation of the Ras/Raf/MEK/ERK pathway by protein interactions. The Biochemical Journal, 351(Pt. 2), 289–305.

    Article  Google Scholar 

  95. Komarova, N. L., & Wodarz, D. (2004, May 4). The optimal rate of chromosome loss for the inactivation of tumor suppressor genes in cancer. Proceedings of the National Academy of Sciences of the United States of America, 101(18), 7017–7021.

    Google Scholar 

  96. Kossenkov, A. V., Peterson, A. J., & Ochs, M. F. (2007). Determining transcription factor activity from microarray data using Bayesian Markov chain Monte Carlo sampling. Studies in Health Technology and Informatics, 129(Pt. 2), 1250–1254.

    Google Scholar 

  97. Kundu, J. K., & Surh, Y.-J. (2008, July-August). Inflammation: Gearing the journey to cancer. Mutation Research, 659(1–2), 15–30.

    Google Scholar 

  98. Lagasse, E. (2008, January). Cancer stem cells with genetic instability: The best vehicle with the best engine for cancer. Gene Therapy, 15(2), 136–142.

    Google Scholar 

  99. Lahav, G., Rosenfeld, N., Sigal, A., Geva-Zatorsky, N., Levine, A. J., Elowitz, M. B., & Alon, U. (2004, February). Dynamics of the p53-MDM2 feedback loop in individual cells. Nature Genetics, 36(2), 147–150.

    Google Scholar 

  100. Lamy, P., Andersen, C. L., Wikman, F. P., & Wiuf, C. (2006). Genotyping and annotation of Affymetrix SNP arrays. Nucleic Acids Research, 34(14), e100.

    Article  Google Scholar 

  101. Lee, D. D., & Seung, H. S. (1999, October). Learning the parts of objects by non-negative matrix factorization. Nature, 401(6755), 788–791.

    Google Scholar 

  102. Leek, J. T., & Storey, J. D. (2007, September). Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genetics, 3(9), 1724–1735.

    Google Scholar 

  103. Lewis, M. T. (2008, October). Faith, heresy and the cancer stem cell hypothesis. Future Oncology, 4(5), 585–589.

    Google Scholar 

  104. Li, H., Fan, X., & Houghton, J. (2007, July 1). Tumor microenvironment: The role of the tumor stroma in cancer. Journal of Cellular Biochemistry, 101(4), 805–815.

    Google Scholar 

  105. Li, H., Cao, Y., Petzold, L. R., & Gillespie, D. T. (2008). Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnology Progress, 24(1), 56–61.

    Article  Google Scholar 

  106. Lister, R., O’Malley, R. C., Tonti-Filippini, J., Gregory, B. D., Berry, C. C., Millar, A. H., & Ecker, J. R. (2008, May 2). Highly integrated single-base resolution maps of the epigenome in arabidopsis. Cell, 133(3), 523–536.

    Google Scholar 

  107. Liu, E. T., Kuznetsov, V. A., & Miller, L. D. (2006, April). In the pursuit of complexity: Systems medicine in cancer biology. Cancer Cell, 9(4), 245–247.

    Google Scholar 

  108. Liu, H. G., You, J., Pan, Y. F., Hu, X. Q., Huang, D. P., & Zhang, X. H. (2009, January 7). Cancer stem cell hierarchy. Stem Cell Reviews. 5, 174.

    Google Scholar 

  109. Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., & Brown, E. L. (1996, December). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology, 14(13), 1675–1680.

    Google Scholar 

  110. Loeb, L. A., Bielas, J. H., & Beckman, R. A. (2008, May 15). Cancers exhibit a mutator phenotype: Clinical implications. Cancer Research, 68(10), 3551–3557.

    Google Scholar 

  111. Macdonald, F., Ford, C. H. J., & Casson, A. G. (2004). Molecular biology of cancer (2nd ed.). London: BIOS Scientific Publishers.

    Google Scholar 

  112. Mantovani, A. (2009, January 1). Cancer: Inflaming metastasis. Nature, 457(7225), 36–37.

    Google Scholar 

  113. Markevich, N. I., Moehren, G., Demin, O. V., Kiyatkin, A., Hoek, J. B., & Kholodenko, B. N. (2004, June). Signal processing at the Ras circuit: What shapes Ras activation patterns? Systems Biology, IEEE Proceedings, 1(1), 104–113.

    Google Scholar 

  114. Michor, F. (2008). Mathematical models of cancer stem cells. Journal of Clinical Oncology, 26, 2854–2861.

    Article  Google Scholar 

  115. Michor, F., Iwasa, Y., Vogelstein, B., Lengauer, C., & Nowak, M. A. (2005, Feburary). Can chromosomal instability initiate tumorigenesis? Seminars in Cancer Biology, 15(1), 43–49.

    Google Scholar 

  116. Mikkelsen, T. S., Hanna, J., Zhang, X., Ku, M., Wernig, M., Schorderet, P., Bernstein, B. E., Jaenisch, R., Lander, E. S., & Meissner, A. (2008, July 3). Dissecting direct reprogramming through integrative genomic analysis. Nature, 454(7200), 49–55.

    Google Scholar 

  117. Mirmohammadsadegh, A., Marini, A., Nambiar, S., Hassan, M., Tannapfel, A., Ruzicka, T., & Hengge, U. R. (2006, July 1). Epigenetic silencing of the PTEN gene in melanoma. Cancer Research, 66(13), 6546–6552.

    Google Scholar 

  118. Moloshok, T. D., Klevecz, R. R., Grant, J. D., Manion, F. J., Speier, W. F., IV., & Ochs, M. F. (2002). Application of Bayesian decomposition for analysing microarray data. Bioinformatics, 18(4), 566–575.

    Google Scholar 

  119. Morange, M. (2007, December 6). The field of cancer research: An indicator of present transformations in biology. Oncogene, 26(55), 7607–7610.

    Google Scholar 

  120. Mukherjee, S., & Speed, T. P. (2008, September 23). Network inference using informative priors. Proceedings of the National Academy of Sciences of the United States of America, 105(38), 14313–14318.

    Google Scholar 

  121. Nielsen, T. O., West, R. B., Linn, S. C., Alter, O., Knowling, M. A., O’Connell, J. X., Zhu, S., Fero, M., Sherlock, G., Pollack, J. R., Brown, P. O., Botstein, D., & van de Rijn, M. (2002, April 13). Molecular characterisation of soft tissue tumours: A gene expression study. Lancet, 359(9314), 1301–1307.

    Google Scholar 

  122. Norton, L., & Massague, J. (2006, August). Is cancer a disease of self-seeding? Nature Medicine, 12(8), 875–878.

    Google Scholar 

  123. Ochs, M. F., & Godwin, A. K. (2003, March). Microarrays in cancer: Research and applications. Biotechniques, (Suppl.), 34, S4–S15.

    Google Scholar 

  124. Ochs, M. F., Stoyanova, R. S., Arias-Mendoza, F., & Brown, T. R. (1999). A new method for spectral decomposition using a bilinear Bayesian approach. Journal of Magnetic Resonance, 137(1), 161–176.

    Article  Google Scholar 

  125. Ochs, M. F., Rink, L., Tarn, C., Mburu, S., Taguchi, T., Eisenberg, B., & Godwin, A. K. (2009). Detection of treatment-induced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data. Cancer Research, 69(23). 9125–9132.

    Article  Google Scholar 

  126. Overall, C. M., & Lopez-Otin, C. (2002, September). Strategies for MMP inhibition in cancer: Innovations for the post-trial era. Nature Reviews. Cancer, 2(9), 657–672.

    Google Scholar 

  127. Paget, S. (1889). The distribution of secondary growths in cancer of the breast. Lancet, 1, 571–573.

    Article  Google Scholar 

  128. Papin, J. A., Hunter, T., Palsson, B. O., & Subramaniam, S. (2005, February). Reconstruction of cellular signalling networks and analysis of their properties. Nature Reviews. Molecular Cell Biology, 6(2), 99–111.

    Google Scholar 

  129. Parkinson, H., Kapushesky, M., Kolesnikov, N., Rustici, G., Shojatalab, M., Abeygunawardena, N., Berube, H., Dylag, M., Emam, I., Farne, A., Holloway, E., Lukk, M., Malone, J., Mani, R., Pilicheva, E., Rayner, T. F., Rezwan, F., Sharma, A., Williams, E., Bradley, X. Z., Adamusiak, T., Brandizi, M., Burdett, T., Coulson, R., Krestyaninova, M., Kurnosov, P., Maguire, E., Neogi, S. G., Rocca-Serra, P., Sansone, S.-A., Sklyar, N., Zhao, M., Sarkans, U., & Brazma, A. (2009, January). ArrayExpress update–from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Research, 37(Database issue), D868–D872.

    Google Scholar 

  130. Parsons, D. W., Jones, S., Zhang, X., Lin, J. C.-H., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Siu, I.-M., Gallia, G. L., Olivi, A., McLendon, R., Rasheed, B. A., Keir, S., Nikolskaya, T., Nikolsky, Y., Busam, D. A., Tekleab, H., Diaz, L. A., Jr., Hartigan, J., Smith, D. R., Strausberg, R. L., Marie, S. K. N., Shinjo, S. M. O., Yan, H., Riggins, G. J., Bigner, D. D., Karchin, R., Papadopoulos, N., Parmigiani, G., Vogelstein, B., Velculescu, V. E., & Kinzler, K. W. (2008, September 26). An integrated genomic analysis of human glioblastoma multiforme. Science, 321(5897), 1807–1812.

    Google Scholar 

  131. Podhajcer, O. L., Benedetti, L. G., Girotti, M. R., Prada, F., Salvatierra, E., & Llera, A. S. (2008, December). The role of the matricellular protein SPARC in the dynamic interaction between the tumor and the host. Cancer Metastasis Reviews, 27(4), 691–705.

    Google Scholar 

  132. Quackenbush, J. (2001, June). Computational analysis of microarray data. Nature Reviews. Genetics, 2(6), 418–427.

    Google Scholar 

  133. Rajagopalan, H., Nowak, M. A., Vogelstein, B., & Lengauer, C. (2003, September). The significance of unstable chromosomes in colorectal cancer. Nature Reviews. Cancer, 3(9), 695–701.

    Google Scholar 

  134. Reya, T., Morrison, S. J., Clarke, M. F., & Weissman, I. L. (2001, November 1). Stem cells, cancer, and cancer stem cells. Nature, 414(6859), 105–111.

    Google Scholar 

  135. Ribba, B., Saut, O., Colin, T., Bresch, D., Grenier, E., & Boissel, J. P. (2006, December 21). A multiscale mathematical model of avascular tumor growth to investigate the therapeutic benefit of anti-invasive agents. Journal of Theoretical Biology, 243(4), 532–541.

    Google Scholar 

  136. Ricke, R. M., van Ree, J. H., & van Deursen, J. M. (2008, September). Whole chromosome instability and cancer: A complex relationship. Trends in Genetics, 24(9), 457–466.

    Google Scholar 

  137. Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D., Dai, H., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., & Friend, S. H. (2000, February 4). Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science, 287(5454), 873–880.

    Google Scholar 

  138. Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., Van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J. C., Lashkari, D., Shalon, D., Myers, T. G., Weinstein, J. N., Botstein, D., & Brown, P. O. (2000, March). Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics, 24(3), 227–235.

    Google Scholar 

  139. Sachs, K., Perez, O., Pe’er, D., Lauffenburger, D. A., & Nolan, G. P. (2005). Causal protein-signaling networks derived from multiparameter single-cell data. Science, 308(5721), 523–529.

    Article  Google Scholar 

  140. Sahai, E. (2007, October). Illuminating the metastatic process. Nature Reviews. Cancer, 7(10), 737–749.

    Google Scholar 

  141. Sandhu, J. S. (2008, July). Prostate cancer and chronic prostatitis. Current Urology Reports, 9(4), 328–332.

    Google Scholar 

  142. Santos, S. D. M., Verveer, P. J., & Bastiaens, P. I. H. (2007, March). Growth factor-induced MAPK network topology shapes ERK response determining PC-12 cell fate. Nature Cell Biology, 9(3), 324–330.

    Google Scholar 

  143. Saul, Z. M., & Filkov, V. (2007). Exploring biological network structure using exponential random graph models. Bioinformatics, 23(19), 2604–2611.

    Article  Google Scholar 

  144. Sauro, H. M., & Kholodenko, B. N. (2004). Quantitative analysis of signaling networks. Progress in Biophysics and Molecular Biology, 86, 5–43.

    Article  Google Scholar 

  145. Schadt, E. E., Li, C., Ellis, B., & Wong, W. H. (2001). Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. Journal of Cellular Biochemistry. Supplement, (Suppl. 37), 120–125.

    Google Scholar 

  146. Schena, M., Shalon, D., Davis, R. W., & Brown, P. O. (1995, October 20). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270(5235), 467–470.

    Google Scholar 

  147. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. O., & Davis, R. W. (1996, October 1). Parallel human genome analysis: Microarray-based expression monitoring of 1,000 genes. Proceedings of the National Academy of Sciences of the United States of America, 93(20), 10614–10619.

    Google Scholar 

  148. Schrader, A. J., Lechner, O., Templin, M., Dittmar, K. E. J., Machtens, S., Mengel, M., Probst-Kepper, M., Franzke, A., Wollensak, T., Gatzlaff, P., Atzpodien, J., Buer, J., & Lauber, J. (2002, April 22). CXCR4/CXCL12 expression and signalling in kidney cancer. British Journal of Cancer, 86(8), 1250–1256.

    Google Scholar 

  149. Segal, E., Yelensky, R., & Koller, D. (2003). Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics, 19(Suppl. 1), i273–i282.

    Article  Google Scholar 

  150. Sell, S. (2007, January). Cancer and stem cell signaling: A guide to preventive and therapeutic strategies for cancer stem cells. Stem Cell Reviews, 3(1), 1–6.

    Google Scholar 

  151. Sharma, S. V., Bell, D. W., Settleman, J., & Haber, D. A. (2007, March). Epidermal growth factor receptor mutations in lung cancer. Nature Reviews. Cancer, 7(3), 169–181.

    Google Scholar 

  152. Shipitsin, M., & Polyak, K. (2008, May). The cancer stem cell hypothesis: In search of definitions, markers, and relevance. Laboratory Investigation, 88(5), 459–463.

    Google Scholar 

  153. Simpson, R. J., & Dorow, D. S. (2001). Cancer proteomics: From signaling networks to tumor markers. Trends in Biotechnology, 19(Suppl. 10), S40–S48.

    Article  Google Scholar 

  154. Singh, S. K., Clarke, I. D., Hide, T., & Dirks, P. B. (2004, September 20). Cancer stem cells in nervous system tumors. Oncogene, 23(43), 7267–7273.

    Google Scholar 

  155. Smith, I. M., Glazer, C. A., Mithani, S. K., Ochs, M. F., Sun, W., Bhan, S., Vostrov, A., Abdullaev, Z., Lobanenkov, V., Gray, A., Liu, C., Chang, S. S., Ostrow, K. L., Westra, W. H., Begum, S., Dhara, M., & Califano, J. (2009). Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer. PLoS ONE, 4(3), e4961.

    Article  Google Scholar 

  156. Soria, J.-C., Lee, H.-Y., Lee, J. I., Wang, L., Issa, J.-P., Kemp, B. L., Liu, D. D., Kurie, J. M., Mao, L., & Khuri, F. R. (2002, May). Lack of PTEN expression in non-small cell lung cancer could be related to promoter methylation. Clinical Cancer Research, 8(5), 1178–1184.

    Google Scholar 

  157. Soukas, A., Cohen, P., Socci, N. D., & Friedman, J. M. (2000, April 15). Leptin-specific patterns of gene expression in white adipose tissue. Genes & Development, 14(8), 963–980.

    Google Scholar 

  158. Soukas, A., Socci, N. D., Saatkamp, B. D., Novelli, S., & Friedman, J. M. (2001, September 7). Distinct transcriptional profiles of adipogenesis in vivo and in vitro. Journal of Chemical Biology, 276(36), 34167–34174.

    Google Scholar 

  159. Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005, October). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America, 102(43), 15545–15550.

    Google Scholar 

  160. Tamada, Y., Kim, S., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S., & Miyano, S. (2003, October). Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics, 19(Suppl. 2), ii227–ii236.

    Google Scholar 

  161. Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E. S., & Golub, T. R. (1999, March 16). Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proceedings of the National Academy of Sciences of the United States of America, 96(6), 2907–2912.

    Google Scholar 

  162. Tanay, A., Sharan, R., & Shamir, R. (2002). Discovering statistically significant biclusters in gene expression data. Bioinformatics, 18(Suppl. 1), S136–S144.

    Article  Google Scholar 

  163. The Cancer Genome Atlas Research Network. (2008, October 23). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455(7216), 1061–1068.

    Google Scholar 

  164. Tibshirani, R., & Hastie, T. (2007). Outlier sums for differential gene expression analysis. Biostatistics, 8(1), 2–8.

    Article  MATH  Google Scholar 

  165. Tozeren, A., Coward, C. W., & Petushi, S. P. (2005, March 7). Origins and evolution of cell phenotypes in breast tumors. Journal of Theoretical Biology, 233(1), 43–54.

    Google Scholar 

  166. van Steensel, B. (2005, June). Mapping of genetic and epigenetic regulatory networks using microarrays. Nature Genetics, 37(Suppl.), S18–S24.

    Google Scholar 

  167. van’t Veer, L. J., & Bernards, R. (2008). Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature, 452(7187), 564–570.

    Google Scholar 

  168. Varambally, S., Yu, J., Laxman, B., Rhodes, D. R., Mehra, R., Tomlins, S. A., Shah, R. B., Chandran, U., Monzon, F. A., Becich, M. J., Wei, J. T., Pienta, K. J., Ghosh, D., Rubin, M. A., & Chinnaiyan, A. M. (2005, November). Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell, 8(5), 393–406.

    Google Scholar 

  169. Vazquez, A., Bond, E. E., Levine, A. J., & Bond, G. L. (2008, December). The genetics of the p53 pathway, apoptosis and cancer therapy. Nature Reviews. Drug Discovery, 7(12), 979–987.

    Google Scholar 

  170. Ventura, A. C., Jackson, T. L., & Merajver, S. D. (2009, January 15). On the role of cell signaling models in cancer research. Cancer Research, 69(2), 400–402.

    Google Scholar 

  171. Vezzoni, L., & Parmiani, G. (2008, September). Limitations of the cancer stem cell theory. Cytotechnology, 58(1), 3–9.

    Google Scholar 

  172. Visvader, J. E., & Lindeman, G. J. (2008, October). Cancer stem cells in solid tumours: Accumulating evidence and unresolved questions. Nature Reviews. Cancer, 8(10), 755–768.

    Google Scholar 

  173. Vogelstein, B., & Kinzler, K. W. (2004, August). Cancer genes and the pathways they control. Nature Medicine, 10(8), 789–799.

    Google Scholar 

  174. von Mering, C., Jensen, L. J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B., & Bork, P. (2007). String 7–recent developments in the integration and prediction of protein interactions. Nucleic Acids Research, 35(Database issue), D358–D362.

    Google Scholar 

  175. Weaver, B. A. A., & Cleveland, D. W. (2006, December). Does aneuploidy cause cancer? Current Opinion in Cell Biology, 18(6), 658–667.

    Google Scholar 

  176. Weinberg, R. A. (2008, June). Mechanisms of malignant progression. Carcinogenesis, 29(6), 1092–1095.

    Google Scholar 

  177. Werbowetski-Ogilvie, T. E., & Bhatia, M. (2008, August). Pluripotent human stem cell lines: What we can learn about cancer initiation. Trends in Molecular Medicine, 14(8), 323–332.

    Google Scholar 

  178. Werhli, A. V., & Husmeier, D. (2007). Reconstructing gene regulatory networks with Bayesian networks by combining expression data with multiple sources of prior knowledge. Statistical Applications in Genetics and Molecular Biology, 6, Article15.

    Google Scholar 

  179. Xing, Y., Kapur, K., & Wong, W. H. (2006). Probe selection and expression index computation of Affymetrix exon arrays. PLoS ONE, 1, e88.

    Article  Google Scholar 

  180. Zakharkin, S. O., Kim, K., Mehta, T., Chen, L., Barnes, S., Scheirer, K. E., Parrish, R. S., Allison, D. B., & Page, G. P. (2005). Sources of variation in Affymetrix microarray experiments. BMC Bioinformatics, 6, 214.

    Article  Google Scholar 

  181. Zhao, H., Ramos, C. F., Brooks, J. D., & Peehl, D. M. (2007, January). Distinctive gene expression of prostatic stromal cells cultured from diseased versus normal tissues. Journal of Cellular Physiology, 210(1), 111–121.

    Google Scholar 

  182. Zhou, X. J., Kao, M.-C. J., Huang, H., Wong, A., Nunez-Iglesias, J., Primig, M., Aparicio, O. M., Finch, C. E., Morgan, T. E., & Wong, W. H. (2005, February). Functional annotation and network reconstruction through cross-platform integration of microarray data. Nature Biotechnology, 23(2), 238–243.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, 550 N Broadway, Suite 1103, Baltimore, MD, 21205, USA

    Elana J. Fertig, Ludmila V. Danilova & Michael F. Ochs

Authors
  1. Elana J. Fertig
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ludmila V. Danilova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michael F. Ochs
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael F. Ochs .

Editor information

Editors and Affiliations

  1. , Institute of Statistics, National Chiao Tung University, Ta Hsueh Road 1001, Hsinchu, 30050, Taiwan, Taiwan R.O.C.

    Henry Horng-Shing Lu

  2. , Department of Empirical Inference, MPI for Intelligent Systems, Spemannstraße 38, Tübingen, 72076, Germany

    Bernhard Schölkopf

  3. School of Medicine, Dept. Epidemiology & Public Health, Yale University, College Street 60, New Haven, 06520, Connecticut, USA

    Hongyu Zhao

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Fertig, E.J., Danilova, L.V., Ochs, M.F. (2011). Cancer Systems Biology. In: Lu, HS., Schölkopf, B., Zhao, H. (eds) Handbook of Statistical Bioinformatics. Springer Handbooks of Computational Statistics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16345-6_25

Download citation

Publish with us

Policies and ethics

Search

Navigation