Skip to main content
Disciplines
Automotive Business IT + Informatics Construction + Real Estate Electrical Engineering + Electronics Energy + Sustainability Insurance + Risk Finance + Banking Management + Leadership Marketing + Sales Mechanical Engineering + Materials
Events
DE
EN
Books
Journals
Topic Page
Marketing
Start single access now
Access for companies
EXTENDED SEARCH
Log in
Top
Published in:
Accuracy Assessment of Consensus Sequence from Shotgun Sequencing Read chapter Read first chapter

2011 | OriginalPaper | Chapter

25. Cancer Systems Biology

Authors : Elana J. Fertig, Ludmila V. Danilova, Michael F. Ochs

Published in: Handbook of Statistical Bioinformatics

Publisher: Springer Berlin Heidelberg

Log in

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

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.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

inform now
previous chapter Computational Drug Target Pathway Discovery: A Bayesian Network Approach
next chapter Comparative Genomics
Literature
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.CrossRef
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.
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.
4.
Alberts, B. (2008). Molecular biology of the cell (5th ed.). New York: Garland Science.
5.
Albini, A., & Sporn, M. B. (2007, February). The tumour microenvironment as a target for chemoprevention. Nature Reviews. Cancer, 7(2), 139–147.
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.
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.
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.
9.
Anderson, A. R. A., & Quaranta, V. (2008, March). Integrative mathematical oncology. Nature Reviews. Cancer, 8(3), 227–234.
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.
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.CrossRef
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.
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.
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.
15.
Bauch, A., & Superti-Furga, G. (2006, April). Charting protein complexes, signaling pathways, and networks in the immune system. Immunological Reviews, 210, 187–207.
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.
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.MathSciNetCrossRef
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.CrossRef
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.CrossRef
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.
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.CrossRef
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.
23.
Blow, J. J., & Gillespie, P. J. (2008, October). Replication licensing and cancer–a fatal entanglement? Nature Reviews. Cancer, 8(10), 799–806.
24.
Bock, C., & Lengauer, T. (2008, January 1). Computational epigenetics. Bioinformatics, 24(1), 1–10.
25.
Bodenreider, O., & Stevens, R. (2006, September). Bio-ontologies: Current trends and future directions. Brief Bioinformatics, 7(3), 256–274.
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.CrossRef
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.
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.
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.
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,.
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.MathSciNetCrossRef
32.
Chiang, A. C., & Massague, J. (2008, December 25). Molecular basis of metastasis. The New England Journal of Medicine, 359(26), 2814–2823.
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.
34.
Claverie, J. M. (1999). Computational methods for the identification of differential and coordinated gene expression. Human Molecular Genetics, 8(10), 1821–1832.CrossRef
35.
Croce, C. M. (2008, January 31). Oncogenes and cancer. The New England Journal of Medicine, 358(5), 502–511.
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.
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.
38.
Dick, J. E. (2008, December 15). Stem cell concepts renew cancer research. Blood, 112(13), 4793–4807.
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.
40.
Duesberg, P., & Li, R. (2003, May-June). Multistep carcinogenesis: A chain reaction of aneuploidizations. Cell Cycle, 2(3), 202–210.
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.
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.
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.
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.CrossRef
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.
46.
Fearon, E. R., & Vogelstein, B. (1990, June 1). A genetic model for colorectal tumorigenesis. Cell, 61(5), 759–767.
47.
Feinberg, A. P., Ohlsson, R., & Henikoff, S. (2006, January). The epigenetic progenitor origin of human cancer. Nature Reviews. Genetics, 7(1), 21–33.
48.
Feinberg, A. P., & Tycko, B. (2004, February). The history of cancer epigenetics. Nature Reviews. Cancer, 4(2), 143–153.
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.
50.
Finkel, T., Serrano, M., & Blasco, M. A. (2007, August 16). The common biology of cancer and ageing. Nature, 448(7155), 767–774.
51.
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.
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.
54.
Gargiulo, G., & Minucci, S. (2009). Epigenomic profiling of cancer cells. International Journal of Biochemistry and Cell Biology, 41(1), 127–135.CrossRef
55.
Gatenby, R. A., & Vincent, T. L. (2003, October 1). An evolutionary model of carcinogenesis. Cancer Research, 63(19), 6212–6220.
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.
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.CrossRef
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.
59.
Ghosh, D., & Chinnaiyan, A. M. (2009, January). Genomic outlier profile analysis: Mixture models, null hypotheses, and nonparametric estimation. Biostatistics, 10(1), 60–69.
60.
Giehl, K., & Menke, A. (2008). Microenvironmental regulation of E-Cadherin-mediated adherens junctions. Frontiers in Bioscience, 13, 3975–3985.CrossRef
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.MathSciNetCrossRef
62.
Gius, D., & Spitz, D. R. (2006, July-August). Redox signaling in cancer biology. Antioxid Redox Signal, 8(7–8), 1249–1252.
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.
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.
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.
66.
Hanahan, D., & Weinberg, R. A. (2000). The hallmarks of cancer. Cell, 100(1), 57–70.CrossRef
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.
68.
Harley, C. B. (2008, March). Telomerase and cancer therapeutics. Nature Reviews. Cancer, 8(3), 167–179.
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.
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.
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.CrossRef
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
85.
Jordan, J. D., Landau, E. M., & Iyengar, R. (2000, October). Signaling networks: The origins of cellular multitasking. Cell, 103, 193–200.
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.
87.
Khalil, I. G., & Hill, C. (2005, January). Systems biology for cancer. Current Opinion in Oncology, 17(1), 44–48.
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.
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.
90.
Kiberstis, P. A., & Travis, J. (2006). Celebrating a glass half-full. Science, 312, 1157.CrossRef
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.
92.
Kinzler, K. W., & Vogelstein, B. (1996, October 18). Lessons from hereditary colorectal cancer. Cell, 87(2), 159–170.
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.
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.CrossRef
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.
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.
97.
Kundu, J. K., & Surh, Y.-J. (2008, July-August). Inflammation: Gearing the journey to cancer. Mutation Research, 659(1–2), 15–30.
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.
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.
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.CrossRef
101.
Lee, D. D., & Seung, H. S. (1999, October). Learning the parts of objects by non-negative matrix factorization. Nature, 401(6755), 788–791.
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.
103.
Lewis, M. T. (2008, October). Faith, heresy and the cancer stem cell hypothesis. Future Oncology, 4(5), 585–589.
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.
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.CrossRef
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.
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.
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.
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.
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.
111.
Macdonald, F., Ford, C. H. J., & Casson, A. G. (2004). Molecular biology of cancer (2nd ed.). London: BIOS Scientific Publishers.
112.
Mantovani, A. (2009, January 1). Cancer: Inflaming metastasis. Nature, 457(7225), 36–37.
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.
114.
Michor, F. (2008). Mathematical models of cancer stem cells. Journal of Clinical Oncology, 26, 2854–2861.CrossRef
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.
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.
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.
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.
119.
Morange, M. (2007, December 6). The field of cancer research: An indicator of present transformations in biology. Oncogene, 26(55), 7607–7610.
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.
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.
122.
Norton, L., & Massague, J. (2006, August). Is cancer a disease of self-seeding? Nature Medicine, 12(8), 875–878.
123.
Ochs, M. F., & Godwin, A. K. (2003, March). Microarrays in cancer: Research and applications. Biotechniques, (Suppl.), 34, S4–S15.
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.CrossRef
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.CrossRef
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.
127.
Paget, S. (1889). The distribution of secondary growths in cancer of the breast. Lancet, 1, 571–573.CrossRef
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.
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.
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.
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.
132.
Quackenbush, J. (2001, June). Computational analysis of microarray data. Nature Reviews. Genetics, 2(6), 418–427.
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.
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.
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.
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.
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.
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.
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.CrossRef
140.
Sahai, E. (2007, October). Illuminating the metastatic process. Nature Reviews. Cancer, 7(10), 737–749.
141.
Sandhu, J. S. (2008, July). Prostate cancer and chronic prostatitis. Current Urology Reports, 9(4), 328–332.
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.
143.
Saul, Z. M., & Filkov, V. (2007). Exploring biological network structure using exponential random graph models. Bioinformatics, 23(19), 2604–2611.CrossRef
144.
Sauro, H. M., & Kholodenko, B. N. (2004). Quantitative analysis of signaling networks. Progress in Biophysics and Molecular Biology, 86, 5–43.CrossRef
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.
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.
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.
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.
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.CrossRef
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.
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.
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.
153.
Simpson, R. J., & Dorow, D. S. (2001). Cancer proteomics: From signaling networks to tumor markers. Trends in Biotechnology, 19(Suppl. 10), S40–S48.CrossRef
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.
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.CrossRef
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.
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.
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.
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.
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.
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.
162.
Tanay, A., Sharan, R., & Shamir, R. (2002). Discovering statistically significant biclusters in gene expression data. Bioinformatics, 18(Suppl. 1), S136–S144.CrossRef
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.
164.
Tibshirani, R., & Hastie, T. (2007). Outlier sums for differential gene expression analysis. Biostatistics, 8(1), 2–8.CrossRefMATH
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.
166.
van Steensel, B. (2005, June). Mapping of genetic and epigenetic regulatory networks using microarrays. Nature Genetics, 37(Suppl.), S18–S24.
167.
van’t Veer, L. J., & Bernards, R. (2008). Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature, 452(7187), 564–570.
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.
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.
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.
171.
Vezzoni, L., & Parmiani, G. (2008, September). Limitations of the cancer stem cell theory. Cytotechnology, 58(1), 3–9.
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.
173.
Vogelstein, B., & Kinzler, K. W. (2004, August). Cancer genes and the pathways they control. Nature Medicine, 10(8), 789–799.
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.
175.
Weaver, B. A. A., & Cleveland, D. W. (2006, December). Does aneuploidy cause cancer? Current Opinion in Cell Biology, 18(6), 658–667.
176.
Weinberg, R. A. (2008, June). Mechanisms of malignant progression. Carcinogenesis, 29(6), 1092–1095.
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.
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.
179.
Xing, Y., Kapur, K., & Wong, W. H. (2006). Probe selection and expression index computation of Affymetrix exon arrays. PLoS ONE, 1, e88.CrossRef
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.CrossRef
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.
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.
Metadata
Title
Cancer Systems Biology
Authors
Elana J. Fertig
Ludmila V. Danilova
Michael F. Ochs
Copyright Year
2011
Publisher
Springer Berlin Heidelberg
Book
Handbook of Statistical Bioinformatics

Print ISBN: 978-3-642-16344-9

Electronic ISBN: 978-3-642-16345-6

Copyright Year: 2011

DOI
https://doi.org/10.1007/978-3-642-16345-6_25

Premium Partner

    Image Credits