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Oncogene-tumor suppressor gene feedback interactions and their control
Algebraic and topological indices of molecular pathway networks in human cancers
1. | Department of Mathematical Sciences, University of Wisconsin – Milwaukee, P.O. Box 413, Milwaukee, WI 53201-0413 |
2. | Newman-Lakka Institute, Tufts University School of Medicine, Boston, MA 02111, United States |
3. | Cross Cancer Institute, University of Alberta, Edmonton, T6G 2E1, Canada |
4. | Cross Cancer Institute and Department of Physics, University of Alberta, Edmonton, T6G 2E1, Canada |
References:
[1] |
R. Albert, H.Jeong and A. L. Barabási, Error and attack tolerance of complex networks, Nature, 406 (2000), 378-382. |
[2] |
W. Alexander, Inhibiting the Akt pathway in cancer treatment, Three leading candidates, Pharmacy and Therapeutics, 36 (2011), 225-227. |
[3] |
F. Berger, P. Gritzmann S. de Vries, Minimum cycle bases for network graphs, Algorithmica, 40 (2004), 51-62.
doi: 10.1007/s00453-004-1098-x. |
[4] |
B. Bollobás, Random Graphs, Cambridge University Press, Cambridge, 2001. |
[5] |
D. Breitkreutz, L. Hlatky, E. Rietman, J. A. Tuszynski, Molecular signaling network complexity is correlated with cancer patient survivability, Proc. Natl. Acad. Sci. USA, 109 (2012), 9209-9212. |
[6] |
N. Chandra and J. Padiadpu, Network approaches to drug discovery, Expert Opin. Drug Discov., 8 (2013), 7-20. |
[7] |
P. Csermely, T. Korcsmáros, H. J. M. Kiss, G. London, R. Nussinov, Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review, Pharmacol. Therapeut., 138 (2013), 333-408. |
[8] |
D. Garlaschelli, F. Ruzzenenti and R. Basosi, Complex networks and symmetry I: A review, Symmetry, 2 (2010), 1683-1709, arXiv:1006.3923.
doi: 10.3390/sym2031683. |
[9] |
D. Holmes, PI3K pathway inhibitors approach junction, Nat. Rev. Drug Discov., 10 (2011), 563-564. |
[10] |
D. W. Huang, B. T. Sherman and R. A. Lempicki, Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists, Nucleic Acid Res., 37 (2009), 1-13. |
[11] |
D. W. Huang, B. T. Sherman and R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature Protocols, 4 (2009), 44-57, http://david.abcc.ncifcrf.gov/ |
[12] |
B. H. Junker, F. Schreiber (editors), Analysis of Biological Networks, John Wiley & Sons, Hoboken, NJ, 2008. |
[13] |
M. Kanehisa and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acid Res., 28 (2000), 23-30, http://www.genome.jp/kegg/. |
[14] |
M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno and M. Hattori, The KEGG resource for deciphering the genome, Nucleic Acid Res., 32 (2004), D277-D280. |
[15] |
H. Katebi, K. A. Sakallah and I. L. Markov, Graph symmetry detection and canonical labeling: Differences and synergies, In A Voronkov, editor, The Alan Turing Centenary, pages 181-195. EasyChair, 2012,http://vlsicad.eecs.umich.edu/BK/SAUCY/. |
[16] |
T. Kavitha, C. Liebchen, K. Mehlhorn, D. Michail, R. Rizzie, T. Ueckerdt and K. A. Zweig, Cycle bases in graphs characterization, algorithms, complexity, and applications, Computer Science Review, 3 (2009), 199-243. |
[17] |
E. V. Koonin, Y. I. Wolf and G. P. Karev (editors), Power Laws, Scale-Free Networks and Genome Biology, Landes Bioscience, Austin, TX, 2006. |
[18] |
A. Ma'ayan and B. D. MacArthur (editors), New Frontiers of Network Analysis in Systems Biology, Springer Verlag, Dordrecht, Heidelberg, New York, London, 2012. |
[19] |
B. D. MacArthur, R. J. Sánchez-García and J. W. Anderson, Symmetry in complex networks, Discr. Appl. Math., 156 (2008), 3525-3531.
doi: 10.1016/j.dam.2008.04.008. |
[20] |
National Cancer Institute, Surveillance, Epidemiology and End Results (SEER) Program, 2013, http://seer.cancer.gov/. |
[21] |
E. A. Rietman, R. L. Karp and J. A. Tuszynski, Review and application of group theory to molecular systems biology, Theor. Biol. Med. Model., 8 (2011), p21. |
[22] |
P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski and T. Ideker, Cytoscape: A software environment for integrated models of biomolecular interaction networks, Genome Res., 13 (2003), 2498-2504. http://cytoscape.org. |
[23] |
K. Takemoto and K. Kihara, Modular organization of cancer signaling networks is associated with patient survivability, BioSystems, 113 (2013), 149-154. |
[24] |
The GAP Group, GAP - Groups, Algorithms, and Programming, University of St Andrews, St Andrews, United Kingdom, 2013. http://www.gap-system.org. |
[25] |
W. Winterbach, P. van Mieghem, M. Reinders, H. Wang and D. de Ridder, Topology of molecular interaction networks, BMC Syst. Biol., 7 (2013), p90. |
[26] |
Y. Xiao, B. D. MacArthur, H. Wang, M. Xiong and W. Wang, Network quotients: Structural skeletons of complex systems, Phys. Rev. E, 78 (2008), 046102, arXiv:0802.4318. |
[27] |
J. D. Zhang and S. Wiemann, KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor, Bioinformatics, 25 (2009), 1470-1471, http://bioconductor.org. |
show all references
References:
[1] |
R. Albert, H.Jeong and A. L. Barabási, Error and attack tolerance of complex networks, Nature, 406 (2000), 378-382. |
[2] |
W. Alexander, Inhibiting the Akt pathway in cancer treatment, Three leading candidates, Pharmacy and Therapeutics, 36 (2011), 225-227. |
[3] |
F. Berger, P. Gritzmann S. de Vries, Minimum cycle bases for network graphs, Algorithmica, 40 (2004), 51-62.
doi: 10.1007/s00453-004-1098-x. |
[4] |
B. Bollobás, Random Graphs, Cambridge University Press, Cambridge, 2001. |
[5] |
D. Breitkreutz, L. Hlatky, E. Rietman, J. A. Tuszynski, Molecular signaling network complexity is correlated with cancer patient survivability, Proc. Natl. Acad. Sci. USA, 109 (2012), 9209-9212. |
[6] |
N. Chandra and J. Padiadpu, Network approaches to drug discovery, Expert Opin. Drug Discov., 8 (2013), 7-20. |
[7] |
P. Csermely, T. Korcsmáros, H. J. M. Kiss, G. London, R. Nussinov, Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review, Pharmacol. Therapeut., 138 (2013), 333-408. |
[8] |
D. Garlaschelli, F. Ruzzenenti and R. Basosi, Complex networks and symmetry I: A review, Symmetry, 2 (2010), 1683-1709, arXiv:1006.3923.
doi: 10.3390/sym2031683. |
[9] |
D. Holmes, PI3K pathway inhibitors approach junction, Nat. Rev. Drug Discov., 10 (2011), 563-564. |
[10] |
D. W. Huang, B. T. Sherman and R. A. Lempicki, Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists, Nucleic Acid Res., 37 (2009), 1-13. |
[11] |
D. W. Huang, B. T. Sherman and R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature Protocols, 4 (2009), 44-57, http://david.abcc.ncifcrf.gov/ |
[12] |
B. H. Junker, F. Schreiber (editors), Analysis of Biological Networks, John Wiley & Sons, Hoboken, NJ, 2008. |
[13] |
M. Kanehisa and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acid Res., 28 (2000), 23-30, http://www.genome.jp/kegg/. |
[14] |
M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno and M. Hattori, The KEGG resource for deciphering the genome, Nucleic Acid Res., 32 (2004), D277-D280. |
[15] |
H. Katebi, K. A. Sakallah and I. L. Markov, Graph symmetry detection and canonical labeling: Differences and synergies, In A Voronkov, editor, The Alan Turing Centenary, pages 181-195. EasyChair, 2012,http://vlsicad.eecs.umich.edu/BK/SAUCY/. |
[16] |
T. Kavitha, C. Liebchen, K. Mehlhorn, D. Michail, R. Rizzie, T. Ueckerdt and K. A. Zweig, Cycle bases in graphs characterization, algorithms, complexity, and applications, Computer Science Review, 3 (2009), 199-243. |
[17] |
E. V. Koonin, Y. I. Wolf and G. P. Karev (editors), Power Laws, Scale-Free Networks and Genome Biology, Landes Bioscience, Austin, TX, 2006. |
[18] |
A. Ma'ayan and B. D. MacArthur (editors), New Frontiers of Network Analysis in Systems Biology, Springer Verlag, Dordrecht, Heidelberg, New York, London, 2012. |
[19] |
B. D. MacArthur, R. J. Sánchez-García and J. W. Anderson, Symmetry in complex networks, Discr. Appl. Math., 156 (2008), 3525-3531.
doi: 10.1016/j.dam.2008.04.008. |
[20] |
National Cancer Institute, Surveillance, Epidemiology and End Results (SEER) Program, 2013, http://seer.cancer.gov/. |
[21] |
E. A. Rietman, R. L. Karp and J. A. Tuszynski, Review and application of group theory to molecular systems biology, Theor. Biol. Med. Model., 8 (2011), p21. |
[22] |
P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski and T. Ideker, Cytoscape: A software environment for integrated models of biomolecular interaction networks, Genome Res., 13 (2003), 2498-2504. http://cytoscape.org. |
[23] |
K. Takemoto and K. Kihara, Modular organization of cancer signaling networks is associated with patient survivability, BioSystems, 113 (2013), 149-154. |
[24] |
The GAP Group, GAP - Groups, Algorithms, and Programming, University of St Andrews, St Andrews, United Kingdom, 2013. http://www.gap-system.org. |
[25] |
W. Winterbach, P. van Mieghem, M. Reinders, H. Wang and D. de Ridder, Topology of molecular interaction networks, BMC Syst. Biol., 7 (2013), p90. |
[26] |
Y. Xiao, B. D. MacArthur, H. Wang, M. Xiong and W. Wang, Network quotients: Structural skeletons of complex systems, Phys. Rev. E, 78 (2008), 046102, arXiv:0802.4318. |
[27] |
J. D. Zhang and S. Wiemann, KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor, Bioinformatics, 25 (2009), 1470-1471, http://bioconductor.org. |
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