, Cancer Gene Census

. Kegg-mapk and . Pathway,

, KEGG p53 signalling pathway

. Kegg-pi3k/akt and . Pathway,

J. P. Alao, The regulation of cyclin D1 degradation : roles in cancer development and the potential for therapeutic invention, Molecular Cancer, vol.6, issue.1, p.1, 2007.

H. R. Andersen, An introduction to binary decision diagrams. Department of Information Technology, Lecture notes for 49285 Advanced Algorithms E97, 1997.

S. Azab and A. Al-hendy, Signal transduction pathways in breast cancer-drug targets and challenges, Breast Cancer-Carcinogenesis, 2011.

A. Barabási and R. Albert, Emergence of scaling in random networks, Science, vol.286, issue.5439, pp.509-512, 1999.

M. Benítez, C. Espinosa-soto, P. Padilla-longoria, and E. R. Alvarez-buylla, Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in arabidopsis epidermis : a dynamic spatial model, BMC Systems Biology, vol.2, issue.1, p.98, 2008.

C. Biane and F. Delaplace, Abduction based drug target discovery using Boolean control network, International Conference on Computational Methods in Systems Biology, pp.57-73, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01522072

C. Biane and F. Delaplace, Causal reasoning on Boolean control networks based on abduction : theory and application to cancer drug discovery, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02264665

C. Biane, F. Delaplace, and T. Melliti, Abductive network action inference for targeted therapy discovery, Electronic Notes in Theoretical Computer Science, vol.335, pp.4-26, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01779429

. Biomarkers-definitions-working, A. J. Group, W. A. Atkinson, V. G. Colburn, D. L. Degruttola et al., Biomarkers and surrogate endpoints : preferred definitions and conceptual framework, Clinical Pharmacology & Therapeutics, vol.69, issue.3, pp.89-95, 2001.

A. Blake, Canonical Expressions in Boolean Algebra, 1938.

R. E. Bryant, Graph-based algorithms for Boolean function manipulation, IEEE Transactions on Computers, vol.100, issue.8, pp.677-691, 1986.

L. N. Burga, H. Hu, A. Juvekar, N. M. Tung, S. L. Troyan et al., Loss of BRCA1 leads to an increase in epidermal growth factor receptor expression in mammary epithelial cells, and epidermal growth factor receptor inhibition prevents estrogen receptor-negative cancers in BRCA1-mutant mice, Breast Cancer Research, vol.13, issue.2, p.30, 2011.

L. Calzone, L. Tournier, S. Fourquet, D. Thieffry, B. Zhivotovsky et al., Mathematical modelling of cell-fate decision in response to death receptor engagement, PLoS Computational Biology, vol.6, issue.3, p.1000702, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00704979

, Cancer Genome Atlas Network et al. Comprehensive molecular portraits of human breast tumours, Nature, vol.490, issue.7418, p.61, 2012.

P. Cheah, The emerging role of RBL2/p130 in multi-step retinoblastoma tumorigenesis, Cancer Biology & Therapy, vol.8, issue.8, pp.718-719, 2009.

G. Ciriello, E. Cerami, C. Sander, and N. Schultz, Mutual exclusivity analysis identifies oncogenic network modules, Genome Research, vol.22, issue.2, pp.398-406, 2012.

M. Cohen-armon, L. Visochek, D. Rozensal, A. Kalal, I. Geistrikh et al., DNA-Independent PARP-1 Activation by Phosphorylated ERK2 Increases Elk1 Activity : A Link to Histone Acetylation, Molecular Cell, vol.25, issue.2, pp.297-308, 2007.

S. Collombet, C. Van-oevelen, J. L. Ortega, W. Abou-jaoudé, B. D. Stefano et al., Logical modeling of lymphoid and myeloid cell specification and transdifferentiation, Proceedings of the National Academy of Sciences of the USA, vol.114, issue.23, pp.5792-5799, 2017.

S. J. Compere, P. Baldacci, A. H. Sharpe, T. Thompson, H. Land et al., The ras and myc oncogenes cooperate in tumor induction in many tissues when introduced into midgestation mouse embryos by retroviral vectors, Proceedings of the National Academy of Sciences of the USA, vol.86, issue.7, pp.2224-2228, 1989.

O. Coudert and J. C. Madre, A unified framework for the formal verification of sequential circuits, IEEE International Conference on Computer-Aided Design, pp.126-129, 1990.

Y. Crama and P. L. Hammer, Boolean Functions : Theory, Algorithms, and Applications, 2011.

M. Cully, H. You, A. J. Levine, and T. W. Mak, Beyond PTEN mutations : the PI3K pathway as an integrator of multiple inputs during tumorigenesis, Nature Reviews Cancer, vol.6, issue.3, pp.184-192, 2006.

J. Demongeot, E. Goles, M. Morvan, M. Noual, and S. Sené, Attraction basins as gauges of robustness against boundary conditions in biological complex systems, PloS One, vol.5, issue.8, p.11793, 2010.

C. Deng, BRCA1 : cell cycle checkpoint, genetic instability, DNA damage response and cancer evolution, Nucleic Acids Research, vol.34, issue.5, pp.1416-1426, 2006.

F. A. Dick, Structure-function analysis of the retinoblastoma tumor suppressor protein-is the whole a sum of its parts ? Cell division, vol.2, p.26, 2007.

G. Didier, E. Remy, and C. Chaouiya, Mapping multivalued onto boolean dynamics, Journal of theoretical biology, vol.270, issue.1, pp.177-184, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00656334

A. E. Emery, F. Muntoni, and R. C. Quinlivan, Duchenne muscular dystrophy, 2015.

P. Eroles, A. Bosch, J. Pérez-fidalgo, and A. Lluch, Molecular biology in breast cancer : Intrinsic subtypes and signaling pathways, Cancer Treatment Reviews, vol.38, issue.6, pp.698-707, 2012.

M. Farago, I. Dominguez, E. Landesman-bollag, X. Xu, A. Rosner et al., Kinase-inactive glycogen synthase kinase 3? promotes wnt signaling and mammary tumorigenesis, Cancer Research, vol.65, issue.13, pp.5792-5801, 2005.

H. Farmer, N. Mccabe, C. J. Lord, A. N. Tutt, D. A. Johnson et al., Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy, Nature, vol.434, issue.7035, pp.917-921, 2005.

A. Fauré, A. Naldi, C. Chaouiya, and D. Thieffry, Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle, Bioinformatics, vol.22, issue.14, pp.124-131, 2006.

E. R. Fearon and B. Vogelstein, A genetic model for colorectal tumorigenesis, Cell, vol.61, issue.5, pp.759-767, 1990.

A. Feber, J. Clark, G. Goodwin, A. R. Dodson, P. H. Smith et al., Amplification and overexpression of E2F3 in human bladder cancer, Oncogene, vol.23, issue.8, p.1627, 2004.

S. A. Forbes, D. Beare, H. Boutselakis, S. Bamford, N. Bindal et al., COSMIC : somatic cancer genetics at highresolution, Nucleic Acids Research, vol.45, issue.D1, pp.777-783, 2016.

Y. H. Goh, J. Yoo, J. H. Noh, and C. Kim, Emerging targeted therapies in advanced bladder cancer, Translational Cancer Research, vol.6, issue.4, pp.666-676, 2017.

D. Hanahan and R. A. Weinberg, Hallmarks of cancer : The next generation, Cell, vol.144, issue.5, pp.646-674, 2011.

T. Helleday, The underlying mechanism for the parp and brca synthetic lethality : clearing up the misunderstandings, Molecular oncology, vol.5, issue.4, pp.387-393, 2011.

L. Hood, J. R. Heath, M. E. Phelps, and B. Lin, Systems biology and new technologies enable predictive and preventative medicine, Science, vol.306, issue.5696, pp.640-643, 2004.

C. D. Hurst, D. C. Tomlinson, S. V. Williams, F. M. Platt, and M. A. Knowles, Inactivation of the Rb pathway and overexpression of both isoforms of E2F3 are obligate events in bladder tumours with 6p22 amplification, Oncogene, vol.27, issue.19, p.2716, 2008.

N. E. Hynes and H. A. Lane, ERBB receptors and cancer : the complexity of targeted inhibitors, Nature Reviews Cancer, vol.5, issue.5, pp.341-354, 2005.

, International Agency for Research on Cancer et al. World cancer factsheet. Cancer Research UK, 2014.

W. G. Kaelin, The concept of synthetic lethality in the context of anticancer therapy, Nature Reviews Cancer, vol.5, issue.9, pp.689-98, 2005.

C. Kandoth, M. D. Mclellan, F. Vandin, K. Ye, B. Niu et al.,

M. A. Mcmichael and . Wyczalkowski, Mutational landscape and significance across 12 major cancer types, Nature, vol.502, issue.7471, pp.333-339, 2013.

M. Kanehisa, M. Furumichi, M. Tanabe, Y. Sato, and K. Morishima, KEGG : new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Research, vol.45, issue.D1, pp.353-361, 2017.
DOI : 10.1093/nar/gkw1092

URL : https://academic.oup.com/nar/article-pdf/45/D1/D353/8846820/gkw1092.pdf

S. A. Kauffman, Metabolic stability and epigenesis in randomly constructed genetic nets, Journal of Theoretical Biology, vol.22, issue.3, pp.437-467, 1969.

D. S. Kaufman, W. U. Shipley, and A. S. Feldman, Bladder cancer. The Lancet, vol.374, pp.239-249, 2009.

K. Kehn, R. Berro, A. Alhaj, M. Bottazzi, W. Yeh et al., Functional consequences of cyclin D1/BRCA1 interaction in breast cancer cells, Oncogene, vol.26, issue.35, pp.5060-5069, 2007.

H. Kitano, A robustness-based approach to systems-oriented drug design, Nature Reviews Drug Discovery, vol.6, issue.3, p.2195, 2007.

E. A. Klein and R. K. Assoian, Transcriptional regulation of the cyclin D1 gene at a glance, Journal of Cell Science, vol.121, pp.3853-3857, 2008.

E. Kumaraswamy, K. L. Wendt, L. A. Augustine, S. R. Stecklein, E. C. Sibala et al., BRCA1 regulation of epidermal growth factor receptor (EGFR) expression in human breast cancer cells involves microRNA146a and is critical for its tumor suppressor function, Oncogene, vol.34, issue.33, pp.4333-4346, 2015.

W. L. Lanier and S. V. Rajkumar, Empiricism and rationalism in medicine : Can 2 competing philosophies coexist to improve the quality of medical care, vol.88, pp.1042-1045, 2013.

R. Layek, A. Datta, M. Bittner, and E. R. Dougherty, Cancer therapy design based on pathway logic, Bioinformatics, vol.27, issue.4, pp.548-555, 2011.

C. Y. Lee, Representation of switching circuits by binary-decision programs, The Bell System Technical Journal, vol.38, issue.4, pp.985-999, 1959.

F. Li, T. Long, Y. Lu, Q. Ouyang, and C. Tang, The yeast cell-cycle network is robustly designed, Proceedings of the National Academy of Sciences of the USA, vol.101, issue.14, pp.4781-4786, 2004.

P. K. Lin and S. P. Khatri, Application of Max-SAT-based ATPG to optimal cancer therapy design, BMC Genomics, vol.13, issue.6, p.5, 2012.

L. Livraghi and J. E. Garber, PARP inhibitors in the management of breast cancer : current data and future prospects, BMC Medicine, vol.13, issue.1, p.1, 2015.

J. Luo, Glycogen synthase kinase 3? (GSK3?) in tumorigenesis and cancer chemotherapy, Cancer Letters, vol.273, issue.2, pp.194-200, 2009.

M. Malanga, J. M. Pleschke, H. E. Kleczkowska, and F. R. Althaus, Poly (ADPribose) binds to specific domains of p53 and alters its DNA binding functions, Journal of Biological Chemistry, vol.273, issue.19, pp.11839-11843, 1998.

P. Marquis, Extending abduction from propositional to first-order logic, Fundamentals of artificial intelligence research, pp.141-155, 1991.

L. D. Mayo and D. B. Donner, The PTEN, Mdm2, p53 tumor suppressoroncoprotein network, Trends in Biochemical Sciences, vol.27, issue.9, pp.462-467, 2002.

W. S. Mcculloch and W. Pitts, A logical calculus of the ideas immanent in nervous activity, The Bulletin of Mathematical Biophysics, vol.5, issue.4, pp.115-133, 1943.

V. A. Mckusick, Mendelian inheritance in man : a catalog of human genes and genetic disorders, vol.1, 1998.

S. Meloche and J. Pouysségur, The ERK1/2 mitogen-activated protein kinase pathway as a master regulator of the G1-to S-phase transition, Oncogene, vol.26, issue.22, p.3227, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00319874

I. Miko, Genetic dominance : genotype-phenotype relationships, Nature Education, vol.1, issue.1, p.140, 2008.

U. M. Moll and O. Petrenko, The MDM2-p53 Interaction. Molecular Cancer Research, vol.1, pp.1001-1008, 2004.

M. K. Morris, J. Saez-rodriguez, P. K. Sorger, and D. A. Lauffenburger, Logicbased models for the analysis of cell signaling networks, Biochemistry, vol.49, issue.15, pp.3216-3224, 2010.

P. Mullan, J. Quinn, and D. Harkin, The role of BRCA1 in transcriptional regulation and cell cycle control, Oncogene, vol.25, issue.43, pp.5854-5863, 2006.

D. Murrugarra, A. Veliz-cuba, B. Aguilar, and R. Laubenbacher, Identification of control targets in Boolean molecular network models via computational algebra, BMC Systems Biology, vol.10, issue.1, p.94, 2016.

Y. Nagata, K. Lan, X. Zhou, M. Tan, F. J. Esteva et al., PTEN activation contributes to tumor inhibition by trastuzumab, and loss of PTEN predicts trastuzumab resistance in patients, Cancer Cell, vol.6, issue.2, pp.117-127, 2004.

S. A. Narod and W. D. Foulkes, BRCA1 and BRCA2 : 1994 and beyond, Nature Reviews Cancer, vol.4, issue.9, pp.665-676, 2004.

, Toward precision medicine : building a knowledge network for biomedical research and a new taxonomy of disease, 2011.

D. Nguyen, M. Zajac-kaye, L. Rubinstein, D. Voeller, J. E. Tomaszewski et al., Poly (ADP-ribose) polymerase inhibition enhances p53-dependent and-independent DNA damage responses induced by DNA damaging agent, Cell Cycle, vol.10, issue.23, pp.4074-4082, 2011.

M. Noual, D. Regnault, and S. Sené, About non-monotony in boolean automata networks, Theoretical Computer Science, vol.504, pp.12-25, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00736641

M. Oeggerli, S. Tomovska, P. Schraml, D. Calvano-forte, S. Schafroth et al., E2F3 amplification and overexpression is associated with invasive tumor growth and rapid tumor cell proliferation in urinary bladder cancer, Oncogene, vol.23, issue.33, p.5616, 2004.

B. Pereira, S. Chin, O. M. Rueda, H. M. Vollan, E. Provenzano et al., The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes, Nature Communications, vol.7, p.11479, 2016.

L. Perfetto, L. Briganti, A. Calderone, A. C. Perpetuini, M. Iannuccelli et al., SI-GNOR : A database of causal relationships between biological entities, Nucleic Acids Research, vol.44, issue.D1, pp.548-554, 2016.

P. C. Phillips, Epistasis -the essential role of gene interactions in the structure and evolution of genetic systems, Nature Reviews Genetics, vol.9, issue.11, pp.855-867, 2008.

W. Quine, On cores and prime implicants of truth functions. The American Mathematical Monthly, vol.66, pp.755-760, 1959.

E. Remy, S. Rebouissou, C. Chaouiya, A. Zinovyev, F. Radvanyi et al., A modelling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis, Cancer Research, p.602, 2015.

F. Robert, Discrete iterations : a metric study, 1986.

C. Romagosa, S. Simonetti, L. Lopez-vicente, A. Mazo, M. Lleonart et al., p16 Ink4a overexpression in cancer : a tumor suppressor gene associated with senescence and high-grade tumors, Oncogene, vol.30, issue.18, p.2087, 2011.

R. W. Ruddon, Cancer Biology, 2007.

J. Saez-rodriguez, L. Simeoni, J. A. Lindquist, R. Hemenway, U. Bommhardt et al., A logical model provides insights into T cell receptor signaling, PLoS Computational Biology, vol.3, issue.8, p.163, 2007.

E. Samson and B. Mills, Circuit Minimization : Algebra and Algorithms for New Boolean Canonical Expressions. Air Force Cambridge Research Center, Office of Technical Services, 1954.

C. Sanchez, C. Lachaize, F. Janody, B. Bellon, L. Röder et al., Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database, Nucleic Acids Research, vol.27, issue.1, pp.89-94, 1999.
URL : https://hal.archives-ouvertes.fr/hal-01662955

T. Santarius, J. Shipley, D. Brewer, M. R. Stratton, and C. S. Cooper, A census of amplified and overexpressed human cancer genes, Nature Reviews Cancer, vol.10, issue.1, p.59, 2010.

L. Shan, X. Li, L. Liu, X. Ding, Q. Wang et al., GATA3 cooperates with PARP1 to regulate CCND1 transcription through modulating histone H1 incorporation, Oncogene, vol.33, issue.24, p.3205, 2014.

M. Spiliotaki, D. Mavroudis, K. Kapranou, H. Markomanolaki, G. Kallergi et al., Evaluation of proliferation and apoptosis markers in circulating tumor cells of women with early breast cancer who are candidates for tumor dormancy, Breast Cancer Research, vol.16, issue.6, p.485, 2014.

V. Stambolic, D. Macpherson, D. Sas, Y. Lin, B. Snow et al., Regulation of PTEN transcription by p53, Molecular Cell, vol.8, issue.2, pp.317-325, 2001.

M. Strnisková, M. Baran?ík, and T. Ravingerová, MItogen-activated protein kinases and their role in regulation of cellular processes, General Physiology and Biophysics, vol.21, issue.3, pp.231-255, 2002.

D. C. Swinney and J. Anthony, How were new medicines discovered ?, Nature Reviews Drug Discovery, vol.10, issue.7, pp.507-519, 2011.

R. Thomas, Boolean formalization of genetic control circuits, Journal of Theoretical Biology, vol.42, issue.3, pp.563-585, 1973.

M. Toshiyuki and J. C. Reed, Tumor suppressor p53 is a direct transcriptional activator of the human bax gene, Cell, vol.80, issue.2, pp.293-299, 1995.

F. Tsuruta, N. Masuyama, and Y. Gotoh, The phosphatidylinositol 3-kinase (PI3K)-Akt pathway suppresses Bax translocation to mitochondria, Journal of Biological Chemistry, vol.277, issue.16, pp.14040-14047, 2002.

B. Vogelstein, N. Papadopoulos, V. E. Velculescu, S. Zhou, L. A. Diaz et al., Cancer genome landscapes. Science, vol.339, issue.6127, pp.1546-1558, 2013.

R. Wang, A. Saadatpour, and R. Albert, Boolean modeling in systems biology : an overview of methodology and applications, Physical Biology, vol.9, issue.5, p.55001, 2012.

X. Wang, A. Q. Fu, M. E. Mcnerney, and K. P. White, Widespread genetic epistasis among cancer genes, Nature Communications, vol.5, 2014.

W. M. Webb, Rationalism, Empiricism, and Evidence-Based Medicine : A Call for a, New Galenic Synthesis. Medicines, vol.5, issue.2, p.40, 2018.

P. L. Welcsh, M. K. Lee, R. M. Gonzalez-hernandez, D. J. Black, M. Mahadevappa et al., BRCA1 transcriptionally regulates genes involved in breast tumorigenesis. Proceedings of the National Academy of Sciences of the USA, vol.99, pp.7560-7565, 2002.

A. K. Witkiewicz, K. E. Knudsen, A. P. Dicker, and E. S. Knudsen, The meaning of p16ink4a expression in tumors : functional significance, clinical associations and future developments, Cell Cycle, vol.10, issue.15, pp.2497-2503, 2011.

A. R. Yallowitz, D. Li, A. Lobko, D. Mott, A. Nemajerova et al., Mutant p53 amplifies epidermal growth factor receptor family signaling to promote mammary tumorigenesis, Molecular Cancer Research, p.360, 2015.

R. Yao, W. J. Lemon, Y. Wang, C. J. Grubbs, R. A. Lubet et al., Altered gene expression profile in mouse bladder cancers induced by hydroxybutyl (butyl) nitrosamine, Neoplasia, vol.6, issue.5, pp.569-577, 2004.

C. Yeang, F. Mccormick, and A. Levine, Combinatorial patterns of somatic gene mutations in cancer, The FASEB Journal, vol.22, issue.8, pp.2605-2622, 2008.

J. G. Zanudo and R. Albert, Cell fate reprogramming by control of intracellular network dynamics, PLoS Computational Biology, vol.11, issue.4, p.1004193, 2015.

H. Zhang, K. Somasundaram, Y. Peng, H. Tian, H. Zhang et al., BRCA1 physically associates with p53 and stimulates its transcriptional activity, vol.16, pp.1713-1721, 1998.

R. Zhang, M. V. Shah, J. Yang, S. B. Nyland, X. Liu et al.,

. Loughran, Network model of survival signaling in large granular lymphocyte leukemia, Proceedings of the National Academy of Sciences of the USA, 2008.

W. Zhang and H. T. Liu, MAPK signal pathways in the regulation of cell proliferation in mammalian cells, Cell Research, vol.12, issue.1, pp.9-18, 2002.

Q. Zhong, N. Simonis, Q. Li, B. Charloteaux, F. Heuze et al.,

M. Cusick and . Vidal, Edgetic perturbation models of human inherited disorders, Molecular Systems Biology, vol.5, issue.321, p.321, 2009.