Utilizando a Ontocancro para traçar o perfil das vias de manutenção da estabilidade genômica
Resumo
O projeto Ontocancro surgiu da necessidade de reunir informações relacionadas ao câncer encontradas em diferentes bases de dados e integrá-las em um único repositório, fornecendo aos pesquisadores dados de interactoma e transcriptoma relacionados as vias metabólicas dos mecanismos de manutenção do genoma (GMM). Além do cruzamento destas informações, este artigo aborda uma metodologia para analisar o perfil destas vias metabólicas utilizando a entropia de Shannon, onde é possível obter um parâmetro quantitativo utilizado para caracterizar a diversidade e a atividade relativa de vias metabólicas.
Referências
Barabási, A. and Oltvai, Z. (2004). Network biology: understanding the cells functional organization. Nature Reviews Genetics, pages 101–113.
Barret, T. and Edgar, R. (2006). Mining microarray data at ncbi’s gene expression omnibus (geo). National Institutes of Health, 338:175–190.
Castro, M. A. A., Filho, J. L. R., Dalmolim, R. J. S., Sinigaglia, M., Moreira, J. C. F., Mombach, J. C. M., and de Almeida, R. M. C. (2009a). Viacomplex: software for lanscape analysis of gene expression networks in genomic context. Bioinformatics, 25:1468–1469.
Castro, M. A. A., Filho, J. L. R., Dalmolin, R. J. S., Sinigaglia, M., Moreira, J. C. F., Mombach, J. C. M., and de Almeida, R. M. C. (2009b). Viacomplex: software for landscape analysis of gene expression networks in genomic context. Bioinformatics, 25:1468–1469.
Castro, M. A. A., Mombach, J. C. M., de Almeida, R. M. C., and Moreira, J. C. F. (2007). Impaired expression of ner gene network in sporadic solid tumors. Nucleic Acids Research, 35:1859–1867.
Éder M. Simão, Cabral, H. B., Castro, M. A. A., Sinigaglia, M., Mombach, J. C. M., and Librelotto, G. R. (2010). Modeling the human genome maintenance network. Physica A, 389:4188–4194.
Giordano, T. J., Kuick, R., Thomas, D. G., Misek, D. E., Vinco, M., Sanders, D., Zhu, Z., Ciampi, R., Roh, M., Shedden, K., Gauger, P., Doherty, G., Thompson, N. W., Hanash, S., Koenig, R. J., and Nikiforov, Y. E. (2005). Molecular classification of pappilary thyroid carcinoma: distinct BRAF, RAS, and RET—PTC mutation-specific gene expression profiles discovered by dna microarray analysis. Oncogene, 24:6646–6656.
Golemis, E. (2002). Protein-Protein Interactions A Molecular Cloning Manual, pages 623–646. Cold Spring Harbor Laboratory Press, New York.
Gruber, T. R. (1993). Toward principles for the design of ontologies used for knowledge sharing. In In Formal Ontology in Conceptual Analysis and Knowledge Representation, Kluwer Academic Publishers, In Press. Substantial revision of paper presented at THE INTERNATIONAL WORKSHOP ON FORMAL ONTOLOGY. Kluwer Academic Publishers.
Halazonetis, T. D. (2008). An oncogene-induced dna damage model for cancer development. Science, 319:1352–1355.
Librelotto, G. R., Ramalho, J. C., and Henriques, P. R. (2006). Metamorphosis: A Topic Maps Based Environment to Handle Heterogeneous Information Resources. In Lecture Notes in Computer Science, volume 3873, pages 14–25. Springer-Verlag GmbH.
Microsoft (2012). Microsoft developer network virtual library. [link].
Schaefer, C. F. (2006). An introduction to the nci pathway interaction database. NCI-Nature Pathway Interaction Database.
Shannon, C. E. (1948). A mathematical theory of communication. The Bell System Technical Journal, 27:379–423, 623–656.
Sinigaglia, M., Filho, J. L. R., Dalmolin, R. J. S., Moreira, J. C. F., de Almeida, R. M. C., Castro, M. A. A., Mombach, J. C. M., and Librelotto, G. R. (2010). Bioinformatics analysis of gene networks involved in genomic stability and cancer. Cancer Biomakers, 13:34–53.
Trapnell, C., Pachter, L., and Salzberg, S. L. (2009). Tophat: discovering splice junctions with rna-seq. Bioinformatics, 25:1105–1111.
Barret, T. and Edgar, R. (2006). Mining microarray data at ncbi’s gene expression omnibus (geo). National Institutes of Health, 338:175–190.
Castro, M. A. A., Filho, J. L. R., Dalmolim, R. J. S., Sinigaglia, M., Moreira, J. C. F., Mombach, J. C. M., and de Almeida, R. M. C. (2009a). Viacomplex: software for lanscape analysis of gene expression networks in genomic context. Bioinformatics, 25:1468–1469.
Castro, M. A. A., Filho, J. L. R., Dalmolin, R. J. S., Sinigaglia, M., Moreira, J. C. F., Mombach, J. C. M., and de Almeida, R. M. C. (2009b). Viacomplex: software for landscape analysis of gene expression networks in genomic context. Bioinformatics, 25:1468–1469.
Castro, M. A. A., Mombach, J. C. M., de Almeida, R. M. C., and Moreira, J. C. F. (2007). Impaired expression of ner gene network in sporadic solid tumors. Nucleic Acids Research, 35:1859–1867.
Éder M. Simão, Cabral, H. B., Castro, M. A. A., Sinigaglia, M., Mombach, J. C. M., and Librelotto, G. R. (2010). Modeling the human genome maintenance network. Physica A, 389:4188–4194.
Giordano, T. J., Kuick, R., Thomas, D. G., Misek, D. E., Vinco, M., Sanders, D., Zhu, Z., Ciampi, R., Roh, M., Shedden, K., Gauger, P., Doherty, G., Thompson, N. W., Hanash, S., Koenig, R. J., and Nikiforov, Y. E. (2005). Molecular classification of pappilary thyroid carcinoma: distinct BRAF, RAS, and RET—PTC mutation-specific gene expression profiles discovered by dna microarray analysis. Oncogene, 24:6646–6656.
Golemis, E. (2002). Protein-Protein Interactions A Molecular Cloning Manual, pages 623–646. Cold Spring Harbor Laboratory Press, New York.
Gruber, T. R. (1993). Toward principles for the design of ontologies used for knowledge sharing. In In Formal Ontology in Conceptual Analysis and Knowledge Representation, Kluwer Academic Publishers, In Press. Substantial revision of paper presented at THE INTERNATIONAL WORKSHOP ON FORMAL ONTOLOGY. Kluwer Academic Publishers.
Halazonetis, T. D. (2008). An oncogene-induced dna damage model for cancer development. Science, 319:1352–1355.
Librelotto, G. R., Ramalho, J. C., and Henriques, P. R. (2006). Metamorphosis: A Topic Maps Based Environment to Handle Heterogeneous Information Resources. In Lecture Notes in Computer Science, volume 3873, pages 14–25. Springer-Verlag GmbH.
Microsoft (2012). Microsoft developer network virtual library. [link].
Schaefer, C. F. (2006). An introduction to the nci pathway interaction database. NCI-Nature Pathway Interaction Database.
Shannon, C. E. (1948). A mathematical theory of communication. The Bell System Technical Journal, 27:379–423, 623–656.
Sinigaglia, M., Filho, J. L. R., Dalmolin, R. J. S., Moreira, J. C. F., de Almeida, R. M. C., Castro, M. A. A., Mombach, J. C. M., and Librelotto, G. R. (2010). Bioinformatics analysis of gene networks involved in genomic stability and cancer. Cancer Biomakers, 13:34–53.
Trapnell, C., Pachter, L., and Salzberg, S. L. (2009). Tophat: discovering splice junctions with rna-seq. Bioinformatics, 25:1105–1111.
Publicado
16/07/2012
Como Citar
PEREIRA, Rafael T.; AZEVEDO, Renato P. de; SIMÃO, Eder M.; MOMBACH, José C. M.; LIBRELOTTO, Giovani R..
Utilizando a Ontocancro para traçar o perfil das vias de manutenção da estabilidade genômica. In: SIMPÓSIO BRASILEIRO DE COMPUTAÇÃO APLICADA À SAÚDE (SBCAS), 12. , 2012, Curitiba/PR.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2012
.
p. 198-207.
ISSN 2763-8952.
