Modeling the Human Genome Maintenance network

Physica A: Statistical Mechanics and its Applications

Volumn 389, Issue 19, 2010, Pages 4188-4194

  Simão, Éder M ^a   Cabral, Heleno B ^c   Castro, Mauro A A ^b   Sinigaglia, Marialva ^b   Mombach, Jos C M ^a   Librelotto, Giovani R ^a  

^a FEDERAL UNIVERSITY OF SANTA MARIA   (Brazil)

^b FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^c CENTRO UNIVERSITÁRIO FRANCISCANO   (Brazil)

Author keywords

Apoptosis; Cancer; Database; DNA repair; Gene expression; Microarray; Pathway; Protein network

Indexed keywords

CELL DEATH; DISEASES; GENE EXPRESSION; MICROARRAYS; PROTEINS;

CANCER; DNA REPAIR; INFORMATION RESOURCE; MAINTENANCE NETWORKS; NETWORK MODELING; PATHWAY; PATHWAY ACTIVITIES; PROTEIN NETWORK;

DATABASE SYSTEMS;

EID: 77955556024     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2010.05.051     Document Type: Article

References (30)

1. J.H.J. HoeijmaKers Genome maintenance mechanisms for preventing cancer Nature 411 2001 366 374
2. Z.H. Wang, J.M. Cummins, and D. Shen Three classes of genes mutated in colorectal cancers with chromosomal instability Cancer Res. 64 2004 2998 3001 (Pubitemid 38581395)
3. D.G. Albertson, C. Collins, F. McCormick, and J.W. Gray Chromosome aberrations in solid tumors Nature Genet. 34 2003 369 376 (Pubitemid 36935328)
4. B. Zhivotovsky, and G. Kroemer Apoptosis and genomic instability Nat. Rev. Mol. Cell. Biol. 5 2004 752 762 (Pubitemid 39208184)
5. P. Duesberg, R. Li, A. Fabarius, and R. Hehlmann The chromosomal basis of cancer Cell Oncol. 27 2005 293 318 (Pubitemid 43000357)
6. P.A. Futreal, L. Coin, M. Marshall, T. Down, T. Hubbard, R. Wooster, N. Rahman, and M.R. Stratton A census of human cancer genes Nature Rev. Cancer 4 2004 177 183 (Pubitemid 38337497)
7. H.H. Heng, G. Liu, S. Bremer, K.J. Ye, J. Stevens, and C.J. Ye Clonal and non-clonal chromosome aberrations and genome variation and aberration Genome 49 2006 195 204 (Pubitemid 43979153)
8. C.E. Jefford, and Irminger-Finger Mechanisms of chromosome instability in cancers Critical Rev. Oncology/Hematology 59 2006 1 14 (Pubitemid 43903279)
9. C. Lengauer, K.W. Kinzler, and B. Vogelstein Genetic instabilities in human cancers Nature 396 1998 643 649 (Pubitemid 29003936)
10. L.M.F. Merlo, J.W. Pepper, B.J. Reid, and C.C. Maley Cancer as an evolutionary and ecological process Nature Rev. Cancer 6 2006 924 935
11. R.N. Venkatesan, J.H. Bielas, and L.A. Loeb Generation of mutator mutants during carcinogenesis DNA Repair 5 2006 294 302
12. M.A.A. Castro, J.C.M. Mombach, R.M.C. Almeida, and J.C.F. Moreira Impaired expression of NER gene network in sporadic solid tumors Nucleic Acids Res. 35 2007 1859 1867
13. NCI http://pid.nci.nih.gov/
14. BioCarta http://www.biocarta.com/
15. Kegg http://www.genome.jp/kegg/
16. Reactome http://www.reactome.org/
17. Prosite http://ca.expasy.org/prosite/
18. Gene Ontology http://www.geneontology.org/
19. String http://www.string.embl.de/
20. G.R. Librelotto, J.C.M. Mombach, M. Sinigaglia, E.M. Simo, H.B. Cabral, and M.A.A. Castro An ontology to integrate transcriptomics and interatomics data involved in gene pathways of genome stability Lect. Notes Bioinform. 5676 2009 164 167
21. BioPAX: Biological pathway exchange language http://www.biopax.org/
22. HGNC http://www.genenames.org/
23. J. Sabates-Bellver, L.G. Van der Filer, M. De Palo, E. Cattaneo, C. Maake, H. Rehraurer, E. Laczko, M.A. Kurowski, B.J. M, M. Menigatti, J. Luz, T.V. Ranalli, V. Gomes, A. Pastorelli, R. Faggiani, M. Anti, J. Jiricny, H. Clevers, and G. Marra Transcriptome profile of human colorectal adenomas Mol. Cancer Res. 5 2007 1263 1275
24. J. Bartkova, Z. Horejsi, A. Koed Kand Kramer, F. Tort, K. Zieger, P. Guldberg, M. Sehested, J.M. Nesland, C. Lukas, T. Orntoft, J. Lukas, and J. Bartek DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis Nature 434 2005 864 870 (Pubitemid 40558993)
25. V.G. Gorgoulis, L.V. Vassiliou, P. Karakaidos, P. Zacharatos, A. Kotsinas, T. Liloglou, M. Venere, R.J. Ditullio, N.G. Kastrinakis, B. Levy, D. Kletsas, A. Yoneta, M. Herlyn, C. Kittas, and T.D. Halazonetis Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions Nature 434 2005 907 913 (Pubitemid 40559004)
26. S. Bakshi, X. Zhang, S. Godoy-Tundidor, R.Y.S. Cheng, M.A. Sartor, M. Medvedovic, and S. Ho Transcriptome analyses in normal prostate epithelial cells exposed to low-dose cadmium: oncogenic and immunomodulations involving the action of tumor necrosis factor Environ. Health Perspect. 116 2008 769 776 (Pubitemid 351943933)
27. C.J. Mungall Obol: integrating language and meaning in bio-ontologies Comp. Funct. Genomics 5 2004 509 520
28. G.R. Librelotto, J.C. Ramalho, P.R. Henriques, J.B. Gassen, and R.C. Turchetti A framework to specify, extract and manage topic maps driven by ontology International Conference on Design of Communication SIGDOC: 2224 September 2008 2008 ACM, DesignLab Lisbon 155 162
29. R.D. Wood, M. Mitchell, J.G. Sgouros, and T. Lindahl Human DNA repair genes Science 291 2001 1284 1289 (Pubitemid 32173086)
30. M.A.A. Castro, J.L. Rybarczyk Filho, R.J.S. Dalmolin, M. Sinigaglia, J.C.F. Moreira, J.C.M. Mombach, and R.M.C. de Almeida ViaComplex: software for landscape analysis of gene expression networks in genomic context Bioinformatics 25 2009 1468 1469