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Modeling the Human Genome Maintenance network

Author

Listed:
  • Simão, Éder M.
  • Cabral, Heleno B.
  • Castro, Mauro A.A.
  • Sinigaglia, Marialva
  • Mombach, José C.M.
  • Librelotto, Giovani R.

Abstract

We present the Ontocancro Database (www.ontocancro.org) illustrated with applications to network modeling and pathway functional analysis. The database compiles information on gene pathways involved in Human Genome Maintenance Mechanisms (GMM) whose dysfunction accounts for cancer and several genetic syndromes. Ontocancro is the most complete, manually curated information resource available providing genomics and interatomics data on 120 GMM pathways (comprising a total of 1435 genes) obtained from curated databases and the literature. It was developed to facilitate the GMM network and functional modeling for the integration of genomic, transcriptomic and interatomic data. The database’s main contribution is the Ontocancro pathways that are expanded versions of standard GMM pathways for including additional genes with evidences of functional involvement in GMM. Using these pathways we find the largest cluster of interacting proteins involving GMM and on it we project a microarray study of adenoma to identify the regions of the network that are highly altered. In the last application we present the dynamical alterations of the pathways in a study of the effect of Cadmium, a known carcinogenic substance, on prostate cells to find that it produces a strong decrease of the pathway activity.

Suggested Citation

  • Simão, Éder M. & Cabral, Heleno B. & Castro, Mauro A.A. & Sinigaglia, Marialva & Mombach, José C.M. & Librelotto, Giovani R., 2010. "Modeling the Human Genome Maintenance network," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(19), pages 4188-4194.
    • Handle: RePEc:eee:phsmap:v:389:y:2010:i:19:p:4188-4194
    DOI: 10.1016/j.physa.2010.05.051
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    References listed on IDEAS

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    1. Christoph Lengauer & Kenneth W. Kinzler & Bert Vogelstein, 1998. "Genetic instabilities in human cancers," Nature, Nature, vol. 396(6712), pages 643-649, December.
    2. Jirina Bartkova & Zuzana Hořejší & Karen Koed & Alwin Krämer & Frederic Tort & Karsten Zieger & Per Guldberg & Maxwell Sehested & Jahn M. Nesland & Claudia Lukas & Torben Ørntoft & Jiri Lukas & Jiri B, 2005. "DNA damage response as a candidate anti-cancer barrier in early human tumorigenesis," Nature, Nature, vol. 434(7035), pages 864-870, April.
    3. Jan H. J. Hoeijmakers, 2001. "Genome maintenance mechanisms for preventing cancer," Nature, Nature, vol. 411(6835), pages 366-374, May.
    4. Vassilis G. Gorgoulis & Leandros-Vassilios F. Vassiliou & Panagiotis Karakaidos & Panayotis Zacharatos & Athanassios Kotsinas & Triantafillos Liloglou & Monica Venere & Richard A. DiTullio & Nikolaos , 2005. "Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions," Nature, Nature, vol. 434(7035), pages 907-913, April.
    Full references (including those not matched with items on IDEAS)

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