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Application of the ANDCell computer system to reconstruction and analysis of associative networks describing potential relationships between myopia and glaucoma

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Russian Journal of Genetics: Applied Research

Abstract

Reconstruction of an associative network, which represents molecular relationships among proteins, metabolites, and molecular processes associated with myopia and glaucoma was performed with the use of the ANDCell computer system which includes a database of knowledge and facts extracted automatically from PubMed. This network contains over 200 proteins and genes and more than 2000 interactions between them, including proteins and genes associated with both open-angle glaucoma and myopia. Reduction of this network and further analysis of molecular pathways revealed candidate genes for simultaneous genotyping of both myopia and open angle glaucoma.

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References

  • Al-Dabbagh, N.M., Al-Dohayan, N., Arfin, M., Tariq, M., Apolipoprotein E Polymorphisms and Primary Glaucoma, Mol. Vis., 2009, vol. 15, pp. 912–919.

    PubMed  CAS  Google Scholar 

  • Alexeev, V.N., Samusenko, I.A., Clinical-Morphological Changes in the Frontal Eye Section, Glaucoma., 2004, no. 1, pp. 3–7.

  • Aman, E.E., Demenkov, P.S., Nemiatov, A., Ivanisenko, V.A., Associative Network Discovery (AND)—Software Package for Automated Reconstruction of Molecular-Genetic Association Network Proc. of the 3rd Moscow Conf. on Computational Molecular Biology. Moscow, Russia, 2007, pp. 33–34.

  • Demenkov, P.S., Aman, E.A., Ivanisenko, V.A., Associative Network Discovery (AND)—a Computer System for Automatic Reconstruction of Associative Knowledge Net about Molecular-Genetic Interactions, Vychislitel’nye tekhnologii., 2008, vol. 13, no. 2, pp. 15–19.

    Google Scholar 

  • Fan, B.J., Wang, D.Y., Fan, D.S., et al., SNPs and Interaction Analysis of Myocilin, Optineurine, and Apolipoprotein E in Primary Open Angle Glaucoma Patients, Mol. Vis., 2005, vol. 11, pp. 625–631.

    PubMed  CAS  Google Scholar 

  • Fingert, J.H., Heon, E., Liebmann, J.M., et al., Variants in Optineurine Gene and Their Association with Tumor Necrosis Factor-alpha Polymorphisms in Japanese Patients with Glaucoma, Invest. Ophthalmol. Vis. Sci., 2004, vol. 45, no. 12, pp. 4359–4367.

    Article  Google Scholar 

  • Fingert, J.H., Heon, E., Liebmann, J.M., et al., Analysis of myocilin mutations in 1703 glaucoma patients from five different populations, Hum. Mol. Genet., 1999, vol. 8, pp. 899–905.

    Article  PubMed  CAS  Google Scholar 

  • Funayama T., Ishikawa K., Ohtake Y. et al., Variants in Optineurine Gene and Their Association with Tumor Necrosis Factor-alpha Polymorphisms in Japanese Patients with Glaucoma, Invest. Ophthalmol. Vis. Sci., 2004, vol. 45, no. 12, pp. 4359–4367.

    Article  PubMed  Google Scholar 

  • Gong, G., Kosoko-Lasaki, O., Haynatzki, G.R., Wilson, M.R., Genetic Dissection of Myocilin Glaucoma, Hum. Mol. Genet., 2004, vol. 13, pp. R91–R102.

    Article  PubMed  CAS  Google Scholar 

  • Grinchuk, O., Kozmik, Z., Wu, X., Tomarev, S., The Optimedin gene is a Downstream Target of Pax6 J. Biol. Chem., 2005, vol. 280, no. 42, pp. 35228–35237.

    Article  PubMed  CAS  Google Scholar 

  • Grocott, T., Frost, V., Maillard, M., et al., Refractive Error and Glaucoma, Acta Ophthalmol. Scand., 2001, vol. 79, pp. 560–566.

    Article  Google Scholar 

  • Grocott T., Frost V., Maillard M. et al., The MH1 domain of Smad3 interacts with Pax6 and represses autoregulation of the Pax6 P1 promoter, Nucl. Acids Res., 2007, vol. 35, pp. 890–901.

    Article  PubMed  CAS  Google Scholar 

  • Han, W., Yap, M.K., Wang, J., Yip, S.P., Family-Based Association Analysis of Hepatocyte Growth Factor (HGF) Gene Polymorphism in High Myopia, Invest. Ophthalmol. Vis. Sci., 2006, vol. 47, no. 6, pp. 2291–2299.

    Article  PubMed  Google Scholar 

  • Hewitt, A.W., Kearns, L.S., Jamienson, R.V., et al., PAX6 Mutations May Be Associated with High Myopia, Ophthalmic Genet., 2007, vol. 28, no. 3., pp. 179–182.

    Article  PubMed  CAS  Google Scholar 

  • Ivanisenko, V.A., Demenkov, P.S., Aman, E.E., et al., Associative Network and Protein Structure Discovery: a Software Complex for Facilitating Search of Targets for Drugs, Drug Design, and Evaluation of Molecular Toxicity, Proc. of the 3rd Intern. Conf. “Basic Science for Medicine”. Novosibirsk, Russia, 2007, p. 92.

  • Kumar, A., Basavaraj, M.G., Gupta, S.K., et al., Role of CYP1B1, MYOC, OPTN, and OPTC Genes in Adult-Onset Primary Open-Angle Glaucoma: Predominance of CYP1B1 Mutations in Indian Patients, Mol. Vis., 2007, vol. 30, no. 13, pp. 667–676.

    Google Scholar 

  • Kwon, Y.H., Chen, W.-C., Tsai, F.-J., Tsai, S.-W., Distributions of p53 Codon 72 Polymorphism in Primary Open Angle Glaucoma, Brit. J. Ophthalmol., 2002, vol. 86, pp. 767–770.

    Article  Google Scholar 

  • Lin H.-J., Chen W.-C., Tsai F.-J., Tsai S.-W. Distributions of p53 codon 72 polymorphism in primary open angle glaucoma, Brit. J. Ophthalmol., 2002, vol. 86, pp. 767–770.

    Article  Google Scholar 

  • Liu, Y., Vollrath, D., Reversal of Mutant Myocilin Non-Secretion and Cell Killing: Implication for Glaucoma Hum. Mol. Genet., 2004, vol. 13, pp. 1193–1204.

    Article  PubMed  CAS  Google Scholar 

  • Loyo-Berríos, N.I., Blustein, J.N., Primary Open-Angle Glaucoma and Myopia: a Narrative Review, WMJ., 2007, vol. 106, pp. 85–95.

    PubMed  Google Scholar 

  • Mitchell, P., Hourihan, F., Sandbach, J., Wang, J.J., The Relationship between Glaucoma and Myopia: the BlueMountain Eye Study, Ophthalmology., 1999, vol. 106, pp. 2010–2015.

    Article  PubMed  CAS  Google Scholar 

  • Momynaliev, K.T., Kashin, S.V., Chelysheva, V.V., et al., Functional Divergence of Helicobacter pylori Related to Early Gastric Cancer, Hum. Mol. Genet., 2005, vol. 14, pp. 725–733.

    Article  Google Scholar 

  • Monemi S., Spaeth G., DaSilva A. et al., Identification of a novel adult-onset primary open-angle glaucoma (POAG) gene on 5q22.1 Hum. Mol. Genet., 2005, vol. 14, pp. 725–733.

    Article  PubMed  CAS  Google Scholar 

  • Nesterov, A.P., Primary Open-Angle Glaucoma: Pathogenesis and Principles of Treatment, Clinical ophthalmology., 2000, vol. 1, no. 1, pp. 47–50.

    Google Scholar 

  • Ng, T.K., Lam, C.Y., Lam, D.S., et al., AC and AG Dinucleotide Repeats in the PAX6 P1 Promoter are Associated with High Myopia, Mol. Vis., 2009, vol. 15, pp. 2239–2248.

    PubMed  CAS  Google Scholar 

  • Petile, K.K., Schäche M., Islam, F.M., et al., Assessment of TGIF as a Candidate Gene for Myopia, Invest. Ophthalmol. Vis. Sci., 2008, vol. 49, no. 1, pp. 49–54.

    Article  Google Scholar 

  • Ploski, J.E., Shamster, M.K., Radu, A., Paired-type Homeodomain Transcription Factors are Imported into the Nucleus by Karyopherin 13. Mol. Cell Biol., 2004, vol. 24, no. 11, pp. 4824–4834.

    Article  PubMed  CAS  Google Scholar 

  • Ponte, F., Giuffre, G., Giammanco, R., Dardanoni, G., Risk Factors of Ocular Hypertension and Glaucoma. The Casteldaccia Eye Stud,y Doc. Ophthalmol., 199, vol. 85, pp. 203–210.

  • Sarfarazi, M., Rezaie, T., Optineurin in Primary Open Angle glaucoma, Ophthalmol. Clin. North. Am., 2003, vol. 6, pp. 529–541.

    Article  Google Scholar 

  • Saw, S.M., Gazzard, G.., Shih-Yen E.C., and Chua W.H., Myopia and Associated Pathological Complications, Ophthal. Physiol. Opt., 2005, vol. 25, pp. 381–391.

    Article  Google Scholar 

  • Song, C.Z., Tian, X., Gelegrter, T.D., Glucocorticoid Receptor Inhibits Transforming Growth Factor-beta Signaling by Directly Targeting the Transcriptional Activation Function of Smad3, Proc. Natl Acad. Sci. USA, 1999, vol. 96, no. 21, pp. 11776–11781.

    Article  PubMed  CAS  Google Scholar 

  • Tang, W.C., Yip, S.P., Lo, K.K., Ng, P.W., et al., Linkage and Association of Myocilin (MYOC) Polymorphisms with High Myopia in a Chinese Population, Mol. Vis., 2007, vol. 13, pp. 534–544.

    PubMed  CAS  Google Scholar 

  • Tao, T., Lan, J., Lukacs, G.L., et al., Importin 13 Regulates Nuclear Import of the Glucocorticoid Receptor in Air-way Epithelial Cells, Am. J. Respir. Cell Mol. Biol., 2006, vol. 35, no. 6, pp. 668–680.

    Article  PubMed  CAS  Google Scholar 

  • Torrado, M., Trivedi, R., Zinovieva, R., et al., Optimedin: a Novel Olfactomedin-Related Protein that Interacts with Myocilin, Hum. Mol. Genet., 2002, vol. 11, no. 11, pp. 1291–1301.

    Article  PubMed  CAS  Google Scholar 

  • Tsai, Y.-Y., Chiang, C.-C., Lin, H.-J., et al. A PAX6 Gene Polymorphism is Associated with Genetic Predisposition to Extreme Myopia, Eye, 2008, vol. 22, pp. 576–581.

    Article  PubMed  CAS  Google Scholar 

  • Volkov, V.V., Glaucoma with Pseudonormal Pressure. M., 2001, p. 275.

  • Vittitow, J.L., Borrás, T., Expression of Optineurin, a Glaucoma-Linked Gene, is Influenced by Elevated Intraocular Pressure, Biochem. Biophys. Res. Commun., 2002, vol. 298, pp. 67–74.

    Article  PubMed  CAS  Google Scholar 

  • Wong, T.Y., Klein, B.E., Klein, R., et al., Refractive Errors, Intraocular Pressure, and Glaucoma in a White Population, Ophthalmology, 2003, vol. 110, pp. 211–217.

    Article  PubMed  Google Scholar 

  • Yanivitch, T., Li, Y.J., Metlapally, R., et al., Hepatocyte Growth Factor and Myopia: Genetic Association Analyses in a Caucasian Population, Mol. Vis., 2009, vol. 15, pp. 1028–1035.

    Google Scholar 

  • Yarkova, E.E., Demenkov, P.S., Ivanisenko, V.A., AND-Cell: a Computer System of Automated Extraction of Knowledge about Molecular Genetic Interactions and Regulations from PubMed Abstracts and Their Representation as Semantic Association Networks Proc of the VI Intern. Conf. on Bioinformatics of Genome Regulation and Structure, Novosibirsk, 2008 (BGRS’2008), Novosibirsk, Russia, 2008, p. 260.

    Google Scholar 

  • Zha, Y., Leung, K.H., Lo, K.K., et al., TGFB1 as a Susceptibility Gene for High Myopia: a Replication Study with New Findings, Opthalmol., 2009, vol. 127, no. 4, pp. 541–548.

    CAS  Google Scholar 

  • Zhang, C., Sweezey, N.B., Gagnon, S., et al., A Novel Karyopherin-β Homolog is Developmentally and Hormonally Regulated in Fetal Lung, Am. J. Respir. Cell Mol. Biol., 2000, vol. 22, no. 4, pp. 451–459.

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia

    O. A. Podkolodnaya, E. E. Yarkova, P. S. Demenkov, V. A. Ivanisenko & N. A. Kolchanov

  2. Novosibirsk State University, Novosibirsk, Russia

    N. A. Kolchanov

  3. Eye Microsurgery Complex Rosmedtekhnologii, Yekaterinburg Branch, Tyumen Office, Tyumen, Russia

    O. S. Konovalova

Authors
  1. O. A. Podkolodnaya
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  2. E. E. Yarkova
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  3. P. S. Demenkov
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  4. O. S. Konovalova
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  5. V. A. Ivanisenko
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  6. N. A. Kolchanov
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Correspondence to O. A. Podkolodnaya.

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Original Russian Text © O.A. Podkolodnaya, E.E. Yarkova, P.S. Demenkov, O.S. Konovalova, V.A. Ivanisenko, N.A. Kolchanov, 2010, published in Informatsionnyi Vestnik Vavilovskogo Obshchestva Genetikov i Selektsionerov, 2010, Vol. 14, No. 1, pp. 106–115.

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Podkolodnaya, O.A., Yarkova, E.E., Demenkov, P.S. et al. Application of the ANDCell computer system to reconstruction and analysis of associative networks describing potential relationships between myopia and glaucoma. Russ J Genet Appl Res 1, 21–28 (2011). https://doi.org/10.1134/S2079059711010059

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  • DOI: https://doi.org/10.1134/S2079059711010059

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