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

Russian Journal of Genetics: Applied Research

Volumn 1, Issue 1, 2011, Pages 21-28

  Podkolodnaya, O A ^a   Yarkova, E E ^a   Demenkov, P S ^a   Konovalova, O S ^c   Ivanisenko, V A ^a   Kolchanov, N A ^a,b  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b NOVOSIBIRSK STATE UNIVERSITY   (Russian Federation)

^c Tyumen Office   (Russian Federation)

Author keywords

associative networks; Automated text mining; glaucoma; myopia

Indexed keywords

ARTICLE; COMPUTER SYSTEM; DISEASE ASSOCIATION; GENETIC ANALYSIS; GENOTYPE; GLAUCOMA; HUMAN; MYOPIA; OPEN ANGLE GLAUCOMA; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS;

EID: 84864753085     PISSN: 20790597     EISSN: 20790600     Source Type: Journal    
DOI: 10.1134/S2079059711010059     Document Type: Article

References (42)

1. 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.
2. Alexeev, V. N., Samusenko, I. A., Clinical-Morphological Changes in the Frontal Eye Section, Glaucoma., 2004, no. 1, pp. 3-7.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. Grocott, T., Frost, V., Maillard, M., et al., Refractive Error and Glaucoma, Acta Ophthalmol. Scand., 2001, vol. 79, pp. 560-566.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. Loyo-Berríos, N. I., Blustein, J. N., Primary Open-Angle Glaucoma and Myopia: a Narrative Review, WMJ., 2007, vol. 106, pp. 85-95.
21. 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.
22. 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.
23. 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.
24. Nesterov, A. P., Primary Open-Angle Glaucoma: Pathogenesis and Principles of Treatment, Clinical ophthalmology., 2000, vol. 1, no. 1, pp. 47-50.
25. 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.
26. 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.
27. 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.
28. 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.
29. Sarfarazi, M., Rezaie, T., Optineurin in Primary Open Angle glaucoma, Ophthalmol. Clin. North. Am., 2003, vol. 6, pp. 529-541.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. Volkov, V. V., Glaucoma with Pseudonormal Pressure. M., 2001, p. 275.
37. 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.
38. 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.
39. 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.
40. 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.
41. 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.
42. 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.