Geometrical study on diseaserelated ncRNAs based on Z-curve method
Yan-Ling Yang, Ji-Hua Wang
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DOI: 10.4236/health.2009.11005   PDF    HTML     5,049 Downloads   8,651 Views  

Abstract

The Z curve is a very useful method for visual-izing and analyzing DNA sequences. It is a three-dimensional space curve that constitutes a unique representation of a given DNA se-quence. It becomes more and more important to study non-coding regions in the recent years. Using Z curve method, 15 disease-related ncRNAs and some snoRNAs and miRNAs sequences are selected from the NONCODE database in this paper, which relate to Alzheimer Disease. The corresponding Z curves of the studied ncRNAs, sequences have been mapped and compared. The statistical features of the Z curves are ob-tained. These features indicate that the ncRNAs sequences playing same roles in the celluar process have almost the same Z-curves. And the base content in these sequences is almost same too.

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Yang, Y. and Wang, J. (2009) Geometrical study on diseaserelated ncRNAs based on Z-curve method. Health, 1, 24-30. doi: 10.4236/health.2009.11005.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] R. Hershberg, S. Altuvia, and H. Margalit, (2003) A survey of small RNA-encoding genes in Escherichia coli, Nucleic Acids Res., 31, 1813-1820.
[2] V. T. Nguyen, T. Kiss, A. A. Michels, and O. Bensaude, (2001) 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes, Nature, 414, 322-325.
[3] Z. Yang, Q. Zhu, K. Luo, and Q. Zhou, (2001) The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription, Nature, 414, 317-322.
[4] S. R. Eddy, (2001) Non-coding RNA genes and the modern RNA world, Nature Rev. Genet., 2, 919-929.
[5] T. Wu, J. Wang, C. N. Liu, Y. Zhang, B. C. Shi, X. P. Zhu, Z. H. Zhang, G. Skogerbo, L. Chen, H. C. Lu, Y. Zhao, and R. S. Chen, (2006) NP Inter: The non-coding RNAs and protein related biomacromolecules database, Nucleic Acids Res., 34, D150-D152.
[6] J. R. Neilson, G. X. Zheng, C. B. Burge, and P. A. Sharp, (2007) Dynamic regulation of miRNA expression in ordered stages of cellular development, Genes & Dev., 21, 578–589.
[7] G. Storz, (2002) An expanding universe of noncoding RNAs, Science, 296, 1260-1263.
[8] T. Zhang, Z. H. Zhang, L. J. Ling, B. C. Shi, and R. S. Chen, (2004) Conservation analysis of small RNA genes in Escherichia coli, Bioinformatics, 20, 599-603.
[9] G. Casadesus, M. A. Smith, S. Basu, J. Hua, D. E. Capobianco, S. L. Siedlak, X. Zhu, and G. Perry, (2007) Increased isoprostane and prostaglandin are prominent in neurons in Alzheimer disease, Mol Neurodegener, 2(2).
[10] K. E. Webster, J. R. Merory, and J. E. Wittwer, (2006) Gait variability in community dwelling adults with Alzheimer disease, Alzheimer Dis Assoc Disord., 20(1), 37-40.
[11] R. Zhang and C. T. Zhang, (1994) Z curves, an intuitive tool for visualizing and analyzing DNA sequences, J. Biomol. Struc. Dyn., 767-782.
[12] C. T. Zhang, R. Zhang, and H. Y. Ou, (2003) The z curve database: A graphic representation of genome sequences, Bioinformatics, 19, 593-599.
[13] F. B. Guo, H. Y. Ou, and C. T. Zhang, (2003) ZCURVE: A new system for recognizing protein-coding genes in bacterial and archaeal genomes., Nucleic Acids Res., 31, 1780-1789.
[14] J. H. Wang, B. Q. Wang, and L. S. Zhang, (2004) Theoretical Study on the Z Curve, J. Biomol., 19(2), 129-135.
[15] C. N. Liu, B. Y. Bai, G. Skogerbo, L. Cai, W. Deng, Y. Zhang, D. B. Bu, Y. Zhao, and R. S. Chen, (2005) NONECODE: An integrated knowledge database of non-coding RNAs, Nucleic Acids Res, 33, D112-D115.
[16] M. Szymanski, V. A. Erdmann, and J. Barciszewski, (2003) Noncoding regulatory RNAs database, Nucleic Acids Res., 31, 429-431.
[17] C. Zwieb, J. Gorodkin, B. Knudsen, J. Burks, and J. Wower, (2003) tmRDB (tmRNA database), Nucleic Acids Res., 31, 446-447.
[18] T. Wu, J. Wang, C. N. Liu, Y. Zhang, B. C. Shi, X. P. Zhu, Z. H. Zhang, G. Skogerbo, L. Chen, H. C. Lu, Y. Zhao, and R. S. Chen, (2006) NP Inter: The non-coding RNAs and protein related biomacromolecules interaction database, Nucleic Acids Res., 34, D150-D152.

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