Abstract—CpG islands are clusters of CG-rich DNA sequences, approximately half of which exist in 5’ region of human housekeeping genes. Using various AI algorithms, previous studies classified CpG islands based on the criteria: length ≥ 200 bp, %GC ≥ 50%, and ObsCpG(Observed CpG)/ExpCpG(Expected CpG) ≥ 0.60. They showed that CpG islands overlap the promoter of all human housekeeping genes and over half of all tissue-specific genes.
Using CpGIE(CpG Island Explorer), we evaluated suggested criteria for the search of CpG island of human gene chromosome 18, 19, 20. Manipulating three different criteria: length, %GC, and ObsCpG/ExpCpG rate, we found most appropriate criteria for CpG detection. One of the most important processes of our assessment is to decide whether the new criteria effectively exclude Alu repeats. Moreover, by assorting association type: promoter-relation, within-relation, end-relation, we confirmed that CpG islands defined by the new criteria showed better function as gene markers.
Index Terms—Bioinformatics, CpG island, gene marker
The authors are with Hankuk Academy of Foreign Studies, Wangsan-ri, Mohyeon-myeon, Cheoin-gu, Yongin-si, Gyeonggi-do, Korea (e-mail: janny4615@naver.com, ljj960819@gmail.com, seonghui12@gmail. com, hjweebee1@naver.com, gwi03186@naver.com).
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Cite: Haewon Kim, Jongjun Lee, Seonghui Yu, Junhyung Bae, Yeonho Jung, and Taeseon Yoon, "Assessment of Criteria Regarding CpG Islands of Their Role as Gene Marker," International Journal of Chemical Engineering and Applications vol. 5, no. 5, pp. 374-378, 2014.
