Assessment of Criteria Regarding CpG Islands of Their Role as Gene Marker

Abstract

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.