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We proposed to use data mining to identify LINE-1 (L1) characteristics that were associated with gene expression in bladder cancer. The data were collected from L1Base and GSE3167. The memory-efficient data structure called FP-Tree was employed to enumerate all frequent item sets. The frequent item sets were then used to produce rules for predicting ˵down regulation″ and ˵not down.″ Each rule was assigned a p-value by means of Chi-square test. No statistically significant rules for ˵down″ had been found, in contrast 692 rules for ˵not down″ were significant with odd ratios ranging from 1.68 to 1.98. All the significant rules were concentrated only in 20 characteristics. We were able to infer the L1 characteristics that down-regulated genes. Those characteristics were number of L1 elements in host genes, full-length intactness, number of CpG islands, conserved 5΄UTR and mutated ORF2. [ABSTRACT FROM AUTHOR]

In mammals, epigenetic modifications play an essential role both in establishing transcription profiles and in organizing DNA architecture within the cell nucleus. Specifically, the role of epigenetic modifications in regulating X-chromosome inactivation, genomic imprinting and tissue-specific expression is widely recognized. In addition, the implied role of epigenetic modifications in cell differentiation and development has recently been highlighted by the recognition of the roles of epigenetic regulators or processes in a number of human diseases, including genetic disorders such as Alpha-thalassemia/mental retardation, X-linked (ATRX), Facioscapulohumeral muscular dystrophy (FSHD), Immunodeficiency-Centromere Instability-Facial anomalies (ICF) and Rett syndrome. Particular attention has been focused on the study of epigenetic alterations in cancer, which is the subject of intense multidisciplinary efforts and has an impact not only in understanding the mechanisms of epigenetic regulation but also in guiding the development of novel and promising therapies for cancer treatment. Initial data about epigenetic changes in cardiovascular, neurological and autoimmune disorders are also starting to emerge. The examples discussed herein not only summarize the widespread association of epigenetic alterations with disease, but also bring to central stage the importance of accomplishing different epigenome projects to understand this fundamental human biological process. [ABSTRACT FROM AUTHOR]