MOTIVATION: DNA methylation has been shown to be spatially dependent across chromosomes. Previous studies have focused on the influence of genomic context on the dependency structure, while not considering differences in dependency structure between individuals. RESULTS: We modeled spatial dependency with a flexible framework to quantify the dependency structure, focusing on inter-individual differences by exploring the association between dependency parameters and technical and biological variables. The model was applied to a subset of the Finnish Twin Cohort study (N = 1611 individuals). The estimates of the dependency parameters varied considerably across individuals, but were generally consistent across chromosomes within individuals. The variation in dependency parameters was associated with bisulfite conversion plate, zygosity, sex and age. The age differences presumably reflect accumulated environmental exposures and/or accumulated small methylation differences caused by stochastic mitotic events, establishing recognizable, individual patterns more strongly seen in older individuals. AVAILABILITY AND IMPLEMENTATION: The twin dataset used in the current study are located in the Biobank of the National Institute for Health and Welfare, Finland. All the biobanked data are publicly available for use by qualified researchers following a standardized application procedure (https://thl.fi/en/web/thl-biobank/for-researchers). A R-script for fitting the dependency structure to publicly available DNA methylation data with the software used in this article is provided in supplementary data. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

This paper describes the overall architecture and design aspects of a hybrid relational and XML database system called System RX. We believe that such a system is fundamental in the evolution of enterprise data management solutions: XML and relational data will co-exist and complement each other in enterprise solutions. Furthermore, a successful XML repository requires much of the same infrastructure that already exists in a relational database management system. Finally, XML query languages have considerable conceptual and functional overlap with relational dataflow engines. System RX is the first truly hybrid system that comingles XML and relational data, giving them equal footing. The new support for XML includes native support for storage and indexing as well as query compilation and evaluation support for the latest industry-standard query languages, SQL/XML and XQuery. By building a hybrid system, we leverage more than 20 years of data management research to advance XML technology to the same standards expected from mature relational systems.