Abstract
The cardiovascular disease (C/VD) database is an integrated and clustered information resource that covers multi-omic studies (microRNA, genomics, proteomics and metabolomics) of cardiovascular-related traits with special emphasis on coronary artery disease (CAD). This resource was built by mining existing literature and public databases and thereafter manual biocuration was performed. To enable integration of omic data from distinct platforms and species, a specific ontology was applied to tie together and harmonise multi-level omic studies based on gene and protein clusters (CluSO) and mapping of orthologous genes (OMAP) across species. CAD continues to be a leading cause of death in the population worldwide, and it is generally thought to be an age-related disease. However, CAD incidence rates are now known to be highly influenced by environmental factors and interactions, in addition to genetic determinants. With the complexity of CAD aetiology, there is a difficulty in research studies to elucidate general elements compared to other cardiovascular diseases. Data from 92 studies, covering 13945 molecular entries (4353 unique molecules) is described, including data descriptors for experimental setup, study design, discovery-validation sample size and associated fold-changes of the differentially expressed molecular features (p-value<0.05). A dedicated interactive web interface, equipped with a multi-parametric search engine, data export and indexing menus are provided for a user-accessible browsing experience. The main aim of this work was the development of a data repository linking clinical information and molecular differential expression in several CVD-related traits from multi-omics studies (genomics, transcriptomics, proteomics and metabolomics). As an example case of how to query and identify data sets within the database framework and concomitantly demonstrate the database utility, we queried CAD-associated studies and performed a systems-level integrative analysis. URL: www.padb.org/cvd
Highlights
Cardiovascular disease (CVD) encompasses many pathological conditions that lead to an integral loss in function of the heart, cardiovascular structures and the circulatory system
Publication-based molecular identifiers were converted to internal identifiers of the Pan-omics Analysis Database (PADB) initiative, which uses the clustered sequences and orthologs (CluSO) identifiers and an ortholog mapping resource (OMAP)
Navigation through the cardiovascular disease (C/VD) database front-end can be either by browsing the study, sample/ demographic, tissue/source or by molecular entry index pages, or alternatively through molecule names, tissue or disease queries in the search interface (S1–S5 Figs)
Summary
Cardiovascular disease (CVD) encompasses many pathological conditions that lead to an integral loss in function of the heart, cardiovascular structures and the circulatory system. In most of the cases the disease remains clinically asymptomatic during the first decades of its development [6], until the surface of the atherosclerotic plaque suffers rupture or erosion, causing formation of a thrombus that obstructs the vessel with deprivation of an adequate blood-flow and consequent ischaemic tissue damage [7]. This leads to severe disease manifestations as myocardial infarction (MI), stroke, or acute coronary disease (ACD) [8]. Despite major improvements in many of the modifiable risk factors, such as smoking habits, alcohol intake, and total cholesterol amongst Western nations over the years [12], CAD still remains the main cause for the majority of cardiovascular events [1]
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