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C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD)
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 e...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231654/ https://www.ncbi.nlm.nih.gov/pubmed/30419069 http://dx.doi.org/10.1371/journal.pone.0207371 |
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author | Fernandes, Marco Patel, Alisha Husi, Holger |
author_facet | Fernandes, Marco Patel, Alisha Husi, Holger |
author_sort | Fernandes, Marco |
collection | PubMed |
description | 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 |
format | Online Article Text |
id | pubmed-6231654 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-62316542018-11-19 C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD) Fernandes, Marco Patel, Alisha Husi, Holger PLoS One Research Article 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 Public Library of Science 2018-11-12 /pmc/articles/PMC6231654/ /pubmed/30419069 http://dx.doi.org/10.1371/journal.pone.0207371 Text en © 2018 Fernandes et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Fernandes, Marco Patel, Alisha Husi, Holger C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD) |
title | C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD) |
title_full | C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD) |
title_fullStr | C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD) |
title_full_unstemmed | C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD) |
title_short | C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD) |
title_sort | c/vddb: a multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (cvd) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231654/ https://www.ncbi.nlm.nih.gov/pubmed/30419069 http://dx.doi.org/10.1371/journal.pone.0207371 |
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