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Integration of cardiac proteome biology and medicine by a specialized knowledgebase
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2013 (English)In: Circulation Research, ISSN 0009-7330, E-ISSN 1524-4571, Vol. 113, no 9, 1043-1053 p.Article in journal (Refereed) Published
Abstract [en]

Rationale: Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. Objective: The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. Methods and results: We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB;, a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10 924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. Conclusions: COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

Place, publisher, year, edition, pages
2013. Vol. 113, no 9, 1043-1053 p.
Keyword [en]
Computational biology, COPaKB, Mitochondria, Omics science, Organelles, Proteomics, Translational medical research, protein, proteome, article, bioinformatics, Caenorhabditis elegans, cardiology, Drosophila, heart muscle, human, nonhuman, phenotype, priority journal
National Category
Biological Sciences Hematology
URN: urn:nbn:se:kth:diva-140053DOI: 10.1161/CIRCRESAHA.113.301151ISI: 000329483800008ScopusID: 2-s2.0-84886089276OAI: diva2:689249
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience

QC 20140120

Available from: 2014-01-20 Created: 2014-01-16 Last updated: 2014-01-30Bibliographically approved

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Odeberg, JacobUhlén, Mathias
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