title: Integration of cardiac proteome biology and medicine by a specialized knowledgebase.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), 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.
authors: From the NHLBI Proteomics Center at UCLA/NHLBI Proteomics Program.
authors: Nobel C
authors: NC
authors: Zong
authors: Haomin
authors: H
authors: Li
authors: Hua
authors: H
authors: Li
authors: Maggie P Y
authors: MP
authors: Lam
authors: Rafael C
authors: RC
authors: Jimenez
authors: Christina S
authors: CS
authors: Kim
authors: Ning
authors: N
authors: Deng
authors: Allen K
authors: AK
authors: Kim
authors: Jeong Ho
authors: JH
authors: Choi
authors: Ivette
authors: I
authors: Zelaya
authors: David
authors: D
authors: Liem
authors: David
authors: D
authors: Meyer
authors: Jacob
authors: J
authors: Odeberg
authors: Caiyun
authors: C
authors: Fang
authors: Hao-Jie
authors: HJ
authors: Lu
authors: Tao
authors: T
authors: Xu
authors: James
authors: J
authors: Weiss
authors: Huilong
authors: H
authors: Duan
authors: Mathias
authors: M
authors: Uhlen
authors: John R
authors: JR
authors: Yates
authors: Rolf
authors: R
authors: Apweiler
authors: Junbo
authors: J
authors: Ge
authors: Henning
authors: H
authors: Hermjakob
authors: Peipei
authors: P
authors: Ping
mesh_terms: D022126:Access to Information; D000818:Animals; D017173:Caenorhabditis elegans; D030562:Databases, Protein; D004059:Diffusion of Innovation; D004330:Drosophila; D006801:Humans; D051188:Knowledge Bases; D051379:Mice; D009124:Muscle Proteins / Q000378:metabolism*; D009206:Myocardium / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012985:Software Design; D049490:Systems Biology; D018511:Systems Integration; D057188:Workflow
chemical_list: D009124:Muscle Proteins
keywords: COPaKB; Omics science; computational biology; mitochondria; organelles; proteomics; translational medical research
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