Yonsei Proteome Research Center and Cancer Proteome Research Center, Department of the Integrated Omics for Biomedical Science, World Class University Graduate Program, Yonsei University, 50 Yonsei-ro, Sudaemoon-ku, Seoul 120-749, Korea.
J Proteome Res. 2013 Jan 4;12(1):106-11. doi: 10.1021/pr3009447. Epub 2012 Dec 19.
In an effort to map the human proteome, the Chromosome-centric Human Proteome Project (C-HPP) was recently initiated. As a member of the international consortium working on this project, our laboratory developed a gene-centric proteomic database called GenomewidePDB, which integrates proteomic data for proteins encoded by chromosomes with transcriptomic data and other information from public databases. As an example case, we chose chromosome 13, which is the largest acrocentric human chromosome with the lowest gene density and contains 326 predicted proteins. All proteins stored in GenomewidePDB are linked to other resources, including neXtProt and Ensembl for protein and gene information, respectively. The Global Proteome Machine database (GPMdb) and the PeptideAtlas are also accessed for observed mass spectrometry (MS) information, while Human Protein Atlas is used for information regarding antibody availability and tissue expression, respectively. Gene ontology disease information is also included. As a pilot work, we constructed this GenomewidePDB with the identified 3615 proteins including 53 chromosome 13-origin proteins that are present in normal human placenta tissue. Thus, developing a comprehensive database containing actual experimental proteomics data will provide a valuable resource for cross chromosomal comparison in the C-HPP community.
为了绘制人类蛋白质组图谱，最近启动了染色体中心人类蛋白质组计划（C-HPP）。作为参与该项目的国际联盟的一员，我们实验室开发了一个称为“全基因组 PDB”的基于基因的蛋白质组数据库，该数据库整合了染色体编码蛋白的蛋白质组数据、转录组数据和来自公共数据库的其他信息。作为一个示例案例，我们选择了 13 号染色体，它是人类最大的近端着丝粒染色体，基因密度最低，包含 326 个预测蛋白。全基因组 PDB 中存储的所有蛋白质都与其他资源相关联，包括 neXtProt 和 Ensembl 分别用于蛋白质和基因信息，还可以访问全球蛋白质组机器数据库（GPMdb）和肽图集以获取观察到的质谱（MS）信息，而人类蛋白质图集则分别用于抗体可用性和组织表达信息。还包括基因本体疾病信息。作为一项初步工作，我们用包括 53 个存在于正常人类胎盘组织中的 13 号染色体起源蛋白在内的 3615 个蛋白构建了这个全基因组 PDB。因此，开发一个包含实际实验蛋白质组学数据的综合数据库将为 C-HPP 社区的跨染色体比较提供有价值的资源。
