GenomewidePDB, a Proteomic Database Exploring the Comprehensive Protein Parts List and Transcriptome Landscape in Human Chromosomes
GenomewidePDB, a Proteomic Database Exploring the Comprehensive Protein Parts List and Transcriptome Landscape in Human Chromosomes
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DOI：
10.1021/pr3009447
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发表时间：
2013-01-01
影响因子：
4.4
通讯作者：
Paik, Young-Ki
中科院分区：
文献类型：
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作者：
Jeong, Seul-Ki;Lee, Hyoung-Joo;Paik, Young-Ki
为了绘制人类蛋白质组图谱，最近启动了以染色体为中心的人类蛋白质组计划（C-HPP）。作为从事该项目的国际联盟的成员，我们的实验室开发了一个以基因为中心的蛋白质组数据库，称为GenomewidePDB，该数据库将染色体编码蛋白质的蛋白质组数据与转录组数据和公共数据库中的其他信息整合在一起。作为一个例子，我们选择了13号染色体，这是最大的近端着丝粒人类染色体，基因密度最低，包含326个预测蛋白质。GenomewidePDB中存储的所有蛋白质都与其他资源相关联，包括分别用于蛋白质和基因信息的neXtProt和Ensembl。全球蛋白质组机器数据库（GPMDB）和PeptideAtlas也可用于观察质谱（MS）信息，而人类蛋白质图谱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。作为试点工作，我们用鉴定的3615种蛋白质构建了这个全基因组PDB，其中包括53种存在于正常人胎盘组织中的13号染色体起源蛋白。因此，开发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。
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 induded. 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.