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.