Here is a brief introduction about the Chinese Chromosome-Centric Human Proteome Database (C-HPD, http://proteomeview.hupo.org.cn/chromosome/), which is also the Chromosome browser of ProteomeView. C-HPD is one layer of ProteomeView, which focuses on chromosome location and gene structure of protein coding genes. As ProteomeView is still in the process of construction, more detailed document will be added soon.
1. What is C-HPD?
The launch of the Chromosome-Centric Human Proteome Project (C-HPP) provides an opportunity to deeply explore the human proteome. Chinese Human Chromosome Proteome Consortium (CCPC) declared to implement proteomic exploration of encoding genes on human chromosome 1, 8 and 20. Under the collaboration of CCPC for these three chromosomal proteome projects, a comprehensive proteome dataset was generated using normal and carcinoma tissues from human liver, colon and stomach. Thirteen cell lines were selected as well, including eight, two and three cell lines for liver, colon and stomach, respectively, for comprehensive proteomics analysis. The details of all proteins identified in this study are presented in C-HPD by a way of tabular visualization.
2. How to browse and search the data in C-HPD?
In C-HPD, all data generated by Chinese Human Chromosome Proteome Consortium (CCPC) is organized by different Chromosome. Chromosome 1, 8 and 20 are three chromosomes declared to be taken by CCPC, the data of which can be accessed by clicking three Circus figures. Also, user can browse data about all 24 chromosomes through links of corresponding chromosomes at bottom of the page.
Similar to the gene display method used by Paik (Nat Biotechnol 2012, 30, (3), 221-223.), a way of tabular visualization is construct to present the data in C-HPD, including the information of protein characterizations and the index of protein and mRNA abundance from this study for each identified genes. Five different colors are used in this table to represent four levels of corresponding data. The top level is marked as green, means the highest quality for protein characterization or top quarter protein/mRNA abundance, then the yellow, red and gray indicating the decreased of quality or abundance. The dark box means that the protein does not contain the characterization or could not be identified in proteome or transcriptome.
Currently, three kinds of keywords can be used to search through the C-HPD, "protein ID", "gene ID" and "protein description". The advanced search will be added in future.
3. How to get the data in C-HPD?
All data in ProteomeView will be available from the "ownload" link. As this database is still in the process of development, the protein and peptide identification of C-HPD and can be accessed by ftp://126.96.36.199/CCPD.
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