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. 2010 Mar;31(3):219-28.
doi: 10.1002/humu.21176.

CanProVar: A Human Cancer Proteome Variation Database

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Free PMC article

CanProVar: A Human Cancer Proteome Variation Database

Jing Li et al. Hum Mutat. .
Free PMC article

Abstract

Identification and annotation of mutated genes or proteins involved in oncogenesis and tumor progression are crucial for both cancer biology and clinical applications. We have developed a human Cancer Proteome Variation Database (CanProVar) by integrating information on protein sequence variations from various public resources, with a focus on cancer-related variations (crVAR). We have also built a user-friendly interface for querying the database. The current version of CanProVar comprises 8,570 crVARs in 2,921 proteins derived from existing genome variation databases and recently published large-scale cancer genome resequencing studies. It also includes 41,541 non-cancer specific variations (ncsVARs) in 30,322 proteins derived from the dbSNP database. CanProVar provides quick access to known crVARs in protein sequences along with related cancer samples, relevant publications, data sources, and functional information such as Gene Ontology (GO) annotations for the proteins, protein domains in which the variation occurs, and protein interaction partners with crVARs. CanProVar also helps reveal functional characteristics of crVARs and proteins bearing these variations. Our analysis showed that crVARs were enriched in certain protein domains. We also showed that proteins bearing crVARs were more likely to interact with each other in the protein interaction network. CanProVar can be accessed from http://bioinfo.vanderbilt.edu/canprovar.

Figures

Figure 1
Figure 1
The system architecture of CanProVar
Figure 2
Figure 2
Proportion of the CanProVar data from different data sources. The sources for cancer-related variations in the CanProVar database include databases COSMIC (C), OMIM (O), HPI (H), TCGA (T) and the publications from Greenman et al. (G) and Sjöblom et al. (S).
Figure 3
Figure 3
Top 20 cancer types ranked by the amount of crVARs in CanProVar
Figure 4
Figure 4
Output view for a protein/gene-based query in CanProVar. The output view for a protein/gene-based query in CanProVar includes three sections: (A) basic information for the protein corresponded to the queried ID, (B) information on the cancer related variations, and (C) validated nsSNPs in the dbSNP database.
Figure 5
Figure 5
Protein interaction partners of the cancer-related proteins MSH6 and MDC1. MSH6 and MDC1 are colored in dark grey. Their interaction partners are colored in light grey if they have cancer-related variations or white otherwise. Solid lines represent interactions between MSH6/MDC1 and their neighbors while dash lines represent interactions between two MSH6- or MDC1-neighbors that have cancer-related variations.

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