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. 2010 Jan;38(Database issue):D658-64.
doi: 10.1093/nar/gkp933. Epub 2009 Nov 9.

dbDEPC: A Database of Differentially Expressed Proteins in Human Cancers

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Free PMC article

dbDEPC: A Database of Differentially Expressed Proteins in Human Cancers

Hong Li et al. Nucleic Acids Res. .
Free PMC article

Abstract

Cancer-related investigations have long been in the limelight of biomedical research. Years of effort from scientists and doctors worldwide have generated large amounts of data at the genome, transcriptome, proteome and even metabolome level, and DNA and RNA cancer signature databases have been established. Here we present a database of differentially expressed proteins in human cancers (dbDEPC), with the goal of collecting curated cancer proteomics data, providing a resource for information on protein-level expression changes, and exploring protein profile differences among different cancers. dbDEPC currently contains 1803 proteins differentially expressed in 15 cancers, curated from 65 mass spectrometry (MS) experiments in peer-reviewed publications. In addition to MS experiments, low-throughput experiment data from the same literatures and cancer-associated genes from external databases were also integrated to provide some validation information. Furthermore, dbDEPC associates differential proteins with important structural variations in the human genome, such as copy number variations or single nucleotide polymorphisms, which might be helpful for explaining changes in protein expression at the DNA level. Data in dbDEPC can be queried by protein identifier, description or sequence; the retrieved protein entry provides the differential expression pattern seen in cancers, along with detailed annotations. dbDEPC is expected to be a reference database for cancer signatures at the protein level. This database is provided at http://dbdepc.biosino.org/index/.

Figures

Figure 1.
Figure 1.
Data content of dbDEPC. (A) Number of differentially expressed human proteins in each cancer. (B) Overlap between dbDEPC and two external databases. (C) Statistics for genomic variations in human genes collected in dbDEPC. For all inclusive representation, circle surface areas in B and C are disproportional so that small numbers can also be shown in the graph.
Figure 2.
Figure 2.
The web interface of dbDEPC. (A) Search page. Proteins can be searched by IPI ID, Entrez gene ID, protein description or sequence. (B) Browse page. Users can browse proteins in multiple selected cancers. (C) Result page for search or browse function. Results summarize protein matches and provide a list of basic protein information. (D) A part of an example protein record. The whole protein page can be found in Supplementary Figure S1, consisting of summary, expression, and annotation sections.
Figure 3.
Figure 3.
(A) Profile page. Users can input a protein list and select cancers of interest to produce an expression heatmap. (B) Example heatmap of differentially expressed proteins in multiple cancers. (C) Number of proteins in multiple cancers. (D) Clustering of cancers based on differentially expressed protein profiles.

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