Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China.
Nucleic Acids Res. 2010 Jan;38(Database issue):D658-64. doi: 10.1093/nar/gkp933. Epub 2009 Nov 9.
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/.
癌症相关研究一直是生物医学研究的焦点。多年来，来自世界各地的科学家和医生的努力已经在基因组、转录组、蛋白质组甚至代谢组水平上产生了大量的数据，并且已经建立了 DNA 和 RNA 癌症特征数据库。在这里，我们提出了一个人类癌症差异表达蛋白数据库 (dbDEPC)，旨在收集经过精心整理的癌症蛋白质组学数据，为蛋白水平表达变化的信息提供资源，并探索不同癌症之间的蛋白谱差异。dbDEPC 目前包含 15 种癌症中 1803 种差异表达的蛋白，这些蛋白是从同行评审出版物中的 65 个质谱 (MS) 实验中整理出来的。除了 MS 实验外，还整合了来自同一文献的低通量实验数据和来自外部数据库的癌症相关基因，以提供一些验证信息。此外，dbDEPC 将差异蛋白与人类基因组中的重要结构变异（如拷贝数变异或单核苷酸多态性）相关联，这可能有助于解释 DNA 水平上蛋白表达的变化。dbDEPC 中的数据可以通过蛋白标识符、描述或序列进行查询；检索到的蛋白条目提供了在癌症中观察到的差异表达模式，以及详细的注释。dbDEPC 有望成为蛋白质水平癌症特征的参考数据库。该数据库可在 http://dbdepc.biosino.org/index/ 上获取。
