Database and web interface
Based on the reported cancer-related gene sets from CGC and CGI, a cancer gene database and a cancer pathway gene database were constructed by the described methods. In total, 436 CGC-originated and 7181 CGI-originated cancer genes were prepared for the reported cancer gene annotation. Additionally, 5,790 CGC-based and 6,744 CGI-based cancer pathway genes were assigned for the annotation of unreported but potential candidate genes (Table 1). The gene ID database for gene symbol conversion, based on HGNC, and the functional annotation database, based on Entrez Gene and UniProt database flat files, were constructed. The types of annotations provided by CaGe are summarized in Table 2.
The main window of the CaGe web interface is shown in Fig. 2 for the cancer gene annotation process. Main menus, located in the upper part of the main window, are linked to the four main functions and home page of the system: 1) home page, 2) cancer gene annotation function, 3) cancer pathway annotation function, 4) cancer gene browsing function, and 5) cancer pathway browsing function. Detailed usages for CaGe are described in the user's guide at http://mgrc.kribb.re.kr/cage/include/cageUserGuide.pdf.