title: Integrative analysis of cancer-related data using CAP.
abstract: The development of human cancer is a highly complex process and can be considered the result of several combined events, such as genetic alterations, disturbance of signal transduction, or failure of immunological surveillance. Cancer-related databases usually focus on specific fields of research, e.g., cancer genetics or cancer immunology, whereas the complexity of cancer genesis requires an integrated analysis of heterogeneous data from several sources. Here we present the cancer-associated protein database (CAP), a novel analysis system for cancer-related data. CAP integrates data from multiple external databases, augments these data with functional annotations, and offers tools for statistical analysis of these data. We have employed CAP to analyze genes that have been found to cause an autoimmune response in cancer. In particular, we explored the connection between the autoimmune response, mutations, and overexpression of these genes. Our preliminary results suggest that mutations are not significant contributors to raising an antibody response against tumor antigens, whereas overexpression seems to play a more important role. We hereby demonstrate how different types of data can be integrated and analyzed successfully, providing interesting results. As the amount of available data is growing rapidly, a combined analysis will play an important role in exploring the genetic and immunological basis of cancer. CAP is freely available at the following web site: http://www.bioinf.uni-sb.de/CAP/.
authors.affiliation: Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
authors.forename: Pierre
authors.initials: P
authors.lastname: Dönnes
authors.forename: Annette
authors.initials: A
authors.lastname: Höglund
authors.forename: Marc
authors.initials: M
authors.lastname: Sturm
authors.forename: Nicole
authors.initials: N
authors.lastname: Comtesse
authors.forename: Christina
authors.initials: C
authors.lastname: Backes
authors.forename: Eckart
authors.initials: E
authors.lastname: Meese
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Lenhof
mesh_terms: D015551:Autoimmunity; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020407:Internet; D009363:Neoplasm Proteins / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics* / Q000276:immunology* / Q000378:metabolism
chemical_list: D009363:Neoplasm Proteins