title: BcCluster: A Bladder Cancer Database at the Molecular Level.
abstract: BACKGROUND
  Bladder Cancer (BC) has two clearly distinct phenotypes. Non-muscle invasive BC has good prognosis and is treated with tumor resection and intravesical therapy whereas muscle invasive BC has poor prognosis and requires usually systemic cisplatin based chemotherapy either prior to or after radical cystectomy. Neoadjuvant chemotherapy is not often used for patients undergoing cystectomy. High-throughput analytical omics techniques are now available that allow the identification of individual molecular signatures to characterize the invasive phenotype. However, a large amount of data produced by omics experiments is not easily accessible since it is often scattered over many publications or stored in supplementary files.
  
  
  OBJECTIVE
  To develop a novel open-source database, BcCluster (http://www.bccluster.org/), dedicated to the comprehensive molecular characterization of muscle invasive bladder carcinoma.
  
  
  METHODS
  A database was created containing all reported molecular features significant in invasive BC. The query interface was developed in Ruby programming language (version 1.9.3) using the web-framework Rails (version 4.1.5) (http://rubyonrails.org/).
  
  
  RESULTS
  BcCluster contains the data from 112 published references, providing 1,559 statistically significant features relative to BC invasion. The database also holds 435 protein-protein interaction data and 92 molecular pathways significant in BC invasion. The database can be used to retrieve binding partners and pathways for any protein of interest. We illustrate this possibility using survivin, a known BC biomarker.
  
  
  CONCLUSIONS
  BcCluster is an online database for retrieving molecular signatures relative to BC invasion. This application offers a comprehensive view of BC invasiveness at the molecular level and allows formulation of research hypotheses relevant to this phenotype.
authors.affiliation: Charité-Universitätsmedizin Berlin, Berlin, Germany; Mosaiques diagnostics GmbH, Hannover, Germany.
authors.forename: Akshay
authors.initials: A
authors.lastname: Bhat
authors.affiliation: Biomedical Research Foundation Academy of Athens , Biotechnology Division, Athens, Greece.
authors.forename: Marika
authors.initials: M
authors.lastname: Mokou
authors.affiliation: Biomedical Research Foundation Academy of Athens , Biotechnology Division, Athens, Greece.
authors.forename: Jerome
authors.initials: J
authors.lastname: Zoidakis
authors.affiliation: Institute for Molecular Cardiovascular Research (IMCAR) , Aachen, Germany.
authors.forename: Vera
authors.initials: V
authors.lastname: Jankowski
authors.affiliation: Biomedical Research Foundation Academy of Athens , Biotechnology Division, Athens, Greece.
authors.forename: Antonia
authors.initials: A
authors.lastname: Vlahou
authors.affiliation: Mosaiques diagnostics GmbH, Hannover, Germany; BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.
authors.forename: Harald
authors.initials: H
authors.lastname: Mischak
keywords: Bladder cancer; bioinformatics; biomarker; data integration; protein interactome; relational database management system; survivin; web application framework