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BcCluster: A Bladder Cancer Database at the Molecular Level.

Akshay Bhat1, Marika Mokou2, Jerome Zoidakis2

  • 1Charité-Universitätsmedizin Berlin, Berlin, Germany; Mosaiques diagnostics GmbH, Hannover, Germany.

Bladder Cancer (Amsterdam, Netherlands)
|July 5, 2016
PubMed
Summary

A new database, BcCluster, centralizes molecular data for muscle invasive bladder cancer (BC). This resource aids researchers in understanding BC invasiveness and developing new hypotheses.

Keywords:
Bladder cancerbioinformaticsbiomarkerdata integrationprotein interactomerelational database management systemsurvivinweb application framework

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Area of Science:

  • Oncology
  • Bioinformatics
  • Genomics

Background:

  • Bladder cancer (BC) presents distinct phenotypes: non-muscle invasive BC with good prognosis and muscle invasive BC with poor prognosis.
  • Muscle invasive BC typically requires systemic chemotherapy and radical cystectomy, with neoadjuvant chemotherapy infrequently used.
  • High-throughput omics technologies identify molecular signatures of invasive BC, but data is often fragmented across publications.

Purpose of the Study:

  • To develop BcCluster, a novel open-source database for comprehensive molecular characterization of muscle invasive bladder carcinoma.
  • To create a centralized repository for accessible molecular data related to BC invasion.
  • To facilitate research into the molecular underpinnings of BC invasiveness.

Main Methods:

  • A database was constructed to house all reported molecular features significant in invasive BC.
  • The query interface was developed using Ruby (version 1.9.3) and the Rails web framework (version 4.1.5).
  • The database integrates data from published literature on BC invasion.

Main Results:

  • BcCluster aggregates data from 112 references, detailing 1,559 statistically significant features related to BC invasion.
  • The database includes 435 protein-protein interaction datasets and 92 significant molecular pathways for BC invasion.
  • Users can retrieve binding partners and pathways for specific proteins, exemplified by survivin.

Conclusions:

  • BcCluster provides an online platform for accessing molecular signatures associated with BC invasion.
  • The database offers a holistic molecular perspective on BC invasiveness.
  • BcCluster supports the formulation of research hypotheses concerning BC invasiveness.