Breast Cancer Research and Treatment

, Volume 139, Issue 3, pp 907–921

ROCK: a resource for integrative breast cancer data analysis

  • Saif Ur-Rehman
  • Qiong Gao
  • Costas Mitsopoulos
  • Marketa Zvelebil
Brief Report

DOI: 10.1007/s10549-013-2593-z

Cite this article as:
Ur-Rehman, S., Gao, Q., Mitsopoulos, C. et al. Breast Cancer Res Treat (2013) 139: 907. doi:10.1007/s10549-013-2593-z

Abstract

Given the steady increase in breast cancer rates in both the developed and developing world, there has been a concerted research effort undertaken worldwide to understand the molecular mechanisms underpinning the disease. The data generated from numerous clinical trials and experimental studies shed light on different aspects of the disease. We present a new version of the ROCK database (rock.icr.ac.uk), which integrates such diverse data types allowing unique analyses of published breast cancer experimental data. We have added several new data types and analysis modules to ROCK, which allow the user to interactively query and research the huge amounts of available experimental data and perform complex correlations across studies and data types such as gene expression, genomic copy number aberrations, micro RNA expression, RNA interference, survival analysis, clinical annotation and signalling protein networks. We present the recent and major functional updates and enhancements to the ROCK resource, including new analysis modules and microRNA and NGS data integration, and illustrate how ROCK can be used to confirm known experimental results as well as generate novel leads and new experimental hypotheses using the Wnt signalling cell surface receptor FZD7 and the Myc oncogene. ROCK provides a unique breast cancer analysis platform of integrated experimental datasets at the genomic, transcriptomic and proteomic level. This paper presents how ROCK has transitioned from being simply a database to an interactive resource useful to the broader breast cancer research community in our effort to facilitate research into the underlying molecular mechanisms of breast cancer.

Keywords

Breast cancer databaseIntegrated data analysisMetadata analysisNext generation sequencingMicro RNAProtein interaction networks

Abbreviations

ROCK

Research Online Cancer Knowledgebase

CNV

Copy number variation

CNA

Copy number alteration

DNA

Deoxyribonucleic acid

RNA

Ribonucleic acid

RNAi

RNA interference

API

Application programming interface

NGS

Next-generation sequencing

CGH

Comparative genomic hybridisation

aCGH

Array CGH

SAM

Significance of microarrays

GO

Gene Ontology

TCGA

The Cancer Genome Atlas

PISA

Protein interactions, surfaces and assemblies

PI

Protein interaction

HPRD

Human Protein Reference Database

STRING

Search tool for the retrieval of interacting genes/proteins

KM

Kaplan–Meier

ERK

Extracellular-signal-regulated kinases

ER

Estrogen receptor

PR

Progesterone receptor

HER2

Human epidermal growth factor receptor

TNBC

Triple negative breast cancer

SVG

Scalable vector graphics

Supplementary material

10549_2013_2593_MOESM1_ESM.pdf (179 kb)
Supplementary material 1 (PDF 178 kb)
10549_2013_2593_MOESM2_ESM.pdf (23 kb)
Supplementary material 2 (PDF 22 kb)

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Saif Ur-Rehman
    • 1
  • Qiong Gao
    • 1
  • Costas Mitsopoulos
    • 1
  • Marketa Zvelebil
    • 1
  1. 1.Breakthrough Breast Cancer Research CentreThe Institute of Cancer ResearchLondonUK