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ROCK: a resource for integrative breast cancer data analysis

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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.

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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

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Acknowledgments

We would like to thank Dr. Borisas Bursteinas and Dr. David Sims for their past contributions in the development of ROCK. We would also like to thank the Breakthrough scientists that have commented on the functionality of ROCK and in particular Dr. Andrea Morandi, Dr. Nick Turner and Dr. Beatrice Howard for their useful advice. This work was supported by the Breakthrough Breast Cancer Research Centre, Institute of Cancer Research. Funding for open access charge: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research.

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The authors declare that they have no competing interests.

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Authors and Affiliations

  1. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK

    Saif Ur-Rehman, Qiong Gao, Costas Mitsopoulos & Marketa Zvelebil

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  1. Saif Ur-Rehman
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  2. Qiong Gao
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  3. Costas Mitsopoulos
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  4. Marketa Zvelebil
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Corresponding author

Correspondence to Marketa Zvelebil.

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S. Ur-Rehman and Q. Gao are joint first authors.

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Ur-Rehman, S., Gao, Q., Mitsopoulos, C. et al. ROCK: a resource for integrative breast cancer data analysis. Breast Cancer Res Treat 139, 907–921 (2013). https://doi.org/10.1007/s10549-013-2593-z

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  • DOI: https://doi.org/10.1007/s10549-013-2593-z

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