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ROCK: a breast cancer functional genomics resource

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Abstract

The clinical and pathological heterogeneity of breast cancer has instigated efforts to stratify breast cancer sub-types according to molecular profiles. These profiling efforts are now being augmented by large-scale functional screening of breast tumour cell lines, using approaches such as RNA interference. We have developed ROCK (rock.icr.ac.uk) to provide a unique, publicly accessible resource for the integration of breast cancer functional and molecular profiling datasets. ROCK provides a simple online interface for the navigation and cross-correlation of gene expression, aCGH and RNAi screen data. It enables the interrogation of gene lists in the context of statistically analysed functional genomic datasets, interaction networks, pathways, GO terms, mutations and drug targets. The interface also provides interactive visualisations of datasets and interaction networks. ROCK collates data from a wealth of breast cancer molecular profiling and functional screening studies into a single portal, where analysed and annotated results can be accessed at the level of a gene, sample or study. We believe that portals such as ROCK will not only afford researchers rapid access to profiling data, but also aid the integration of different data types, thus enhancing the discovery of novel targets and biomarkers for breast cancer.

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Acknowledgements

The authors would like to thank Dr. Amar Sabri Ahmad, Dr. Jorge Reis-Filho, Dr. Chris Lord and Prof. Alan Ashworth of the Institute for comments on the manuscript. We acknowledge funding from Breakthrough Breast Cancer and NHS funding to the NIHR Biomedical Research Centre. Funding to pay the Open Access publication charges for this article was provided by Breakthrough Breast Cancer.

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There are no conflicts of interest.

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Authors and Affiliations

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

    David Sims, Borisas Bursteinas, Qiong Gao, Ekta Jain, Alan MacKay, Costas Mitsopoulos & Marketa Zvelebil

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  1. David Sims
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  2. Borisas Bursteinas
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  3. Qiong Gao
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Correspondence to Marketa Zvelebil.

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Sims, D., Bursteinas, B., Gao, Q. et al. ROCK: a breast cancer functional genomics resource. Breast Cancer Res Treat 124, 567–572 (2010). https://doi.org/10.1007/s10549-010-0945-5

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