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Database (Oxford). 2012 Dec 15;2012:bas055. doi: 10.1093/database/bas055. Print 2012.

CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data.

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1
North West Cancer Research Fund Institute, Bangor University, Bangor, Gwynedd LL57 2UW, UK. julia.feichtinger@gmail.com

Abstract

The identification of novel candidate markers is a key challenge in the development of cancer therapies. This can be facilitated by putting accessible and automated approaches analysing the current wealth of 'omic'-scale data in the hands of researchers who are directly addressing biological questions. Data integration techniques and standardized, automated, high-throughput analyses are needed to manage the data available as well as to help narrow down the excessive number of target gene possibilities presented by modern databases and system-level resources. Here we present CancerMA, an online, integrated bioinformatic pipeline for automated identification of novel candidate cancer markers/targets; it operates by means of meta-analysing expression profiles of user-defined sets of biologically significant and related genes across a manually curated database of 80 publicly available cancer microarray datasets covering 13 cancer types. A simple-to-use web interface allows bioinformaticians and non-bioinformaticians alike to initiate new analyses as well as to view and retrieve the meta-analysis results. The functionality of CancerMA is shown by means of two validation datasets.

PMID:
23241162
PMCID:
PMC3522872
DOI:
10.1093/database/bas055
[Indexed for MEDLINE]
Free PMC Article
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