title: CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data.
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.
authors.affiliation: North West Cancer Research Fund Institute, Bangor University, Bangor, Gwynedd LL57 2UW, UK. julia.feichtinger@gmail.com
authors.forename: Julia
authors.initials: J
authors.lastname: Feichtinger
authors.forename: Ramsay J
authors.initials: RJ
authors.lastname: McFarlane
authors.forename: Lee D
authors.initials: LD
authors.lastname: Larcombe
mesh_terms: D022126:Access to Information; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020407:Internet; D015201:Meta-Analysis as Topic; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D015203:Reproducibility of Results; D014584:User-Computer Interface; D057188:Workflow