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Information about CancerMA


CancerMA is an integrated bioinformatic analytical pipeline to automate the identification of novel candidate cancer markers/targets by means of analysing the expression profiles of a user-supplied gene list across publicly-available cancer microarray experimentally derived data sets. Using meta-analysis approaches the expression profiles for a given cancer type are pooled resulting in an enhancement of statistical power.
Analysis Process consists of i processing of user-supplied gene lists; ii filtering the microarray cancer data with the user-supplied list; iii individual microarray data analysis; iv microarray meta-analysis; v annotation, and data presentation. User-supplied data is provided via an online portal, and results are returned online with graphical visualisation and searchable lists. The analysis process is implemented in R/Bioconductor, MySQL and Perl.
Aim of CancerMA is the identification of novel candidate markers and therapeutic targets by means of microarray meta-analysis, as it is a key challenge in the fight against cancer.
This is a task that can be facilitated by putting accessible approaches to analysing the current wealth of "omic"-scale data in the hands of researchers directly addressing biological questions. Establishing a simple-to-use pipeline puts a standardised, automated, high throughput analysis in the hands of biologists; helping to narrow down the excessive number of target gene possibilities presented by modern databases and systems-level resources to a manageable number of putative candidates which can be followed up in the laboratory.
Available Data Sets were obtained from GEO or ArrayExpress. A total of 80 cancer microarray data sets covering 13 cancer types are available. Accession numbers can be found here.
About Us

Project leader (Bioinformatics) - Lee Larcombe
Project leader (Biology) - Ramsay McFarlane
Design & Development - Julia Feichtinger
Implementation

Pipeline: R, Bioconductor, MySQL and Perl
Web interface: HTML/CSS, Perl, MySQL, jQuery and       Twitter Bootstrap
CancerESTis the sister project of CancerMA! It's based on EST data and allows you to search for suitable cancer antigenes as well. Check it out!

   
© Bangor 2012