View Example Dataset
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
the expression profiles for a given cancer type are pooled resulting in an enhancement of statistical power.
processing of user-supplied gene lists;
filtering the microarray cancer data with the user-supplied list;
individual microarray data analysis;
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
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
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
. A total of 80 cancer microarray data sets covering 13 cancer types are available. Accession numbers can be found
North West Cancer Research Fund
Welsh Assembly Government
Project leader (Bioinformatics) - Lee Larcombe
Project leader (Biology) - Ramsay McFarlane
Design & Development - Julia Feichtinger
Web interface: HTML/CSS,
is 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