The proposed method is tested here through its initial application to a microarray database related to cervix cancer 13 and the results are successfully validated through the information available in the literature for the selected genes.
We propose a novel method to compare microarray experiments at the pathway level, this method consists of two steps: first, generate pathway signatures, a set of descriptors recapitulating the biologically meaningful pathways related to some clinical/biological variable of interest, second, use these signatures to interrogate microarray databases.
Although there are some existing microarray databases, they have their own storage structure and implementation.
Over the past years, microarray databases have increased rapidly in size.
The GPX system comprises two MIAME-compliant microarray databases, GPX Repository and GPX Discovery.
A list of microarray databases analyzed in the present study.
Each of six human tumor types (prostate, breast, lung, colon, ovary, and pancreas) was used in the 〈〈profile search〉〉 function in the Oncomine database to find the available microarray datasets related to the specific cancer type.
The first results on the application of the proposed method include the analysis of the microarray database used by Wong et al. 13 related to cervix cancer.
Specifically, we have built a database that gathers all the public microarray data related to muscle studies from GEO [ 13].
Following the recommendations of a previous study (Jeffares et al. 2008), we downloaded the "Stress Series" data related to the AtGenExpress Project from the microarray database of the Nottingham Arabidopsis Stock Center (http://arabidopsis.info/, last accessed October 9, 2011).
