The super cohort is comprised of 15 distinct breast cancer cohorts for which corresponding microarray data and clinical annotation were publicly accessible from microarray databases including the Gene Expression Omnibus (National Center for Biotechnology Information, USA), ArrayExpress (European Bioinformatics Institute, UK) and caArray (National Cancer Institute, NIH, USA).
To assess whether overexpression of these proteins might be related to gene amplification, we extracted in silico microarray data from a public database including 40 SCLC samples and 23 cell lines.
These cell lines showed low expression of the ER, HER2 and claudin 3, claudin 4 and claudin 7. We identified those genes whose expression distinguished each human tumor subtype using significance analysis of microarrays (SAM) in our UNC337 tumor database, including a list defining the normal breast-like group.
Public high-throughput microarray databases that include GEO and ArrayExpress were searched to collect NSCLC-related DNA methylation microarray data.
In contrast to existing microarray database resources, the FunGenES database includes a state of the art tools for the interactive visualization of gene to gene relationships.
The database includes analyzed global microarray expression profiles generated in hosts infected with the plant pathogenic bacterium X. fastidiosa, which causes Pierce's disease in grapevines.
Finally, the database includes 14 processed global microarray expression profile sets.
The belief that such wealth of genomic information the community could not afford to lose has led to the development of microarray standards [1], [2] and databases including two major public microarray repositories, Gene Expression Omnibus (GEO) [3] and ArrayExpress [4], in the hope of enabling mining and exploration of newly acquired data space.
The MYC Target Gene database includes MYC responsive genes identified in independent studies by SAGE, DNA microarray, subtractive hybridization, ChIP, northern/western blot or RT-PCR.
The intended users of the database include any genomics researchers facing the persistent challenges of sensitivity for biomarker discovery and cross-platform microarray comparisons.
