Due to the change of gene sequence and annotation, 2% of probes have changed their corresponding genes within a 4-month interval in the latest Affymetrix mouse chip. Microarray results need to be perpetually re-evaluated with the latest probe annotations.
We built an automated system to decode microarray platforms from NCBI Gene Expression Omnibus (GEO). We also built a web server to enable users to re-annotate their microarray results and find existing experiments with cross-platform comparison. The system relates probe IDs to Entrez Gene identifiers through a universal gene identifier table for all species.
This approach shows comparable accuracy and 6 times greater coverage as compared to the gene annotation files released by GEO based on probe sequences. Some microarray data sets deposited in GEO can not be re-used due to the missing gene annotations. Mandates are suggested to standardize the probe annotation to enable the downstream secondary usage. The initial paper describing AILUN has been accepted in Nature Methods (2007).
View Project's Website: http://ailun.stanford.edu