Flow chart for matching data from two gene expression platforms. SAGE tags were converted into Unigene clusters using data from the CGAP website. Accession numbers from Affymetrix GeneChips were also converted to their corresponding Unigene cluster. Platforms are matched according to their Unigene cluster and only unambiguous Unigene clusters are selected. Finally, data are filtered for tag counts >0 and present calls on microarray platforms. 1. In the complete process of annotation a large number of tags or probe sets lost due to the following reasons: SAGE: 11733 tags with no annotation, 13113 tags with no reliable annotation, 913 tags with multiple Unigene Clusters, 80 tags belonging to linker sequences, 20 tags belonging to repetitive sequences, 22 tags belonging to mitochondrial DNA; Affymetrix: 1795 Probe sets no longer belong to a Unigene Cluster (Build 160). The remaining 20488 probe sets represent 13727 unique Unigene clusters. 2. Unambiguous Unigene clusters refer to those clusters that occur only once within each platform.