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Genome Wide Profiling of Paired Cancerous and Normal Breast Tissues and Rapid Interpretation of Gene Expression Data

cted for cluster analysis using the GeneSpring Software application for all 12 samples (Figure 4). Twodimensional clustering analysis was obtained from gene expression values based on the similarity of their foldchange patterns. The nomal and metastasis tumor tissue samples formed their own distinct clusters and were easily distinguishable with this analysis. For the primary tumor samples, the expression pattern of patient 1 is close to that of the normal tissue sample cluster, whereas the expression pattern of patient 2 is closer to that of the metastasis tumor sample cluster.

Gene Classification

The gene annotation provided in the Oracle Database is an important component of the Expression Array System. This versatile tool empowers researchers to quickly find useful information on genes of interest and make direct data comparisons between platforms and laboratories using annotation such as gene name and symbol, RefSeq, NMs, LocusLink, dBEST, etc.

In addition the Oracle Database includes, when known, gene annotation that pertains to gene molecular function and biological processes. Two classification systems are employed; the Panther Classification system devised by Celera Genomics and the publicly available Gene Ontology (GO) annotations. In this study we used the Panther classifications to rapidly interpret gene expression data from the various normal and diseased tissue states.

For instance, among the 2,508 genes studied in this experiment, 200 genes differentially expressed between normal and cancer tissues with p-values < 0.01 were classified by the Panther system to be involved in various signal transduction pathways. This was considered notable since the signal transduction pathway has been implicated in breast cancer. Figure 4B shows the cluster analysis of the differential expression levels of these genes. From this analysis we can
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