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Analysis of Microarray Data

fter amplification of total RNA (2 g) from HCT116 and RKO cells using the MessageAmp Kit.


Hierarchical clustering analysis of the data obtained from 6912 elements was carried out using UPGMA (Unweighted Pair Group Method with Arithmetic Mean) analysis (see sidebar "Clustering Methods Used for Analyzing Microarray Data"), with an ordering function based on the input rank. This data is represented as a dendrogram (tree graph) with the closest branches of the tree representing arrays with similar gene expression patterns. Figure 3 depicts the hierarchical clustering data from all 6912 elements. The results indicate that there are broad similarities between arrays hybridized with aRNA or mRNA. Even though the overall signal patterns found on the aRNA and mRNA hybridized arrays are similar, a small subset of regions show differential expression (RKO/HCT116) signals between the aRNA and mRNA samples.

Figure 3. Hierarchical Clustering Analysis of All Array Elements. Hierarchical clustering data of all the elements in a HCl array. A dendrogram (tree graph) epicts the grouping of the genes based on the similarity between them. UPGMA analysis (unweighted average) was carried out using the "Euclidean Distance" to determine the similarity measure and the input rank as the ordering function. A subset of all the columns constituting the complete data is shown in this figure.


To obtain statistically significant data for the sub-regions that were distinct between the aRNA and mRNA (91 elements), a weighted average (WPGMA) analysis was carried out. The hierarchical clustering of these 91 elements is depicted in Figure 4. It is evident that there are very few genes that
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