next up previous contents
Next: 3.3.6 Confrontation with sample Up: 3.3 Data analysis Previous: 3.3.4 Clustering profiles   Contents

3.3.5 Comparing profiles

VAMP proposes several data manipulation procedures for the profiles such as loading any type of profile (CGH, expression, LOH, ChIP chip) for a given sample. A typical application of VAMP is the simultaneous visualization of the DNA alterations and gene under- and over-expression in a region (see Figures 3.46 and 3.47). In the case of one-color microarrays (such as Affymetrix) the user can define a reference profile and compute the ratio with a test profile: he can easily compare the ratio of gene expression with the DNA alteration.

Figure 3.46: Transcriptome Load - The user can load expression profiles The user can load and visualize one expression profiles which is connected to Array-CGH.
Image VampCGHvsTRS0

In the example below we compare array-CGH (top profile) versus transcriptome ratio (second profile in descending order), computed for Affymetrix U95 array of a bladder tumor sample and of a reference sample. This confrontation pinpoints the probable implication of the oncogene cyclin D1 in this tumor. The third and fourth profiles in descending order correspond to a reference profile (average normal bladder tissue profile) and the profile of the tumor under study, respectively. The second profile is the ratio of the fourth to the reference profile.

Figure 3.47: CGH vs Transcriptome. An icon at the left of each profile shows the type of loaded profile.
Image VampCGHvsTRS


next up previous contents
Next: 3.3.6 Confrontation with sample Up: 3.3 Data analysis Previous: 3.3.4 Clustering profiles   Contents
2007 - Institut Curie Bioinformatics unit