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Chordoma Low-Template Microarray Analysis

Chordoma is a malignant bone cancer that de- velops from notochordal remnants. The MUG-Chor1 chor- doma cell line shows a phenotypic anomaly, as it comprises two subpopulations, which were separated by micromanip- ulation and analysed with Affymetrix microarrays. Such a low-template microarray analysis, however, poses a diffi- cult statistical problem, as the variances between biologi- cal replicates are high, whereas the biological differences are modest. Hence statistical approaches to increase the detection power are required. Firstly, we have applied a filtering step, which could slightly improve the detection power. Secondly, we have conducted a gene set test shift- ing the analysis from single gene level to gene set level, as such techniques are more sensitive in detecting moderate changes when these changes affect a set of related genes.