Advanced spot quality analysis in two-colour microarray experiments

BMC Research Notes

Table 3 p-values of selected GO categories resulted from the different conditions of analysis.

GO term	MAIA	GP-standard	GP-weak	GP-medium	GP-strong
Kinase activity	0.000	0.002	0.000	0.088	0.849
Regulation of cell cycle	0.001	0.039	0.014	0.013	0.201
Hormone receptor binding	0.006	0.006	0.073	0.093	0.307
Wnt receptor activity	0.016	0.732	0.053	0.258	1.000
Actin cytoskeleton	0.063	0.088	0.134	0.164	0.102
Transcriptional repressor activity	0.003	0.007	0.000	0.017	0.029
Transcriptional activator activity	0.026	0.352	0.177	0.685	0.439
Vitamin D receptor binding	0.005	0.003	0.013	0.041	1.000
Regulation of cell growth	0.066	0.094	0.016	0.022	0.868

Several biological categories with a well-established role in epithelial to mesenchymal transition (EMT) were selected for comparison in terms of the p-values. p-values obtained for the GP-strong gene list have the weakest statistical meaning. Statistical results yielded from GP-standard, weak, and medium filtering are in mutual agreement. MAIA gave the best p-values among all tested spot quality approaches. Presented categories were obtained with FDR < 0.3.

ISSN: 1756-0500