Stress associated gene expression in blood cells is related to outcome in radiotherapy treated head and neck cancer patients

Table 2 Summary of GSEA analysis comparing whole blood gene expression profiles of poor-responders (PR) to responders (R) with regard to pre-RT gene expression levels and response to RT

Stress and defence relevant gene set database (keyword)	Number of gene sets in collection	HNSCC patients whole blood
	HG-U133-plus2	Baseline expression pre-RT		Change during RT
		PR > R	R > PR	PR > R	R > PR
Apoptosis	273	29	0	0	91
Cell and cycle	311	38	1	0	85
Cytokine*	239	41	0	0	89
Hypoxi*	63	5	0	0	25
Antioxidant*	10	8	0	0	4
Immune* and response	116	10	0	0	37
Stress and response	59	5	0	0	11
DNA and repair	80	12	0	0	13
Cancer	699	75	1	4	152
Tox*	136	23	0	1	49
C3 TFT	583	18	11	0	4

The number of stress and defence-relevant gene sets that were higher expressed in one group compared to the other are given for each gene set collection. FDR (false discovery rate) < 5%.
Affymetrix HG-U133-plus2 chips were used to analyze the whole blood RNA. A gene set browser provided by Broad institute at www.broad.mit.edu/gsea/ was used to obtain the stress-associated gene set collections. Detailed information regarding the regulated gene sets is given in online Additional files 2-5. *indicates that truncated search keywords were used to create the gene set collections. C3TFT is a pre-defined gene set collections.

ISSN: 1471-2407