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

Table 3 Summary of GSEA analysis comparing radioresistant (RR) with radiosensitive (RS) HNSCC xenografts in nude mice and HNSCC tumour tissue versus normal epithelial cells

Stress and defence relevant gene set database (keyword)	Number of gene sets in collection		HNSCC tumour cell xenografts (GEOD-9716) Baseline pre-RT		HNSCC tumour versus controls (GEOGSE6791) Baseline pre-RT
	HG-U133-plus2	HG-U133A	RR> RS	RS>RR	HNSCC>ctr	ctr>HNSCC
Apoptosis	271	272	30	1	163	1
Cell and cycle	308	309	63	1	200	2
Cytokine*	239	236	33	0	104	2
Hypoxi*	63	63	7	0	41	0
Antioxidant*	10	10	2	0	2	0
Immune* and response	114	114	23	0	55	1
Stress and response	59	58	6	0	0	0
DNA and repair	80	79	14	0	57	0
Cancer	699	687	103	14	373	9
Tox*	137	140	16	2	70	2
C3 TFT	582	587	5	2	83	1

The number of stress and defence-relevant gene sets that were more highly expressed in one group relative to the other is given for each gene set collection. False discovery rate (FDR) <5%.
Affymetrix HG-U133A microarray chips were used in the GEOD-9716 dataset while Affymetrix HG-U133-plus2 chips were used in the GSE6791 dataset. A gene set browser provided by the 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 6-9. *indicates that truncated search keywords were used to create the gene set collections. C3TFT is a pre-defined gene set collection.

ISSN: 1471-2407