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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

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

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
  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%.
  2. 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.