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Table 4 Microarray profiles of radiation response in the NCI60 cell lines

From: Microenvironmental genomic alterations reveal signaling networks for head and neck squamous cell carcinoma

Gene Group

Genes

Tested

Statistic Q

Expected Q

sd of Q

p-value

Epithelium Network (EN)

21

20

0.12173

0.68791

0.70898

0.82857

Stroma Network (SN)

32

27

8.9873

6.0567

3.4807

0.2

Intersection of EN & SN

14

13

0.14672

1.0085

1.0742

0.85714

Hot/Cold spots in SN

14

11

7.2921

5.187

6.0014

0.28571

Hot/Cold spots in EN

9

8

0.050848

0.096741

0.05459

0.77143

Genes within 250 K of Epithelium Markers

79

61

18.863

8.8517

9.2183

0.17143

Genes within 250 K of Stroma Markers

235

151

56.296

10.686

10.746

0.02857

  1. The network genes identified for stroma and epithelium of HNSCC as well as genes within 250 kb of stroma- and epithelium-associated markers are tested via Global Test [29], a statistical test scoring for association of the expression profile of groups of genes for outcome (e.g. response to radiation treatment: resistant/sensitive). Overall seven sets of genes were tested, and only hot- and cold-spot-associated genes within the stroma network (red/blue colored nodes in Figure 2) was shown to be significant, i.e., expression profiles of stroma-associated genes at hot-/cold-spots are associated with increased sensitivity to radiation. mRNA expression profiles are acquired from GEO (GSE9714), a study reporting gene expression profiles of radiosensitive and radioresistant human head and neck tumor cell lines [30].