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Table 2 Enriched clusters of gene annotation terms for U251 (human) tumor genes up-regulated (A) or down-regulated (B) by metronomic CPA treatment

From: Transcriptional profiling provides insights into metronomic cyclophosphamide-activated, innate immune-dependent regression of brain tumor xenografts

Cluster name

Cluster enrichment score

Number of genes (top term)

p-value (top term)

A. Up-regulated tumor gene clusters

Inflammatory/defense response to wounding

9.15

63

3.91E-12

Signal peptide/glycoprotein/secreted

6.01

190

7.67E-13

Histone/nucleosome core

5.02

17

3.00E-12

Integral plasma membrane

4.29

83

1.29E-06

Cytokine activity

3.38

20

1.68E-04

Induction/regulation of apoptosis

3.26

31

7.73E-06

Response to bacterium/cytokine stimulus

2.99

21

6.36E-05

Positive regulation of (innate) immune system

2.72

29

1.72E-07

B. Down-regulated tumor gene clusters

Extracellular signal

5.04

81

2.75E-08

Cell adhesion

2.92

37

1.12E-04

Skeletal system development

2.70

22

1.24E-04

Extracellular matrix

2.61

25

1.98E-05

EGF-like

2.58

19

2.58E-06

Blood vessel development

2.54

17

8.45E-04

  1. Analysis was based on genes that respond consistently after both 2 and 3 CPA/6-day treatment cycles (i.e., treatment days 12 and 18) at |fold-change| >1.5 and p-value < 104. Shown are clusters with enrichment scores >2.5 whose top term contains >15 genes. Also shown is the number of genes and p-value for the top term in each cluster. See Additional file 1: Tables S2A and S2B for a more complete listing of significant enrichment clusters and associated gene lists.