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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.