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