Interaction of a traditional Chinese Medicine (PHY906) and CPT-11 on the inflammatory process in the tumor microenvironment

Table 1 Summary of differentially expressed tumor genes among treatment groups.

Tumor Microenvironment	Test	Number of genes < 0.001 and (<0.05 total/annotated)*	Pt p-value for <0.001 cutoff^†
Four way	F test	1,132	< 0.001
PBS vs PHY906	t test	117/113 (1,759/1,664)	< 0.001
PBS vs CPT-11	t test	570/557 (2,630/2,513)	< 0.001
PBS vs CPT-11+PHY906	t test	798/774 (3,347/3,190)	< 0.001
CPT-11 vs CPT-11+PHY906	t test	93/91 (1,556/1,477)	< 0.001

Number of sample: PBS = 10; PHY906 = 9; CPT-11 = 10; CPT-11 + PHY906 = 9; Total 38
*Cutoff of p-value < 0.05 was used to select genes for IPA; In parentheses are the number of genes identified at <0.05 level and with an annotated function that could be used for IPA; ^†although the pt test p-value is shown for the <0.001 analyses, identical results were obtained for the lower stringency analyses. Details concerning comparisons among other tissues and treatments are provided in the extended table as an additional file (Additional file 2, Table S2).
Note. Pt test: permutation test