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

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

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

  1. Number of sample: PBS = 10; PHY906 = 9; CPT-11 = 10; CPT-11 + PHY906 = 9; Total 38
  2. *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).
  3. Note. Pt test: permutation test