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Table 2 Validation of microarray gene expression data

From: Deciphering cellular states of innate tumor drug responses

Symbol Assay ID Tumors Metastases
   CtR CtS Ratio p value CtR CtS Ratio p value
Fully validated genes          
   CHEK1* CHEK1-Hs00176236_m1 30.3 30.9 2.2 2.11E-02 29.8 31.9 4.0 2.87E-03
   CHEK2* CHEK2-Hs00200485_m1 29.3 30.1 2.5 3.40E-04 29.0 30.9 2.0 8.33E-03
   COL4A2 COL4A2-Hs00300500_m1 25.2 23.5 -3.7 1.60E-06 24.9 23.5 -4.3 5.27E-07
   COL6A1 COL6A1-Hs00242448_m1 24.8 21.9 -6.6 3.45E-08 25.9 24.6 -2.0 9.54E-03
   COL6A2 COL6A2-Hs00365167_m1 24.8 21.6 -8.6 8.66E-08 25.1 24.0 -2.8 5.40E-05
   FOS FOS-Hs00170630_m1 21.5 21.1 -2.7 2.36E-03 22.1 21.6 -3.0 2.86E-06
   HRASLS3 HRASLS3-Hs00272992_m1 27.6 25.2 -5.6 3.42E-07 25.7 25.7 -2.4 2.14E-05
   LAMB1 LAMB1-Hs00158620_m1 24.6 23.4 -2.4 5.25E-04 25.3 24.1 -2.8 8.46E-06
   MMP11 MMP11-Hs00171829_m1 25.4 23.6 -3.1 1.85E-05 25.6 23.0 -10.2 2.46E-08
   PEA15 PEA15-Hs00269428_m1 24.4 23.5 -2.4 4.52E-04 24.5 23.7 -2.3 2.50E-05
   RAD51 RAD51-Hs00153418_m1 26.6 27.7 2.3 9.81E-03 26.2 28.0 3.0 4.23E-03
   RECQL4* RECQL4-Hs00171627_m1 27.6 28.3 2.1 1.26E-03 27.0 29.0 3.7 2.41E-03
   RERG RERG-Hs00262869_m1 31.8 28.5 -11.1 5.07E-12 31.2 30.5 -3.4 2.10E-06
   RRAGD RRAGD-Hs00222001_m1 29.6 27.0 -7.8 1.74E-07 28.5 26.9 -3.0 2.60E-05
   SERPINF1 SERPINF1-Hs00171467_m1 26.1 23.7 -3.5 2.52E-05 24.6 24.7 n/a n/a
   TGFBI TGFBI-Hs00165908_m1 23.9 22.0 -5.4 2.35E-06 24.0 21.6 -6.7 7.27E-08
   TP53 TP53-Hs00153340_m1 24.0 25.2 2.5 7.00E-03 24.0 25.4 2.9 3.21E-03
   BCL2 BCL2-Hs00608023_m1 29.7 29.5 n/a n/a 29.2 29.5 1.1 6.86E-01
   E2F4 E2F4-Hs00608098_m1 23.0 22.6 -1.1 8.34E-01 22.8 23.2 -1.3 1.94E-01
   ITGB6 ITGB6-Hs00168458_m1 27.5 27.8 -1.0 9.16E-01 26.9 27.7 -1.0 9.32E-01
   RAD52 RAD52-Hs00172536_m1 29.4 28.5 -1.9 1.12E-02 28.5 28.6 -1.1 5.42E-01
   TOP1 TOP1-Hs00243257_m1 25.1 24.8 -1.1 7.89E-01 24.6 26.2 1.1 8.14E-01
Validated genes          
   CASP1 CASP1-Hs00354832_m1 26.6 27.6 2.1 5.91E-03 28.6 28.3 -1.5 1.80E-01
   MAD2L1 MAD2L1-Hs00829154_g1 26.7 27.5 2.0 9.91E-03 27.0 27.7 1.4 2.72E-01
False discoveries          
   ABCA2 ABCA2-Hs00242232_m1 26.2 26.0 1.0 9.94E-01 25.9 26.0 -1.1 6.59E-01
   ABL1* ABL1-Hs00245445_m1 26.2 25.7 -1.3 3.05E-01 26.2 26.1 -1.3 2.91E-01
   TOP2B TOP2B-Hs00172259_m1 25.4 25.1 -1.2 3.19E-01 25.1 25.6 -1.1 5.46E-01
   CES2 CES2-Hs00187279_m1 26.2 24.6 -2.8 5.41E-04 24.2 24.6 2.0 2.33E-02
   JUN JUN-Hs00277190_s1 22.8 22.1 -1.6 1.86E-02 22.1 22.3 -2.5 9.00E-06
   TGFB1 TGFB1-Hs00171257_m1 25.8 23.8 -3.5 2.70E-06 24.8 24.5 -2.2 5.83E-05
  1. Q-PCR validation step on a series of 30 genes. For each gene, symbol and TaqMan® assay (assay ID) are indicated; asterisks refer to TaqMan® single assays. Genes displayed in bold were considered for further Q-PCR analysis of new samples from additional patients (compare Figure 3 and Additional data file 7); italics refer to genes selected as not significantly differentially expressed with microarrays. The threshold cycle CtS refer to chemo-sensitive states and CtR to resistant states; the expression changes (ratio) are specified as negative (down-regulated) or positive (up-regulated) values between resistant versus sensitive samples. Adjusted p values were computed using z statistics with false discovery rate corrections (α = 0.05). n/a, not analyzed.