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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.
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Genome Biology

ISSN: 1474-760X

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