Table 3

Validation of differentially expressed miRNAs using PCR.

miRNA

NGS normal

NGS tumor

NGS fc

PCR fc

Consistent?


has-let-7b

32 594.1

16 107.1

0.49

0.46

Y

hsa-let-7c

7 710.1

2 439.1

0.32

0.44

Y

hsa-miR-22

69 532.1

24 576.1

0.35

0.24

Y

hsa-miR-125b

44 624.1

6 613.1

0.15

0.37

Y

hsa-miR-143

38 419.1

17 359.1

0.45

0.14

Y

hsa-miR-144

3 548.1

351.1

0.10

0.30

Y

hsa-miR-145

28 682.1

6 435.1

0.22

0.26

Y

hsa-miR-193a-5p

1 836.1

298.1

0.16

0.27

Y

hsa-miR-193b

2 469.1

1 058.1

0.43

0.30

Y

hsa-miR-199b-5p

1 608.1

1 055.1

0.66

0.83

Y

hsa-miR-320a

16 734.1

3 060.1

0.18

0.75

Y

hsa-miR-378

12 610.1

1 542.1

0.12

0.24

Y

hsa-miR-497

8 005.1

2 010.1

0.25

0.29

Y

hsa-miR-99a

31 360.1

5 548.1

0.18

0.16

Y

hsa-miR-141

5007.1

14 541.1

2.90

5.88

Y

hsa-miR-375

240.1

2 372.1

9.88

37.95

Y

hsa-miR-425

592.1

2 529.1

4.27

1.93

Y

hsa-miR-203

197.1

1 045.1

5.30

9.80

Y

hsa-miR-342-3p

350.1

1 331.1

3.80

3.43

Y

hsa-miR-182

316.1

1 653.1

5.23

11.86

Y

hsa-miR-200b

1 362.1

4 162.1

3.06

12.61

Y

hsa-miR-183

118.1

1 067.1

9.04

6.12

Y

hsa-miR-423-3p

2 446.1

1 993.1

0.81

5.96

N


NGS normal and NGS tumor denote miRNA relative read counts (TPM) in normal and tumor tissues. The NGS fold change (NGS fc) values are the quotients of miRNA read counts in normal tissue divided by those in tumor tissue. The PCR fold change (PCR fc) values are the quotients of miRNA expression levels, relative to U6 in normal tissue, divided by those in tumor tissue, averaged from 4 independent experiments

Chang et al. BMC Genomics 2012 13(Suppl 7):S18   doi:10.1186/1471-2164-13-S7-S18

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