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Table 3 Small RNA-Seq analysis of NPC FFPE tissue

From: Methods and matrices: approaches to identifying miRNAs for Nasopharyngeal carcinoma

Down-regulated

miRNA

MiRDeep (logFC)

MiRExpress (logFC)

Family

NPC ref.

hsa-let-7b-5p,hsa-let-7b

−1.23

−1.17

let-7/98/4458/4500

[36, 50, 51]

hsa-miR-100-5p,hsa-mir-100

−1.72

−1.57

miR-99ab/100

[36, 50, 52–54]

hsa-miR-1251,hsa-mir-1251

−5.69

−5.44

miR-1251

-

hsa-miR-1269a,hsa-mir-1269a

−6.44

-

miR-1269/1269b

-

hsa-miR-1269b,hsa-mir-1269b

−7.73

−6.14

miR-1269/1269b

-

hsa-miR-130a-3p,hsa-mir-130a

−2.82

−2.72

miR-130 ac/301ab/301b/301b-3p/454/721/4295/3666

[50, 52, 54]

hsa-miR-133a,hsa-mir-133a-1

−3.75

−3.63

miR-133abc

-

hsa-miR-133a,hsa-mir-133a-2

−3.75

−3.63

miR-133abc

-

hsa-miR-133b,hsa-mir-133b

−2.68

−2.74

miR-133abc

-

hsa-miR-136-5p,hsa-mir-136

−2.89

−2.77

miR-136

-

hsa-miR-139-5p,hsa-mir-139

−2.08

−2.04

miR-139-5p

[50, 52, 54]

hsa-miR-143-3p,hsa-mir-143

−1.64

−1.40

miR-143/1721/4770

[36, 50, 52, 54]

hsa-miR-145-5p,hsa-mir-145

−2.77

−2.86

miR-145

[36]

hsa-miR-152,hsa-mir-152

−1.72

-

miR-148ab-3p/152

[50, 52]

hsa-miR-187-3p,hsa-mir-187

−3.15

-

miR-187

[52]

hsa-miR-195-3p,hsa-mir-195

−2.37

−3.02

miR-15abc/16/16abc/195/322/424/497/1907

[50]

hsa-miR-195-5p,hsa-mir-195

−3.06

−2.29

miR-15abc/16/16abc/195/322/424/497/1907

[52]

hsa-miR-199a-5p,hsa-mir-199a-1

−2.46

−2.60

miR-199ab-5p

[55]

hsa-miR-199a-5p,hsa-mir-199a-2

−2.46

−2.60

miR-199ab-5p

[55]

hsa-mir-199b-5p,hsa-miR-199b

-

−2.10

miR-199ab-5p

[52]

hsa-miR-204-5p,hsa-mir-204

−4.68

−4.62

miR-204/204b/211

[52]

hsa-miR-214-3p,hsa-mir-214

−2.79

−2.83

miR-214/761/3619-5p

-

hsa-miR-3065-5p,hsa-mir-3065

−3.73

−3.60

miR-545/3065/3065-5p

-

hsa-miR-335-5p,hsa-mir-335

−2.71

−2.68

miR-335/335-5p

-

hsa-miR-376a-5p,hsa-mir-376a-1

−3.96

−3.75

miR-376abd/376b-3p

-

hsa-miR-376b-5p,hsa-mir-376b

−3.45

-

miR-376abd/376b-3p

-

hsa-miR-376c-5p,hsa-mir-376c

−3.45

-

miR-376c/741-5p

-

hsa-miR-4423-5p,hsa-mir-4423

−6.24

−6.51

miR-4423-5p

-

hsa-miR-450a-5p,hsa-mir-450a-1

-

−2.06

miR-450a/451a

-

hsa-miR-450a-5p,hsa-mir-450a-2

-

−2.05

miR-450a/451a

-

hsa-miR-4792,hsa-mir-4792

−1.53

-

miR-4792

-

hsa-miR-488-3p,hsa-mir-488

−4.86

−4.46

miR-488

-

hsa-miR-497-3p,hsa-mir-497

−3.63

-

miR-15abc/16/16abc/195/322/424/497/1907

[50, 52]

hsa-miR-497-5p,hsa-mir-497

−2.53

−2.46

miR-15abc/16/16abc/195/322/424/497/1907

[50, 52]

hsa-miR-504,hsa-mir-504

−3.31

-

miR-504/4725-5p

-

hsa-miR-539-5p,hsa-mir-539

−6.68

-

miR-300/381/539-3p

-

hsa-miR-542-3p,hsa-mir-542

−2.02

−1.96

miR-542-3p

-

hsa-miR-556-3p,hsa-mir-556

−5.18

-

miR-556-5p

-

hsa-miR-574-3p,hsa-mir-574

−1.32

−1.25

miR-574-3p

-

hsa-miR-585,hsa-mir-585

−2.51

-

miR-585

-

hsa-miR-874,hsa-mir-874

−1.68

−1.56

miR-874

-

hsa-miR-887,hsa-mir-887

−1.90

−1.99

miR-887

-

hsa-miR-891a,hsa-mir-891a

−7.14

−6.86

miR-891a

-

Up-regulated

miRNA

MiRDeep (logFC)

MiRExpress (logFC)

Family

NPC ref.

hsa-mir-1268a,hsa-miR-1268a

-

2.89

miR-1268/1268b

-

hsa-mir-1268b,hsa-miR-1268b

-

2.59

miR-1268/1268b

-

hsa-miR-1303,hsa-mir-1303

1.61

1.62

miR-1303

-

hsa-miR-1304-3p,hsa-mir-1304

1.56

-

miR-1304

-

hsa-miR-1305,hsa-mir-1305

2.84

-

miR-1305

-

hsa-mir-15b-5p,hsa-miR-15b

-

1.09

miR-15abc/16/16abc/195/322/424/497/1907

[52]

hsa-miR-184,hsa-mir-184

4.84

5.22

miR-184

-

hsa-mir-21-3p,hsa-miR-21

-

1.41

miR-21/590-5p

-

hsa-mir-27a-3p,hsa-miR-27a

-

1.15

miR-27abc/27a-3p

-

hsa-miR-205-3p,hsa-mir-205

2.77

2.65

miR-205/205ab

[52]

hsa-miR-205-5p,hsa-mir-205

2.87

2.84

miR-205/205ab

[52]

hsa-miR-25-5p,hsa-mir-25

2.21

2.15

miR-25/32/92abc/363/363-3p/367

[52]

hsa-miR-4677-3p,hsa-mir-4677

1.52

1.74

miR-4677-3p

-

hsa-mir-4791,hsa-miR-4791

-

2.67

miR-3201/4791

-

hsa-mir-548n,hsa-miR-548n

-

3.79

miR-548abakhjiwy/548abcd-5p/559

-

hsa-miR-6510-3p,hsa-mir-6510

2.22

-

miR-6510-3p

-

hsa-miR-92a-3p,hsa-mir-92a-1

1.32

-

miR-25/32/92abc/363/363-3p/367

-

hsa-miR-92a-3p,hsa-mir-92a-2

1.28

-

miR-25/32/92abc/363/363-3p/367

-

hsa-mir-944,hsa-miR-944

-

1.47

miR-944

-

EBV specific (All up-regulated)

miRNA

MiRDeep (logFC)

MiRExpress (logFC)

 

ebv-miR-BART1-3p,ebv-mir-BART1

4.54

4.55

 

ebv-miR-BART1-5p,ebv-mir-BART1

4.37

4.37

ebv-miR-BART10-3p,ebv-mir-BART10

4.43

4.41

ebv-miR-BART10-5p,ebv-mir-BART10

4.24

4.49

ebv-miR-BART12,ebv-mir-BART12

3.52

3.47

ebv-miR-BART13-3p,ebv-mir-BART13

2.64

2.55

ebv-miR-BART13-5p,ebv-mir-BART13

4.29

4.32

ebv-miR-BART14-3p,ebv-mir-BART14

3.63

3.61

ebv-miR-BART14-5p,ebv-mir-BART14

3.78

3.83

ebv-miR-BART15,ebv-mir-BART15

3.70

3.68

ebv-miR-BART16,ebv-mir-BART16

3.52

3.53

ebv-miR-BART17-3p,ebv-mir-BART17

4.45

4.44

ebv-miR-BART17-5p,ebv-mir-BART17

4.81

4.72

ebv-miR-BART18-3p,ebv-mir-BART18

3.73

3.28

ebv-miR-BART18-5p,ebv-mir-BART18

4.44

4.44

ebv-miR-BART19-3p,ebv-mir-BART19

3.51

3.47

ebv-miR-BART19-5p,ebv-mir-BART19

4.58

-

ebv-miR-BART2-5p,ebv-mir-BART2

3.79

3.72

ebv-miR-BART20-3p,ebv-mir-BART20

3.41

3.39

ebv-miR-BART20-5p,ebv-mir-BART20

4.55

4.62

ebv-miR-BART21-3p,ebv-mir-BART21

2.79

2.71

ebv-miR-BART21-5p,ebv-mir-BART21

3.51

3.50

ebv-miR-BART22,ebv-mir-BART22

3.97

3.93

ebv-miR-BART3-3p,ebv-mir-BART3

4.13

3.83

ebv-miR-BART3-5p,ebv-mir-BART3

4.66

4.50

ebv-miR-BART4-3p,ebv-mir-BART4

3.78

3.66

ebv-miR-BART4-5p,ebv-mir-BART4

3.37

3.32

ebv-miR-BART5-3p,ebv-mir-BART5

4.20

3.82

ebv-miR-BART5-5p,ebv-mir-BART5

3.97

3.89

ebv-miR-BART6-3p,ebv-mir-BART6

4.34

4.29

ebv-miR-BART6-5p,ebv-mir-BART6

4.49

4.35

ebv-miR-BART7-3p,ebv-mir-BART7

4.18

4.15

ebv-miR-BART7-5p,ebv-mir-BART7

5.77

5.76

ebv-miR-BART8-3p,ebv-mir-BART8

4.31

4.26

ebv-miR-BART8-5p,ebv-mir-BART8

4.65

4.63

ebv-miR-BART9-3p,ebv-mir-BART9

4.18

4.05

ebv-miR-BART9-5p,ebv-mir-BART9

4.47

4.45

  
  1. Five FFPE samples previously analyzed by microarray were submitted for RNA-Seq and analyzed via both miRExpress and miRDeep tools. Significantly dysregulated miRNAs are listed in Table 3.
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Journal of Translational Medicine

ISSN: 1479-5876

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