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Table 1 Differential microRNA expression in Rasless MEFs

From: Reversible, interrelated mRNA and miRNA expression patterns in the transcriptome of Rasless fibroblasts: functional and mechanistic implications

12-D 4OHT-TREATED MEFs (RASLESS)

6-D 4OHT-TREATED

BRAF-RESCUED

MEK1-RESCUED

Pairwise comparison to control K-Ras lox cells

miRNA probeset ID

miRNA name

family

Chromosome, strand and cluster

Genecodis prediction

d-value

p-value

q-value

R-fold vs. Control

R-fold vs. Control

R-fold vs. Rasless

R-fold vs. Rasless

mmu-let-7b_st

mmu-let-7b

let-7

Chrom 15 (+): let-7c-2 | let-7b

7.95E-06

-2.2

0.02

0.05

0.68

n.a.

n.a.

n.a.

mmu-let-7c_st

mmu-let-7c

let-7

Chrom 16 (+): mir-99a | let-7c-1

2.89E-06

-1.41

0.09

0.17

0.78

n.a.

n.a.

n.a.

mmu-let-7b-star_st

mmu-let-7b*

let-7

Chrom 15 (+): let-7c-2 | let-7b

1.86E-21

-1.36

0.1

0.15

0.63

n.a.

n.a.

n.a.

mmu-miR-206_st

mmu-miR-206

mir-1

Chrom 1 (+): mir-206 | mir-133b

 

2.76

0.01

0.03

1.78

n.a.

0.05

0.13

mmu-miR-10b_st

mmu-miR-10b

mir-10

Chrom 2 (+)

 

2.17

0.02

0.05

2.26

n.a.

n.a.

n.a.

mmu-miR-125b-3p_st

mmu-miR-125b-3p

mir-125

Chrom 9 (+)

7.97E-06 (1.13E-07)

-3.91

0.00

0.03

0.32

n.a.

3.8

3.42

mmu-miR-125b-5p_st

mmu-miR-125b-5p

mir-125

Chrom 9 (+)

 

-1.71

0.05

0.09

0.75

n.a.

2.18

2.29

mmu-miR-125a-3p_st

mmu-miR-125a-3p

mir-125

Chrom 17 (+): mir-99b | let-7e | mir-125a

 

-1.67

0.05

0.09

0.45

n.a.

n.a.

n.a.

mmu-miR-129-3p_st

mmu-miR-129-3p

mir-129

Chrom 2 (-)

4.56E-06

5.63

0.00

0.02

6.02

n.a.

n.a.

n.a.

mmu-miR-130b_st

mmu-miR-130b

mir-130

Chrom 16 (-): mir-301b | mir-130b

6.71E-17

-3.2

0.01

0.03

0.45

n.a.

n.a.

1.96

mmu-miR-132_st

mmu-miR-132

mir-132

Chrom 11 (+): mir-212 | mir-132

6.39E-17

-2.45

0.01

0.04

0.11

n.a.

17.75

3.61

mmu-miR-212_st

mmu-miR-212

mir-132

Chrom 11 (+): mir-212 | mir-132

1.05E-14

-1.95

0.03

0.07

0.21

n.a.

11.18

1.47

mmu-miR-487b_st

mmu-miR-487b

mir-154

Chrom 12 (+): mir-495 | mir-667 | mir-376c | mir-654 | mir-376b | mir-376a | mir-300 | mir-381 | mir-487b | mir-539 | mir-544 | mir-382 | mir-134 | mir-668 | mir-485 | mir-453

8.76E-11

3.25

0.01

0.03

3.45

n.a.

n.a.

n.a.

mmu-miR-155_st

mmu-miR-155

mir-155

Chrom 16 (+)

2.44E-08

-3.11

0.01

0.03

0.16 # [0.47]

n.a. # [1.1]

7.5 # [10.68]

4.38 # [6.26]

mmu-miR-17-star_st

mmu-miR-17*

mir-17

Chrom 14 (+): mir-17 | mir-18a | mir-19a | mir-20a | mir-19b-1 | mir-92a-1

 

-5.05

0.00

0.02

0.32

n.a.

3.47

2.69

mmu-miR-18a_st

mmu-miR-18a

mir-17

Chrom 14 (+): mir-17 | mir-18a | mir-19a | mir-20a | mir-19b-1 | mir-92a-1

(5.42E-08)

-4.84

0.00

0.03

0.38

n.a.

4.0

2.46

mmu-miR-20b_st

mmu-miR-20b

mir-17

Chrom X (-): mir-106a | mir-18b | mir-20b | mir-19b-2 | mir-92a-2 | mir-363

7.42E-17

-4.22

0.00

0.03

0.21

0.29

9.88

5.93

mmu-miR-106a_st

mmu-miR-106a

mir-17

Chrom X (-): mir-106a | mir-18b | mir-20b | mir-19b-2 | mir-92a-2 | mir-363

8.87E-14

(1.25E-06)

-3.38

0.01

0.03

0.19 # [0.15]

n.a. # [0.86]

6.84 # [7.75]

6.07 # [13.58]

mmu-miR-106b-star_st

mmu-miR-106b*

mir-17

Chrom 5 (-): mir-106b | mir-93 | mir-25

 

-2.99

0.01

0.03

0.29

n.a.

4.92

5.28

mmu-miR-17_st

mmu-miR-17

mir-17

Chrom 14 (+): mir-17 | mir-18a | mir-19a | mir-20a | mir-19b-1 | mir-92a-1

1.08E-15

(3.84E-07)

-2.87

0.01

0.03

0.37 # [0.27]

n.a. # [0.58]

5.74 # [6.1]

3.48 # [9.01]

mmu-miR-20a_st

mmu-miR-20a

mir-17

Chrom 14 (+): mir-17 | mir-18a | mir-19a | mir-20a | mir-19b-1 | mir-92a-1

(7.38E-07)

-2.58

0.01

0.04

0.37 # [0.24]

n.a. # [0.55]

5.13 # [5.8]

3.57 # [7.85]

mmu-miR-93-star_st

mmu-miR-93*

mir-17

Chrom 5 (-): mir-106b | mir-93 | mir-25

 

-2.44

0.01

0.04

0.42

0.33

2.58

2.15

mmu-miR-106b_st

mmu-miR-106b

mir-17

Chrom 5 (-): mir-106b | mir-93 | mir-25

2.82E-11

-2.25

0.02

0.05

0.46

n.a.

2.17

3.07

mmu-miR-93_st

mmu-miR-93

mir-17

Chrom 5 (-): mir-106b | mir-93 | mir-25

4.77E-14 (4.35E-06)

-1.84

0.04

0.08

0.64

n.a.

2.19

2.4

mmu-miR-181d_st

mmu-miR-181d

mir-181

Chrom 8 (-): mir-181c | mir-181d

7.13E-10

-3.24

0.01

0.03

0.23

n.a.

5.63

4.29

mmu-miR-181b_st

mmu-miR-181b

mir-181

Chrom 1 (+): mir-181a-1 | mir-181b-1

1.40E-09

-1.43

0.09

0.13

0.68

n.a.

n.a.

n.a.

mmu-miR-181a-1-star_st

mmu-miR-181a-1*

mir-181

Chrom 1 (+): mir-181a-1 | mir-181b-1

1.37E-08

5.4

0.00

0.02

8.55

5.5

n.a.

1.68

mmu-miR-182_st

mmu-miR-182

mir-182

Chrom 6 (-): mir-183 | mir-96 | mir-182

4.24E-11

-2.21

0.02

0.05

0.52

n.a.

22.16

13.95

mmu-miR-183_st

mmu-miR-183

mir-183

Chrom 6 (-): mir-183 | mir-96 | mir-182

2.68E-07

-2.26

0.02

0.05

0.62

n.a.

28.07

18.61

mmu-miR-185_st

mmu-miR-185

mir-185

Chrom 16 (-)

 

2.38

0.02

0.04

1.39

n.a.

0.23

0.25

mmu-miR-215_st

mmu-miR-215

mir-192

Chrom 1 (+): mir-194-1 | mir-215

5.61E-10

2.89

0.01

0.03

4.3

n.a.

6.23

5.21

mmu-miR-193_st

mmu-miR-193

mir-193

Chrom 11 (+)

4.31E-08

-1.73

0.05

0.09

0.47

0.3

2.33

2.36

mmu-miR-207_st

mmu-miR-207

mir-207

Chrom 4 (+)

 

-1.44

0.08

0.13

0.61

n.a.

n.a.

1.69

mmu-miR-21_st

mmu-miR-21

mir-21

Chrom 11 (-)

6.39E-09

-1.74

0.05

0.09

0.31

n.a.

n.a.

2.53

mmu-miR-214_st

mmu-miR-214

mir-214

Chrom 1 (+): mir-199a-2 | mir-214

1.58E-08 (1.13E-07)

-3.02

0.01

0.03

0.54

n.a.

n.a.

n.a.

mmu-miR-214-star_st

mmu-miR-214*

mir-214

Chrom 1 (+): mir-199a-2 | mir-214

 

-2.59

0.01

0.05

0.26

n.a.

n.a.

3.02

mmu-miR-222_st

mmu-miR-222

mir-221

Chrom X (-): mir-222 | mir-221

6.41E-08

-5.43

0.00

0.02

0.47

n.a.

5.76

7.49

mmu-miR-221_st

mmu-miR-221

mir-221

Chrom X (-): mir-222 | mir-221

1.64E-15

-3.04

0.01

0.03

0.54

n.a.

5.21

6.11

mmu-miR-23b_st

mmu-miR-23b

mir-23

Chrom 13 (+): mir-23b | mir-27b | mir-3074-1 | mir-24-1

1.92E-07

2.24

0.02

0.05

1.43

n.a.

0.17

0.43

mmu-miR-92a_st

mmu-miR-92a

mir-25

Chrom 14 (+): mir-17 | mir-18a | mir-19a | mir-20a | mir-19b-1 | mir-92a-1

3.92E-10

-7.12

0.00

0.02

0.24

n.a.

6.59

4.41

mmu-miR-25_st

mmu-miR-25

mir-25

Chrom 5(-): mir-106b | mir-93 | mir-25

1.03E-10

-2.68

0.01

0.03

0.38 # [0.51]

n.a. # [0.62]

2.76 # [2.9]

4.96 # [5.08]

mmu-miR-92b_st

mmu-miR-92b

mir-25

Chrom 3 (-)

1.67E-09

-1.69

0.05

0.09

0.61

n.a.

2.2

2.35

mmu-miR-27a_st

mmu-miR-27a

mir-27

Chrom 8 (+): mir-23a | mir-27a | mir-24-2 | mir-3074-2

6.34E-07

2.89

0.01

0.03

1.57

n.a.

n.a.

0.54

mmu-miR-27b_st

mmu-miR-27b

mir-27

Chrom 13 (+): mir-23b | mir-27b | mir-3074-1 | mir-24-1

5.98E-07

3.86

0.00

0.03

1.93

n.a.

0.07

0.23

mmu-miR-28-star_st

mmu-miR-28*

mir-28

Chrom 16 (+)

6.88E-07

-1.36

0.10

0.15

0.63

n.a.

n.a.

n.a.

mmu-miR-29a_st

mmu-miR-29a

mir-29

Chrom 6 (-): mir-29b-1 | mir-29a

8.04E-10 (5.02E-07)

-4.57

0.00

0.03

0.28

n.a.

8.13

12.61

mmu-miR-294-star_st

mmu-miR-294*

mir-290

Chrom 7 (+): mir-290 | mir-291a | mir-292 | mir-291b | mir-293 | mir-294 | mir-295

4.58E-08

2.41

0.01

0.04

3.19

n.a.

n.a.

2.81

mmu-miR-296-3p_st

mmu-miR-296-3p

mir-296

Chrom 2 (-): mir-298 | mir-296

 

-3.21

0.01

0.03

0.42

n.a.

n.a.

2.1

mmu-miR-30c-2-star_st

mmu-miR-30c-2*

mir-30

Chrom 1 (+)

 

-2.18

0.02

0.05

0.43

n.a.

n.a.

n.a.

mmu-miR-30c_st

mmu-miR-30c

mir-30

Chrom 4 (-): mir-30f | mir-30e | mir-30c-1

2.40E-15

2.06

0.03

0.06

2.05

n.a.

n.a.

n.a.

mmu-miR-30a_st

mmu-miR-30a

mir-30

Chrom 1 (+)

2.41E-14

2.77

0.01

0.03

1.69

n.a.

n.a.

0.39

mmu-miR-30b_st

mmu-miR-30b

mir-30

Chrom 15 (-): mir-30d | mir-30b

6.64E-17

3.88

0.00

0.03

2.67

n.a.

n.a.

n.a.

mmu-miR-31_st

mmu-miR-31

mir-31

Chrom 4 (-)

(3.84E-07)

-2.87

0.01

0.03

0.64

n.a.

2.12

1.88

mmu-miR-320_st

mmu-miR-320

mir-320

Chrom 14 (+)

7.97E-07

-1.39

0.09

0.14

0.73

n.a.

n.a.

n.a.

mmu-miR-322-star_st

mmu-miR-322*

mir-322

Chrom X (-): mir-322 | mir-503 | mir-351 | mir-542 | mir-450a-2 | mir-450a-1 | mir-450b

6.72E-13

-1.72

0.05

0.09

0.37

n.a.

n.a.

1.77

mmu-miR-328_st

mmu-miR-328

mir-328

Chrom 8 (-)

 

-1.98

0.03

0.07

0.39

n.a.

n.a.

n.a.

mmu-miR-335-5p_st

mmu-miR-335-5p

mir-335

Chrom 6 (+)

5.76E-06

4.65

0.00

0.03

9.44 # [3.88]

n.a. # [0.47]

n.a. # [0.01]

n.a # [0.16]

mmu-miR-34c-star_st

mmu-miR-34c*

mir-34

Chrom 9 (-): mir-34b | mir-34c

9.47E-11

-1.39

0.09

0.14

0.46

n.a.

n.a.

0.28

mmu-miR-342-5p_st

mmu-miR-342-5p

mir-342

Chrom 12 (+)

 

-1.83

0.04

0.08

0.58

0.47

n.a.

n.a.

mmu-miR-351_st

mmu-miR-351

mir-351

Chrom X (-): mir-322 | mir-503 | mir-351 | mir-542 | mir-450a-2 | mir-450a-1 | mir-450b

(2.36E-06)

-2.01

0.03

0.06

0.22

n.a.

n.a.

3.61

mmu-miR-365_st

mmu-miR-365

mir-365

Chrom 16 (+): mir-193b | mir-365-1

 

4.32

0.00

0.03

4.75

n.a.

0.21

0.32

mmu-miR-376a_st

mmu-miR-376a

mir-368

Chrom 12 (+): mir-494 | mir-679 | mir-1193 | mir-666 | mir-543 | mir-495 | mir-667 | mir-376c | mir-654 | mir-376b | mir-376a | mir-300 | mir-381 | mir-487b | mir-539 | mir-544 | mir-382

1.84E-10

2.17

0.02

0.05

2.31

n.a.

n.a.

n.a.

mmu-miR-376b_st

mmu-miR-376b

mir-368

Chrom 12 (+): mir-329 | mir-494 | mir-679 | mir-1193 | mir-666 | mir-543 | mir-495 | mir-667 | mir-376c | mir-654 | mir-376b | mir-376a | mir-300 | mir-381 | mir-487b | mir-539 | mir-544

1.89E-09

4.35

0.00

0.03

3.24

2.05

n.a.

n.a.

mmu-miR-378_st

mmu-miR-378

mir-378

Chrom 18 (-)

 

-2.92

0.01

0.03

0.27

n.a.

0.24

1.91

mmu-miR-411_st

mmu-miR-411

mir-379

Chrom 12 (+): mir-379 | mir-411 | mir-299a | mir-299b | mir-380 | mir-1197 | mir-323 | mir-758 | mir-329 | mir-494 | mir-679 | mir-1193 | mir-666 | mir-543 | mir-495 | mir-667

2.81E-10

2.26

0.02

0.05

2.72

n.a.

n.a.

n.a.

mmu-miR-423-5p_st

mmu-miR-423-5p

mir-423

Chrom 11 (-)

(2.68E-09)

-2.41

0.01

0.04

0.41

n.a.

n.a.

n.a.

mmu-miR-423-3p_st

mmu-miR-423-3p

mir-423

Chrom 11 (-)

(7.44E-08)

-1.89

0.03

0.07

0.49

n.a.

2.22

1.9

mmu-miR-433-star_st

mmu-miR-433*

mir-433

Chrom 12 (+): mir-337 | mir-3544 | mir-540 | mir-665 | mir-3070a | mir-3070b | mir-431 | mir-433 | mir-127 | mir-434 | mir-432 | mir-3071 | mir-136

 

-2.25

0.02

0.05

0.59

n.a.

n.a.

n.a.

mmu-miR-455_st

mmu-miR-455

mir-455

Chrom 4 (+)

9.31E-07

-2.88

0.01

0.03

0.23

n.a.

n.a.

n.a.

mmu-miR-466f_st

mmu-miR-466f

mir-467

Chrom 2 (+): mir-466m | mir-466f-1 | mir-669f | mir-669e | mir-669b | mir-669d | mir-466f-2 | mir-669l | mir-669d-2 | mir-466f-3 | mir-297a-2 | mir-466o | mir-467c | mir-466b-1 | mir-669a-3 | mir-669k | mir-467a-1 | mir-466b-8 | mir-669a-1

 

-3.48

0.00

0.03

0.25

n.a.

n.a.

n.a.

mmu-miR-467a_st

mmu-miR-467a

mir-467

Chrom 2 (+): mir-466m | mir-466f-1 | mir-669f | mir-669e | mir-669b | mir-669d | mir-466f-2 | mir-669l | mir-669d-2 | mir-466f-3 | mir-297a-2 | mir-466o | mir-467c | mir-466b-1 | mir-669a-3 | mir-669k | mir-467a-1 | mir-466b-8 | mir-669a-1 | mir-669g | mir-669j | mir-467a-2 | mir-466e | mir-669a-4 | mir-467b | mir-466c-1 | mir-669a-5 | mir-467a-3 | mir-466c-2 | mir-669a-6 | mir-467a-4

7.61E-08

-3.38

0.01

0.03

0.52

0.46

n.a.

n.a.

mmu-miR-466f-5p_st

mmu-miR-466f-5p

mir-467

Chrom 2 (+): mir-466m | mir-466f-1 | mir-669f | mir-669e | mir-669b | mir-669d | mir-466f-2 | mir-669l | mir-669d-2 | mir-466f-3 | mir-297a-2 | mir-466o | mir-467c | mir-466b-1 | mir-669a-3 | mir-669k | mir-467a-1 | mir-466b-8 | mir-669a-1

1.86E-07

-2.8

0.01

0.03

0.32

n.a.

n.a.

n.a.

mmu-miR-466f-3p_st

mmu-miR-466f-3p

mir-467

Chrom 2 (+): mir-466m | mir-466f-1 | mir-669f | mir-669e | mir-669b | mir-669d | mir-466f-2 | mir-669l | mir-669d-2 | mir-466f-3 | mir-297a-2 | mir-466o | mir-467c | mir-466b-1 | mir-669a-3 | mir-669k | mir-467a-1 | mir-466b-8 | mir-669a-1

2.94E-17

-1.99

0.03

0.07

0.54

n.a.

3.54

2.36

mmu-miR-466j_st

mmu-miR-466j

mir-467

Chrom 10 (+)

 

-1.56

0.07

0.11

0.48

n.a.

n.a.

n.a.

mmu-miR-669c_st

mmu-miR-669c

mir-467

Chrom 2 (+): mir-669a-11 | mir-467a-10 | mir-466b-3 | mir-669a-12 | mir-467e | mir-466p | mir-467d | mir-466a | mir-297c | mir-669c | mir-669a-2 | mir-297b | mir-466d | mir-669m-1 | mir-669m-2 | mir-466n | mir-669o | mir-466g | mir-466h | mir-297a-3 | mir-466l | mir-297a-4 | mir-669i | mir-669h

8.81E-11

-1.34

0.11

0.15

0.48

n.a.

n.a.

n.a.

mmu-miR-467e-star_st

mmu-miR-467e*

mir-467

Chrom 2 (+): mir-467a-8 | mir-466b-7 | mir-669p-2 | mir-467a-9 | mir-466b-2 | mir-669a-10 | mir-669a-11 | mir-467a-10 | mir-466b-3 | mir-669a-12 | mir-467e | mir-466p | mir-467d | mir-466a | mir-297c | mir-669c | mir-669a-2 | mir-297b | mir-466d | mir-669m-1 | mir-669m-2 | mir-466n | mir-669o | mmir-466g | mir-466h

4.32E-09

3.57

0.00

0.03

3.2

n.a.

3.88

1.57

mmu-miR-493_st

mmu-miR-493

mir-493

Chrom 12 (+): mir-673 | mir-493 | mir-337 | mir-3544 | mir-540 | mir-665 | mir-3070a | mir-3070b

 

-1.59

0.06

0.11

0.52

n.a.

3.02

n.a.

mmu-miR-503_st

mmu-miR-503

mir-503

Chrom X (-): mir-322 | mir-503 | mir-351 | mir-542 | mir-450a-2 | mir-450a-1 | mir-450b

2.84E-06

-2.58

0.01

0.04

0.25

0.23

2.75

2.95

mmu-miR-574-5p_st

mmu-miR-574-5p

mir-574

Chrom 5 (+)

(5.07E-06)

-3.32

0.01

0.03

0.43

n.a.

n.a.

n.a.

mmu-miR-652_st

mmu-miR-652

mir-652

Chrom X (+)

1.72E-07

-1.59

0.06

0.11

0.67

n.a.

n.a.

1.48

mmu-miR-665_st

mmu-miR-665

mir-665

Chrom 12 (+): mir-493 | mir-337 | mir-3544 | mir-540 | mir-665 | mir-3070a | mir-3070b | mir-431 | mir-433 | mir-127 | mir-434 | mir-432 | mir-3071 | mir-136

(2.89E-06)

-1.72

0.05

0.09

0.32

n.a.

4.99

2.88

mmu-miR-670_st

mmu-miR-670

mir-670

Chrom 2 (-)

 

2.11

0.02

0.06

3.48

n.a.

n.a.

n.a.

mmu-miR-672_st

mmu-miR-672

mir-672

Chrom X (-):

 

-1.47

0.08

0.13

0.22

n.a.

n.a.

1.48

mmu-miR-674_st

mmu-miR-674

mir-674

Chrom 2 (+)

 

-2.21

0.02

0.05

0.68

n.a.

n.a.

2.76

mmu-miR-675-3p_st

mmu-miR-675-3p

mir-675

Chrom 7 (-)

2.79E-07

3.48

0.00

0.03

3.3

n.a.

n.a.

n.a.

mmu-miR-708_st

mmu-miR-708

mir-708

Chrom 7 (+)

6.41E-06

-1.74

0.05

0.09

0.47

n.a.

0.27

0.35

mmu-miR-744_st

mmu-miR-744

mir-744

Chrom 11 (-)

(1.89E-07)

-1.69

0.05

0.09

0.68

n.a.

n.a.

n.a.

mmu-miR-877-star_st

mmu-miR-877*

mir-877

Chrom 17 (-)

 

-2.8

0.01

0.03

0.47

n.a.

n.a.

n.a.

mmu-miR-877_st

mmu-miR-877

mir-877

Chrom 17 (-)

(2.52E-07)

-1.36

0.1

0.15

0.5

n.a.

n.a.

1.68

mmu-miR-883b-3p_st

mmu-miR-883b-3p

mir-883

Chrom X (-): mir-463 | mir-741 | mir-471 | mir-883b | mir-883a | mir-742

6.72E-11

4.13

0.00

0.03

6.57

n.a.

3.15

1.94

mmu-miR-99b-star_st

mmu-miR-99b*

mir-99

Chrom 17 (+): mir-99b | let-7e | mir-125a

 

-3.6

0.00

0.03

0.38

n.a.

2.33

2.03

mmu-miR-100_st

mmu-miR-100

mir-99

Chrom 9 (+): mir-100 | let-7a-2

(1.13E-07)

-1.97

0.03

0.07

0.56

n.a.

n.a.

1.68

mmu-miR-1196_st

mmu-miR-1196

 

Chrom 14 (-)

 

-3.74

0.00

0.03

0.27

n.a.

n.a.

n.a.

mmu-miR-714_st

mmu-miR-714

  

2.06E-06

-2.29

0.02

0.05

0.35

n.a.

9.4

6.12

mmu-miR-805_st

mmu-miR-805

 

Death miR entry: maps to the Mt genome and overlaps a Mt tRNA sequence.

2.75E-06

-2.26

0.02

0.05

0.58

n.a.

n.a.

2.04

mmu-miR-709_st

mmu-miR-709

 

Chrom 18 (+)

2.87E-08

-1.85

0.04

0.08

0.58

n.a.

n.a.

1.72

mmu-miR-705_st

mmu-miR-705

 

Chrom 6 (-)

 

-1.8

0.04

0.08

0.4

n.a.

2.35

n.a.

mmu-miR-1187_st

mmu-miR-1187

 

Chrom 5 (-)

 

-1.76

0.05

0.09

0.38

n.a.

n.a.

n.a.

mmu-miR-699_st

mmu-miR-699

 

Death miR entry: appears to be a fragment of RNase MRP RNA (Paul Gardner pers comm)

 

-1.58

0.07

0.11

0.52

n.a.

2.75

1.57

mmu-miR-712_st

mmu-miR-712

 

mir-712a and mir-712b sequences map to the same genomic locus in mouse genome assembly NCBI36

 

-1.38

0.1

0.14

0.41

n.a.

8.61

2.91

mmu-miR-1192_st

mmu-miR-1192

 

Chrom 19 (+)

 

3.55

0.00

0.03

5.61

4.17

2.85

n.a.

mmu-miR-719_st

mmu-miR-719

 

Chrom 14 (-)

9.32E-08

4.51

0.00

0.03

5.79

n.a.

n.a.

n.a.

mmu-miR-706_st

mmu-miR-706

 

Chrom 6 (-)

1.79E-08

5.19

0.00

0.02

4.98

2.66

n.a.

n.a.

  1. List of 103 differentially expressed microRNAs (77 repressed and 26 induced) identified by means of pair-wise SAM contrasts (FDR = 0.1) comparing the microarray-generated miRNA transcriptional profile of 12-day 4OHT Rasless MEFs with that of control untreated K-Raslox MEFs. The last three columns on the right show data corresponding to independent pair-wise comparisons between 6-day 4OHT-treated MEFs and untreated K-Raslox control MEFs, and comparisons between BRAF-rescued or MEK1-rescued cells and Rasless MEFs (all three also at the same FDR = 0.1). The differentially expressed miRNAs are identified by the Affymetrix miRNA probeset ID, miRNA name, miRNA family, Chromosome location and miRNA cluster to which they belong (using updated data from the miRBase database (http://www.mirbase.org/). All miRNA members of the same cluster that show concomitant differential expression in Rasless cells are written in bold. The Genecodis prediction column shows the p-values of statistical significance for predictions of the indicated miRNAs made by Genecodis analysis of the list of repressed or induced (in parenthesis) mRNAs of Rasless cells (Additional file 1: Table S1). d-value quantifies the degree of overexpression (positive values) or repression (negative values) and is a parameter measuring the statistical distance separating the calculated expression value of each gene probeset from the null hypothesis (no-change). p-value is a statistical measurement indicating the probability of random expression for that probeset. q-value is the estimated FDR at the highest p-value for which the probeset would be statistically significant. R-fold is a measurement of the fold-change of a probeset in the collection of the microarrays provided by the SAM algorithm. Independent confirmation of the microarray-generated R-fold values of differential expression for several randomly selected miRNAs was obtained by means of qRT-PCR using specific primers which generated the data indicated by the # symbols and the actual fold values included in the square [parenthesis]. “n.a.”: not applicable at FDR = 0.1. In some cases, the BRAF- and MEK1-rescued samples showed the opposite transcriptional behavior (reversion) in comparison with the Rasless samples but their respective R-fold parameters are still shown here as “n.a.” because the corresponding FDR value of the overall contrasts was higher than 0.1 under the experimental conditions used.
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BMC Genomics

ISSN: 1471-2164

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