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Table 1 Ranking of RNA-binding proteins (RBPs) for the experiments: KD-SRSF1, KD-FUS and KD-TARDBP (CLIP p-value < 0.05; limma p-value < 0.05; |log2 FC| > 0.58). Four groups of columns are separated by thick vertical black lines are shown: i) knock down (KD) genes and RBP of the ranking; ii) the prediction using the pipeline presented in this work (CLIP experiments); iii) differential expression (knock-down vs normal) and iv) the same prediction using previous algorithms based on RBPs’ consensus binding motifs –represented as Position Weighted Matrices (PWMs). NA: the PWM is not available for this RBP. N.S.: non-significant

From: Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data

Experiment

RBP

Ranking by CLIP p-value (out of 195)

Differentially spliced hits (Expected)

Differentially spliced hits (Found)

CLIP p-value (Fisher)

Expression Fold change (log2)

limma adjusted p-value

Ranking by PWM p-value (out of 123)

PWM p-value

KD-SRSF1

SRSF1

10

396

620

5 .16E-24

−1 .54

9 .18E-29

13

8.32E-04

LIN28B

20

561

747

3 .75E−15

0 .96

7 .76E-14

NA

NA

UCHL5

27

261

384

1 .03E-13

-1 .52

7 .61E-21

NA

NA

SF3A3

37

266

324

7 .03E-11

−0 .83

2 .77E-22

NA

NA

HNRNPD

46

69

164

2 .94E− 08

−0 .63

1 .49E-16

15

1 .11E−03

EFTUD2

62

454

520

1 .29E-05

-0 .66

2 .69E−19

NA

NA

TAF15

115

83

149

4 .75E− 02

−0 .78

5 .05E-17

NA

NA

KD-FUS

FUS

11

375

465

2 .35E−09

-1 .09

9 .77E− 02

112

N.S.

LIN28A

25

163

219

1 .78E− 06

0 .69

1 .43E-01

1

9 .54E-02

FBL

56

49

73

3 .12E-04

-0 .81

3 .10E-01

NA

NA

YBX3

64

145

182

4 .94E-04

-0 .79

2 .08E-01

NA

NA

CPSF2

109

40

52

2 .58E-02

-0 .70

9 .91E-02

NA

NA

KD-TARDBP

TARDBP

20

688

746

2 .10E-05

-0 .87

2 .16E-02

13

1 .30E-02

RBM22

26

160

205

6 .69E-05

0 .64

1 .93E-02

NA

NA

PTBP2

58

144

174

3 .74E-03

-0 .60

4 .57E-02

NA

NA

SF3A3

68

223

255

7 .86E-03

0 .64

7 .83E-02

NA

NA

FBL

81

49

63

1 .81E-02

0 .89

1 .14E-01

NA

NA

RBP

83

37

49

1 .92E-02

0 .68

1 .69E-02

NA

NA