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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