Table 5. Summarised results of the differential expression analysis of androgen-regulated isoforms between tumour and normal tissue samples in the TCGA PRAD cohort.
| Isoform 1 | Isoform 2 | PSI | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Event type | Change with androgens (LNCap) | log2FC | Av.Expr.
(TPM) |
FDR | log2FC | Av.Expr.
(TPM) |
FDR | Delta
PSI |
Av. PSI | FDR | Consistency
of change in tumours |
| LIG4 | Alternative promoter | Induction of promoter 2 | -0.81 | 1.77 | 4.31E-02 | -1.53 | 1.28 | 4.48E-05 | 0.06 | 0.597300667 | 9.85E-02 | Opposite |
| TACC2 | Alternative promoter | Repression of promoter 1 | -0.80 | 2.42 | 5.51E-03 | 0.18 | 6.22 | 6.06E-01 | -0.16 | 0.284239843 | 2.95E-05 | Consistent |
| TPD52 | Alternative promoter | Induction of promoter 2 | -0.34 | 0.17 | 5.45E-01 | 1.87 | 39.20 | 1.23E-09 | 0.00 | 0.011365308 | 8.11E-06 | Consistent |
| NUP93 | Alternative promoter | Induction of promoter 1 | 0.25 | 25.52 | 6.45E-04 | 0.31 | 7.20 | 6.08E-01 | 0.01 | 0.828738669 | 7.52E-01 | Consistent |
| RLN1 | Alternative promoter | Repression of promoter 2 | -0.45 | 133.50 | 4.97E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| AP2S1 | Alternative promoter | Induction of promoter 2 | 0.48 | 191.44 | 2.24E-05 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| RLN2 | Alternative promoter | Induction of promoter 1 | 0.48 | 5.07 | 2.41E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| PIK3R1 | Alternative promoter | Repression of promoter 2 | -1.79 | 7.15 | 3.26E-12 | -1.79 | 1.26 | 8.20E-06 | -0.02 | 0.820282185 | 7.52E-01 | Consistent |
| MAPRE2 | Alternative promoter | Switch to promoter 2 | 1.17 | 1.52 | 1.22E-01 | -0.34 | 0.07 | 1.96E-01 | 0.09 | 0.730349729 | 4.67E-02 | Opposite |
| NDUFAF4 | Alternative promoter | Repression of promoter 2 | 0.55 | 0.06 | 5.86E-02 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| DCXR | Alternative promoter | Repression of promoter 2 | 0.68 | 623.07 | 2.05E-05 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| PEX10 | Alternative promoter | Switch to promoter 2 | 0.92 | 75.55 | 7.84E-06 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| SNAPC2 | Alternative promoter | Switch to promoter 2 | 0.38 | 5.42 | 1.23E-01 | 0.22 | 37.58 | 3.20E-02 | -0.01 | 0.130583106 | 8.29E-01 | Inconclusive |
| ATP6V0D1 | Alternative promoter | Repression of promoter 2 | -0.12 | 109.86 | 1.42E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| ARRDC1 | Alternative promoter | Induction of promoter 2 | 0.46 | 12.78 | 2.34E-05 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| DENND1A | Alternative promoter | Repression of promoter 2 | 0.04 | 7.09 | 9.11E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| KLHL36 | Alternative promoter | Induction of promoter 2 | -0.38 | 10.58 | 4.61E-06 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| RAB3IL1 | Alternative promoter | Repression of promoter 2 | 0.34 | 0.28 | 5.07E-01 | 0.05 | 4.68 | 6.91E-01 | 0.01 | 0.062673984 | 4.28E-01 | Inconclusive |
| ACER3 | Alternative promoter | Repression of promoter 2 | 0.13 | 6.32 | 8.52E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| OSBPL1A | Alternative promoter | Induction of promoter 2 | 0.14 | 4.11 | 5.75E-01 | -1.06 | 3.56 | 3.44E-09 | 0.17 | 0.522207286 | 1.03E-08 | Opposite |
| TRIM16 | Alternative promoter | Induction of promoter 2 | -0.65 | 6.87 | 1.03E-14 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| VSIG10L | Alternative promoter | Induction of promoter 1 | -1.01 | 1.91 | 5.49E-04 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| SEPT5 | Alternative promoter | Repression of promoter 2 | 0.80 | 11.47 | 1.79E-09 | 1.09 | 3.86 | 1.82E-06 | -0.03 | 0.749615358 | 1.90E-01 | Opposite |
| HMGCR | Alternative promoter | Repression of promoter 1 | -0.86 | 0.59 | 1.07E-01 | -0.55 | 17.41 | 1.09E-02 | 0.00 | 0.029105295 | 9.62E-01 | Inconclusive |
| RDH13 | Alternative promoter | Induction of promoter 1 | 1.67 | 2.10 | 1.31E-08 | 0.72 | 0.05 | 5.88E-03 | 0.00 | 0.962155441 | 9.33E-02 | Consistent |
| GPRIN2 | Alternative promoter | Repression of promoter 2 | -- | -- | -- | -0.48 | 3.31 | 3.98E-02 | -- | -- | -- |
Not
assessed |
| CLK3 | Alternative promoter | Repression of promoter 1 | 0.10 | 31.34 | 1.07E-01 | -- | 0.04 | -- | 0.00 | 0.998537929 | 6.18E-01 | Inconclusive |
| RNH1 | Alternative promoter | Induction of promoter 1 | -0.16 | 4.38 | 7.95E-01 | -0.19 | 6.56 | 5.74E-01 | 0.00 | 0.375368151 | 7.52E-01 | Inconclusive |
| ZFAND6 | Alternative promoter | Repression of promoter 2 | -0.10 | 37.63 | 6.33E-01 | -1.51 | 2.29 | 5.59E-03 | 0.03 | 0.935657481 | 3.73E-02 | Consistent |
| CDIP1 | Alternative promoter | Repression of promoter 2 | 0.77 | 0.35 | 1.16E-01 | -1.83 | 3.70 | 2.77E-11 | 0.06 | 0.142411928 | 1.46E-03 | Consistent |
| YIF1B | Alternative promoter | Switch to promoter 2 | 0.50 | 2.52 | 3.18E-01 | 2.83 | 3.08 | 1.60E-04 | -0.32 | 0.497841217 | 1.64E-02 | Consistent |
| LIMK2 | Alternative promoter | Switch to promoter 2 | -0.90 | 6.80 | 1.50E-03 | 0.58 | 10.99 | 1.10E-05 | -0.19 | 0.382613244 | 2.85E-06 | Consistent |
| TSC22D3 | Alternative promoter | Repression of promoter 1 | -- | 35.48 | -- | -1.08 | 173.59 | 8.13E-15 | 0.01 | 0.203019277 | 2.97E-01 | Inconclusive |
| ALDH1A3 | Alternative promoter | Repression of promoter 1 | 0.71 | 279.09 | 7.51E-03 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| TRABD | Alternative promoter | Switch to promoter 2 | 1.57 | 21.80 | 3.42E-02 | 0.87 | 0.54 | 1.18E-01 | 0.00 | 0.958501941 | 5.17E-01 | Inconclusive |
| LIMCH1 | Alternative promoter | Repression of promoter 2 | -- | 0.01 | -- | -- | -- | -- | -- | -- | -- |
Not
assessed |
| GMFB | Alternative promoter | Induction of promoter 2 | -0.11 | 11.91 | 7.54E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| MLST8 | Alternative promoter | Switch to promoter 1 | 0.87 | 0.19 | 9.88E-04 | 1.51 | 4.90 | 9.60E-03 | 0.02 | 0.121241399 | 5.81E-01 | Inconclusive |
| TLE3 | Alternative promoter | Induction of promoter 2 | 0.10 | 0.10 | 8.70E-01 | -0.20 | 5.14 | 4.28E-01 | 0.00 | 0.02562604 | 6.14E-01 | Inconclusive |
| UBA1 | Alternative promoter | Repression of promoter 1 | 0.21 | 23.51 | 1.39E-01 | 0.01 | 131.71 | 9.46E-01 | 0.01 | 0.190009964 | 2.99E-01 | Inconclusive |
| TNRC6B | Alternative promoter | Repression of promoter 2 | 0.18 | 2.27 | 3.34E-02 | -0.43 | 0.03 | 4.15E-01 | 0.00 | 0.988593061 | 3.56E-02 | Inconclusive |
| FDFT1 | Alternative promoter | Repression of promoter 2 | -0.57 | 94.14 | 1.13E-07 | -1.07 | 1.05 | 5.62E-12 | 0.00 | 0.986642757 | 2.13E-02 | Consistent |
| GREB1 | Alternative promoter | Induction of promoter 2 | 1.45 | 1.01 | 6.45E-04 | 0.28 | 1.48 | 3.21E-01 | 0.14 | 0.378280864 | 3.40E-02 | Inconclusive |
| NCAPD3 | Alternative promoter | Induction of promoter 2 | 0.16 | 75.75 | 6.55E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| SLC36A4 | Alternative promoter | Induction of promoter 2 | -0.91 | 2.15 | 1.60E-03 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| KLC2 | Alternative promoter | Repression of promoter 1 | 0.47 | 0.27 | 4.16E-01 | -0.76 | 3.64 | 8.12E-02 | 0.00 | 0.1048405 | 4.53E-01 | Inconclusive |
| RAP1GAP | Alternative promoter | Repression of promoter 1 | 1.94 | 3.42 | 3.45E-08 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| TMEM79 | Alternative promoter | Repression of promoter 1 | 0.21 | 3.77 | 7.91E-01 | -1.40 | 1.67 | 2.05E-05 | 0.19 | 0.399443544 | 5.07E-02 | Inconclusive |
| NR4A1 | Alternative promoter | Induction of promoter 2 | -0.40 | 1.86 | 2.34E-01 | -0.74 | 5.81 | 7.87E-03 | 0.06 | 0.292753045 | 2.53E-01 | Opposite |
| ZNF32 | Alternative promoter | Repression of promoter 2 | 0.03 | 67.26 | 7.14E-01 | 0.03 | 4.12 | 7.14E-01 | 0.00 | 0.942446541 | 1.00E+00 | Inconclusive |
| C1QTNF3 | Alternative promoter | Induction of promoter 1 | -0.30 | 3.41 | 4.67E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| UBE2D3 | Alternative promoter | Switch to promoter 2 | -0.50 | 8.00 | 5.09E-04 | -0.13 | 0.32 | 8.18E-01 | -0.01 | 0.953413055 | 5.49E-01 | Inconclusive |
| KRT8 | Alternative promoter | Repression of promoter 1 | -0.08 | 2.08 | 8.55E-01 | 0.48 | 697.27 | 1.26E-05 | 0.00 | 0.003455479 | 9.85E-02 | Inconclusive |
| ELOVL1 | Alternative promoter | Induction of promoter 2 | -0.10 | 100.07 | 1.38E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| RCAN1 | Alternative promoter | Induction of promoter 2 | -0.31 | 1.39 | 4.66E-01 | -1.40 | 6.90 | 4.40E-07 | 0.09 | 0.2372612 | 1.64E-02 | Opposite |
| SORBS3 | Alternative promoter | Induction of promoter 2 | 0.21 | 6.33 | 6.20E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| MAT2A | Alternative 3' end | Repression of isoform 2 | -0.36 | 102.47 | 6.63E-02 | 0.27 | 13.41 | 2.87E-01 | -0.03 | 0.888519015 | 5.32E-03 | Inconclusive |
| CNNM2 | Alternative 3' end | Induction of isoform 1 | 0.67 | 0.44 | 2.73E-05 | -0.79 | 1.22 | 5.96E-03 | 0.13 | 0.331082656 | 3.31E-05 | Consistent |
| TMEM125 | Alternative 3' end | Induction of isoform 1 | -- | -- | -- | 0.45 | 40.70 | 9.40E-04 | -- | -- | -- |
Not
assessed |
| CBWD2 | Alternative 3' end | Induction of isoform 2 | 0.00 | 16.56 | 9.88E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| NDUFV3 | Alternative exon | Switch to isoform 2 (exon excluded) | -0.09 | 12.98 | 2.36E-01 | 0.54 | 56.19 | 4.17E-07 | -0.07 | 0.201011 | 2.54E-08 | Consistent |
| ZNF678 | Alternative exon | Switch to isoform 2 (exon excluded) | 0.32 | 0.97 | 2.23E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| ZNF121 | Alternative exon | Switch to isoform 2 (exon excluded) | 0.90 | 0.08 | 5.97E-03 | 0.02 | 3.09 | 9.28E-01 | 0.00 | 0.037899858 | 9.85E-02 | Inconclusive |
| SPATC1L | Alternative exon | Induction of isoform 2 (exon included) | 0.35 | 36.98 | 4.71E-02 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| MOCOS | Alternative exon | Switch to isoform 2 (exon excluded) | -0.82 | 2.24 | 1.14E-09 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| RBM45 | Alternative exon | Switch to isoform 2 (exon included) | 0.25 | 7.85 | 9.96E-07 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| MIPEP | Alternative exon | Repression of isoform 2 (exon excluded) | 0.87 | 49.00 | 9.53E-04 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| BBS4 | Alternative exon | Induction of isoform 2 (exon included) | 0.02 | 21.63 | 9.71E-01 | -- | -- | -- | -- | -- | -- |
Not
assessed |
| FAM195A | Alternative exon | Switch to isoform 1 (exon exluded) | 0.87 | 43.81 | 4.03E-08 | 0.99 | 5.57 | 1.01E-08 | -0.01 | 0.884563881 | 2.50E-01 | Inconclusive |
| LINC01133 | Alternative exon | Induction of isoform 1 (exon excluded) | -- | -- | -- | -1.58 | 2.77 | 1.39E-08 | 0.00 | -- | -- |
Not
assessed |
| SS18 | Alternative exon | Switch to isoform 2 (exon excluded) | -1.47 | 3.70 | 1.97E-02 | -0.14 | 33.31 | 1.18E-02 | -0.07 | 0.087763421 | 2.88E-02 | Consistent |
| RHOC | Alternative exon | Switch to isoform 2 (exon excluded) | 0.62 | 1.48 | 3.71E-06 | 0.13 | 153.20 | 1.96E-01 | 0.00 | 0.009830219 | 1.46E-03 | Inconclusive |
| ZNF226 | Retained intron | Switch to isoform 1 (intron included) | -0.13 | 2.48 | 5.37E-01 | -0.08 | 13.49 | 7.40E-01 | -0.01 | 0.184522223 | 8.77E-01 | Inconclusive |