Table 7. Summarised results of the correlation analysis of androgen-regulated isoforms expression with tumour stage in the TCGA PRAD cohort (related to Figure 4 and Supplementary Figure 5).
| Isoform 1 | Isoform 2 | PSI | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Gene | Event type | Change with androgens
(LNCap) |
Rho | FDR | Rho | FDR | Rho | FDR | Consistency
of change with stage |
| LIG4 | Alternative promoter | Induction of promoter 2 | -0.04 | 6.05E-01 | 0.02 | 6.82E-01 | -0.09 | 1.82E-01 | Inconclusive |
| TACC2 | Alternative promoter | Repression of promoter 1 | -0.08 | 1.74E-01 | -0.05 | 4.47E-01 | -0.04 | 5.65E-01 | Inconclusive |
| TPD52 | Alternative promoter | Induction of promoter 2 | -0.02 | 7.85E-01 | -0.02 | 6.82E-01 | -0.02 | 7.95E-01 | Inconclusive |
| NUP93 | Alternative promoter | Induction of promoter 1 | -0.12 | 3.95E-02 | 0.03 | 6.65E-01 | -0.05 | 4.43E-01 | Opposite |
| RLN1 | Alternative promoter | Repression of promoter 2 | -0.22 | 1.82E-05 | -- | -- | -- | -- | Not assessed |
| AP2S1 | Alternative promoter | Induction of promoter 2 | -0.04 | 5.51E-01 | -- | -- | -- | -- | Not assessed |
| RLN2 | Alternative promoter | Induction of promoter 1 | -0.16 | 5.68E-03 | -- | -- | -- | -- | Not assessed |
| PIK3R1 | Alternative promoter | Repression of promoter 2 | -0.02 | 7.92E-01 | 0.11 | 5.92E-02 | -0.14 | 3.27E-02 | Opposite - |
| MAPRE2 | Alternative promoter | Switch to promoter 2 | -0.02 | 7.56E-01 | -0.02 | 6.82E-01 | 0.03 | 1.00E+00 | Inconclusive |
| NDUFAF4 | Alternative promoter | Repression of promoter 2 | 0.08 | 1.89E-01 | -- | -- | -- | -- | Not assessed |
| DCXR | Alternative promoter | Repression of promoter 2 | -0.30 | 6.32E-10 | -- | -- | -- | -- | Not assessed |
| PEX10 | Alternative promoter | Switch to promoter 2 | 0.10 | 9.95E-02 | -- | -- | -- | -- | Not assessed |
| SNAPC2 | Alternative promoter | Switch to promoter 2 | 0.13 | 2.87E-02 | -0.23 | 5.57E-06 | 0.20 | 2.40E-04 | Opposite |
| ATP6V0D1 | Alternative promoter | Repression of promoter 2 | -0.11 | 5.43E-02 | -- | -- | -- | -- | Not assessed |
| ARRDC1 | Alternative promoter | Induction of promoter 2 | 0.08 | 2.06E-01 | -- | -- | -- | -- | Not assessed |
| DENND1A | Alternative promoter | Repression of promoter 2 | -0.01 | 8.49E-01 | -- | -- | -- | -- | Not assessed |
| KLHL36 | Alternative promoter | Induction of promoter 2 | -0.10 | 1.04E-01 | -- | -- | -- | -- | Not assessed |
| RAB3IL1 | Alternative promoter | Repression of promoter 2 | 0.08 | 1.71E-01 | 0.33 | 4.58E-12 | 0.00 | 9.75E-01 | Opposite |
| ACER3 | Alternative promoter | Repression of promoter 2 | 0.16 | 4.77E-03 | -- | -- | -- | -- | Not assessed |
| OSBPL1A | Alternative promoter | Induction of promoter 2 | 0.04 | 5.38E-01 | 0.13 | 1.59E-02 | -0.07 | 2.88E-01 | Consistent |
| TRIM16 | Alternative promoter | Induction of promoter 2 | 0.06 | 3.95E-01 | -- | -- | -- | -- | Not assessed |
| VSIG10L | Alternative promoter | Induction of promoter 1 | -0.12 | 5.43E-02 | -- | -- | -- | -- | Not assessed |
| SEPT5 | Alternative promoter | Repression of promoter 2 | 0.11 | 7.96E-02 | 0.07 | 2.54E-01 | -0.01 | 8.89E-01 | Inconclusive |
| HMGCR | Alternative promoter | Repression of promoter 1 | 0.00 | 9.91E-01 | -0.04 | 5.77E-01 | 0.04 | 6.25E-01 | Inconclusive |
| RDH13 | Alternative promoter | Induction of promoter 1 | -0.03 | 7.33E-01 | 0.10 | 7.19E-02 | -0.12 | 9.32E-02 | Inconclusive |
| GPRIN2 | Alternative promoter | Repression of promoter 2 | -- | -- | 0.03 | 6.48E-01 | -- | -- | Not assessed |
| CLK3 | Alternative promoter | Repression of promoter 1 | -0.15 | 6.05E-03 | 0.02 | 7.76E-01 | 0.02 | 8.63E-01 | Consistent |
| RNH1 | Alternative promoter | Induction of promoter 1 | -0.02 | 7.92E-01 | 0.10 | 6.12E-02 | -0.08 | 2.28E-01 | Inconclusive |
| ZFAND6 | Alternative promoter | Repression of promoter 2 | 0.03 | 6.50E-01 | 0.04 | 5.78E-01 | -0.04 | 6.05E-01 | Inconclusive |
| CDIP1 | Alternative promoter | Repression of promoter 2 | 0.10 | 1.04E-01 | 0.02 | 7.82E-01 | 0.06 | 3.78E-01 | Inconclusive |
| YIF1B | Alternative promoter | Switch to promoter 2 | -0.01 | 8.87E-01 | -0.10 | 6.71E-02 | 0.06 | 3.97E-01 | Inconclusive |
| LIMK2 | Alternative promoter | Switch to promoter 2 | 0.00 | 9.67E-01 | -0.05 | 4.72E-01 | 0.00 | 9.75E-01 | Inconclusive |
| TSC22D3 | Alternative promoter | Repression of promoter 1 | -0.13 | 3.44E-02 | -0.07 | 2.54E-01 | -0.03 | 6.59E-01 | Consistent |
| ALDH1A3 | Alternative promoter | Repression of promoter 1 | -0.18 | 7.69E-04 | -- | -- | -- | -- | Not assessed |
| TRABD | Alternative promoter | Switch to promoter 2 | 0.06 | 3.95E-01 | -0.03 | 6.48E-01 | 0.03 | 7.83E-01 | Inconclusive |
| LIMCH1 | Alternative promoter | Repression of promoter 2 | 0.02 | 7.85E-01 | -- | -- | -- | -- | Not assessed |
| GMFB | Alternative promoter | Induction of promoter 2 | 0.07 | 2.57E-01 | -- | -- | -- | -- | Not assessed |
| MLST8 | Alternative promoter | Switch to promoter 1 | 0.10 | 8.19E-02 | 0.15 | 6.14E-03 | 0.02 | 7.83E-01 | Inconclusive |
| TLE3 | Alternative promoter | Induction of promoter 2 | 0.03 | 6.38E-01 | -0.11 | 3.84E-02 | 0.04 | 5.65E-01 | Opposite |
| UBA1 | Alternative promoter | Repression of promoter 1 | 0.12 | 5.43E-02 | 0.00 | 9.72E-01 | 0.06 | 3.99E-01 | Inconclusive |
| TNRC6B | Alternative promoter | Repression of promoter 2 | -0.04 | 6.31E-01 | -0.03 | 6.48E-01 | 0.02 | 7.83E-01 | Inconclusive |
| FDFT1 | Alternative promoter | Repression of promoter 2 | -0.05 | 4.82E-01 | 0.04 | 5.46E-01 | -0.08 | 2.28E-01 | Inconclusive |
| GREB1 | Alternative promoter | Induction of promoter 2 | -0.11 | 7.48E-02 | -0.18 | 7.01E-04 | 0.01 | 8.96E-01 | Opposite |
| NCAPD3 | Alternative promoter | Induction of promoter 2 | -0.23 | 1.82E-05 | -- | -- | -- | -- | Not assessed |
| SLC36A4 | Alternative promoter | Induction of promoter 2 | 0.07 | 2.59E-01 | -- | -- | -- | -- | Not assessed |
| KLC2 | Alternative promoter | Repression of promoter 1 | -0.03 | 6.33E-01 | 0.13 | 1.81E-02 | -0.08 | 2.78E-01 | Inconclusive |
| RAP1GAP | Alternative promoter | Repression of promoter 1 | 0.02 | 7.85E-01 | -- | -- | -- | -- | Not assessed |
| TMEM79 | Alternative promoter | Repression of promoter 1 | -0.08 | 1.71E-01 | 0.16 | 1.97E-03 | -0.10 | 1.20E-01 | Inconclusive |
| NR4A1 | Alternative promoter | Induction of promoter 2 | 0.01 | 8.49E-01 | -0.06 | 3.69E-01 | 0.08 | 2.62E-01 | Inconclusive |
| ZNF32 | Alternative promoter | Repression of promoter 2 | -0.15 | 6.70E-03 | 0.02 | 7.34E-01 | -0.08 | 2.33E-01 | Inconclusive |
| C1QTNF3 | Alternative promoter | Induction of promoter 1 | 0.03 | 6.74E-01 | -- | -- | -- | -- | Not assessed |
| UBE2D3 | Alternative promoter | Switch to promoter 2 | 0.20 | 2.96E-04 | 0.07 | 2.17E-01 | -0.02 | 7.83E-01 | Inconclusive |
| KRT8 | Alternative promoter | Repression of promoter 1 | -0.04 | 6.05E-01 | -0.24 | 2.72E-06 | 0.04 | 6.05E-01 | Inconclusive |
| ELOVL1 | Alternative promoter | Induction of promoter 2 | 0.13 | 2.87E-02 | -- | -- | -- | -- | Not assessed |
| RCAN1 | Alternative promoter | Induction of promoter 2 | 0.09 | 1.26E-01 | -0.01 | 8.69E-01 | 0.10 | 1.20E-01 | Inconclusive |
| SORBS3 | Alternative promoter | Induction of promoter 2 | 0.11 | 7.96E-02 | -- | -- | -- | -- | Not assessed |
| MAT2A | Alternative 3' end | Repression of isoform 2 | 0.01 | 9.35E-01 | 0.18 | 7.83E-04 | -0.21 | 8.42E-05 | Opposite |
| CNNM2 | Alternative 3' end | Induction of isoform 1 | 0.05 | 3.95E-01 | 0.05 | 4.47E-01 | -0.04 | 6.05E-01 | Inconclusive |
| TMEM125 | Alternative 3' end | Induction of isoform 1 | -- | -- | -0.16 | 2.80E-03 | -- | -- | Not assessed |
| CBWD2 | Alternative 3' end | Induction of isoform 2 | 0.08 | 1.74E-01 | -- | -- | -- | -- | Not assessed |
| NDUFV3 | Alternative exon | Switch to isoform 2 (exon
excluded) |
0.11 | 7.48E-02 | -0.05 | 4.72E-01 | 0.11 | 1.00E-01 | Inconclusive |
| ZNF678 | Alternative exon | Switch to isoform 2 (exon
excluded) |
-0.02 | 7.43E-01 | -- | -- | -- | -- | Not assessed |
| ZNF121 | Alternative exon | Switch to isoform 2 (exon
excluded) |
-0.08 | 1.80E-01 | 0.03 | 6.48E-01 | -0.09 | 1.82E-01 | Inconclusive |
| SPATC1L | Alternative exon | Induction of isoform 2
(exon included) |
-0.10 | 9.95E-02 | -- | -- | -- | -- | Not assessed |
| MOCOS | Alternative exon | Switch to isoform 2 (exon
excluded) |
0.03 | 6.33E-01 | -- | -- | -- | -- | Not assessed |
| RBM45 | Alternative exon | Switch to isoform 2 (exon
included) |
0.08 | 1.71E-01 | -- | -- | -- | -- | Not assessed |
| MIPEP | Alternative exon | Repression of isoform 2
(exon excluded) |
-0.16 | 4.48E-03 | -- | -- | -- | -- | Not assessed |
| BBS4 | Alternative exon | Induction of isoform 2
(exon included) |
-0.06 | 3.85E-01 | -- | -- | -- | -- | Not assessed |
| FAM195A | Alternative exon | Switch to isoform 1 (exon
exluded) |
0.06 | 3.37E-01 | 0.10 | 6.85E-02 | -0.10 | 1.20E-01 | Inconclusive |
| LINC01133 | Alternative exon | Induction of isoform 1
(exon excluded) |
-- | -- | 0.00 | 9.72E-01 | -- | -- | Not assessed |
| SS18 | Alternative exon | Switch to isoform 2 (exon
excluded) |
0.04 | 5.68E-01 | -0.04 | 5.46E-01 | 0.06 | 3.97E-01 | Inconclusive |
| RHOC | Alternative exon | Switch to isoform 2 (exon
excluded) |
0.15 | 6.05E-03 | 0.11 | 3.84E-02 | 0.11 | 1.00E-01 | Inconclusive |
| ZNF226 | Retained intron | Switch to isoform 1 (intron
included) |
-0.03 | 6.64E-01 | -0.09 | 1.23E-01 | 0.07 | 3.35E-01 | Inconclusive |