Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000159023
1 Isoform Switch
Summary Plot
Only the isoforms with fraction > 5% are shown below.
Notes on IDR and IDR_w_binding: As the prediction of Intrinsically Disordered Regions (IDR) and Intrinsically Disordered Binding Regions (IDBR) are done by two different tools we require two things to annotate the Intrinsically Disordered Binding Regions (IDBR). Firstly the IDBR (predicted by ANCHOR2) must be a region of at least 15 amino acids (after the smoothing). Secondly the fraction of the IDBR which overlaps the IDR predictions (done by IUPred3, again after smoothing) must be at least 80%. When that is the case the IDR type will be annotated as “IDR_w_binding_region” instead of just “IDR”. The current default parameters have not been rigorously tested and should be considered experimental.
For the function of any other domain, please Click HERE to search it through Pfam database.
Results
| isoform_id | gene_id | condition_1 | condition_2 | gene_name | gene_biotype | iso_biotype | gene_overall_mean | gene_value_1 | gene_value_2 | gene_stderr_1 | gene_stderr_2 | gene_log2_fold_change | iso_overall_mean | iso_value_1 | iso_value_2 | iso_stderr_1 | iso_stderr_2 | iso_log2_fold_change | IF_overall | IF1 | IF2 | dIF | isoform_switch_q_value | gene_switch_q_value | PTC | codingPotential |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000490308 | ENSG00000159023 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | EPB41 | protein_coding | retained_intron | 45.62901 | 37.53715 | 63.17677 | 5.772333 | 2.298735 | 0.7509191 | 8.3176134 | 5.4749454 | 15.560136 | 0.9541050 | 1.0280720 | 1.5052324 | 0.1557958 | 0.1541667 | 0.2471000 | 0.09293333 | 4.731834e-01 | 1.886805e-11 | FALSE | TRUE |
| ENST00000647103 | ENSG00000159023 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | EPB41 | protein_coding | protein_coding | 45.62901 | 37.53715 | 63.17677 | 5.772333 | 2.298735 | 0.7509191 | 7.8899309 | 6.3894870 | 12.539626 | 1.4543428 | 1.3363324 | 0.9716162 | 0.1640375 | 0.1660667 | 0.1987667 | 0.03270000 | 8.118261e-01 | 1.886805e-11 | FALSE | TRUE |
| MSTRG.706.24 | ENSG00000159023 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | EPB41 | protein_coding | 45.62901 | 37.53715 | 63.17677 | 5.772333 | 2.298735 | 0.7509191 | 10.8678833 | 11.9524987 | 9.494508 | 2.7633156 | 0.2928426 | -0.3318349 | 0.2627917 | 0.3111000 | 0.1505000 | -0.16060000 | 3.252394e-04 | 1.886805e-11 | FALSE | TRUE | |
| MSTRG.706.26 | ENSG00000159023 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | EPB41 | protein_coding | 45.62901 | 37.53715 | 63.17677 | 5.772333 | 2.298735 | 0.7509191 | 0.8871524 | 3.8307062 | 0.000000 | 1.3709050 | 0.0000000 | -8.5852278 | 0.0258000 | 0.1024667 | 0.0000000 | -0.10246667 | 1.886805e-11 | 1.886805e-11 | FALSE | TRUE | |
| MSTRG.706.40 | ENSG00000159023 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | EPB41 | protein_coding | 45.62901 | 37.53715 | 63.17677 | 5.772333 | 2.298735 | 0.7509191 | 5.5122253 | 0.6201653 | 11.878738 | 0.6201653 | 1.2959990 | 4.2377215 | 0.0923125 | 0.0157000 | 0.1871667 | 0.17146667 | 7.872467e-02 | 1.886805e-11 | FALSE | TRUE |
- Note:
- The comparisons made can be identified as “from ‘condition_1’ to ‘condition_2’”, meaning ‘condition_1’ is considered the ground state and ‘condition_2’ the changed state. This also means that a positive dIF value indicates that the isoform usage is increased in ‘condition_2’ compared to ‘condition_1’. Since the ‘isoformFeatures’ entry is the most relevant part of the switchAnalyzeRlist object, the most-used standard methods have also been implemented to work directly on isoformFeatures.
2 Differential Exon Usage
Counts
All exons whithin this gene region are shown and numbering below.
Expression
All exons whithin this gene region are shown and numbering below.
Splicing
All exons whithin this gene region are shown and numbering below.
Transcripts
All isoforms whithin this gene region are shown below.
Results
| groupID | featureID | exonBaseMean | dispersion | pvalue | padj | seqnames | start | end | width | strand | HEK293_TMG_6hB | HEK293_OSMI2_6hA | log2fold_HEK293_OSMI2_6hA_HEK293_TMG_6hB |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000159023 | E001 | 0.0000000 | 1 | 28886996 | 28887026 | 31 | + | ||||||
| ENSG00000159023 | E002 | 0.0000000 | 1 | 28887027 | 28887072 | 46 | + | ||||||
| ENSG00000159023 | E003 | 0.2617363 | 1.463869e-01 | 1.952988e-01 | 1 | 28887073 | 28887090 | 18 | + | 0.000 | 0.235 | 11.364 | |
| ENSG00000159023 | E004 | 0.3926045 | 4.639079e-01 | 1.964988e-01 | 1 | 28887091 | 28887091 | 1 | + | 0.000 | 0.307 | 13.022 | |
| ENSG00000159023 | E005 | 1.0468253 | 5.508356e-02 | 2.214583e-01 | 1 | 28887092 | 28887097 | 6 | + | 0.196 | 0.449 | 1.669 | |
| ENSG00000159023 | E006 | 1.6597277 | 5.746735e-02 | 6.731042e-01 | 8.183011e-01 | 1 | 28887098 | 28887099 | 2 | + | 0.384 | 0.500 | 0.604 |
| ENSG00000159023 | E007 | 1.8211433 | 3.249348e-02 | 8.436851e-01 | 9.214326e-01 | 1 | 28887100 | 28887102 | 3 | + | 0.433 | 0.502 | 0.349 |
| ENSG00000159023 | E008 | 1.8211433 | 3.249348e-02 | 8.436851e-01 | 9.214326e-01 | 1 | 28887103 | 28887108 | 6 | + | 0.433 | 0.502 | 0.349 |
| ENSG00000159023 | E009 | 3.0399334 | 5.450880e-02 | 3.334626e-01 | 5.720105e-01 | 1 | 28887109 | 28887111 | 3 | + | 0.671 | 0.546 | -0.552 |
| ENSG00000159023 | E010 | 5.5223800 | 5.512007e-03 | 1.582055e-01 | 3.740871e-01 | 1 | 28887112 | 28887116 | 5 | + | 0.878 | 0.731 | -0.580 |
| ENSG00000159023 | E011 | 8.1415619 | 4.977385e-03 | 2.708204e-02 | 1.185376e-01 | 1 | 28887117 | 28887118 | 2 | + | 1.051 | 0.835 | -0.812 |
| ENSG00000159023 | E012 | 11.2048178 | 2.583707e-02 | 1.885895e-01 | 4.151752e-01 | 1 | 28887119 | 28887123 | 5 | + | 1.140 | 1.030 | -0.400 |
| ENSG00000159023 | E013 | 28.4750908 | 2.107540e-02 | 2.030996e-02 | 9.696921e-02 | 1 | 28887124 | 28887171 | 48 | + | 1.542 | 1.367 | -0.602 |
| ENSG00000159023 | E014 | 36.0413419 | 1.133462e-02 | 1.553306e-02 | 8.009897e-02 | 1 | 28887172 | 28887210 | 39 | + | 1.629 | 1.486 | -0.486 |
| ENSG00000159023 | E015 | 0.9097275 | 1.501117e-01 | 1.138157e-02 | 1 | 28893371 | 28893740 | 370 | + | 0.000 | 0.500 | 14.478 | |
| ENSG00000159023 | E016 | 1.2428501 | 2.617412e-01 | 9.416159e-01 | 1 | 28893741 | 28893837 | 97 | + | 0.336 | 0.328 | -0.048 | |
| ENSG00000159023 | E017 | 0.2027342 | 3.272342e-02 | 4.209274e-01 | 1 | 28914528 | 28914543 | 16 | + | 0.000 | 0.136 | 12.600 | |
| ENSG00000159023 | E018 | 0.4054685 | 3.987408e-01 | 2.512254e-01 | 1 | 28914544 | 28914550 | 7 | + | 0.000 | 0.248 | 12.651 | |
| ENSG00000159023 | E019 | 1.3640294 | 4.230846e-01 | 1.714749e-01 | 1 | 28914551 | 28914561 | 11 | + | 0.110 | 0.533 | 3.064 | |
| ENSG00000159023 | E020 | 1.3640294 | 4.230846e-01 | 1.714749e-01 | 1 | 28914562 | 28914566 | 5 | + | 0.110 | 0.533 | 3.064 | |
| ENSG00000159023 | E021 | 1.3640294 | 4.230846e-01 | 1.714749e-01 | 1 | 28914567 | 28914568 | 2 | + | 0.110 | 0.533 | 3.064 | |
| ENSG00000159023 | E022 | 1.3640294 | 4.230846e-01 | 1.714749e-01 | 1 | 28914569 | 28914571 | 3 | + | 0.110 | 0.533 | 3.064 | |
| ENSG00000159023 | E023 | 1.7034289 | 3.745465e-01 | 5.094671e-01 | 7.075617e-01 | 1 | 28914572 | 28914573 | 2 | + | 0.273 | 0.531 | 1.458 |
| ENSG00000159023 | E024 | 3.0330522 | 2.712390e-01 | 7.214535e-01 | 8.490660e-01 | 1 | 28914574 | 28914578 | 5 | + | 0.522 | 0.655 | 0.596 |
| ENSG00000159023 | E025 | 15.3699140 | 3.066835e-03 | 6.314996e-03 | 4.127436e-02 | 1 | 28914579 | 28914600 | 22 | + | 1.072 | 1.353 | 0.994 |
| ENSG00000159023 | E026 | 20.5680192 | 4.053435e-03 | 4.238393e-03 | 3.048221e-02 | 1 | 28914601 | 28914625 | 25 | + | 1.198 | 1.469 | 0.942 |
| ENSG00000159023 | E027 | 75.6133569 | 5.627061e-04 | 4.724719e-01 | 6.818584e-01 | 1 | 28914626 | 28914768 | 143 | + | 1.849 | 1.922 | 0.245 |
| ENSG00000159023 | E028 | 0.1308682 | 3.092858e-02 | 4.223072e-01 | 1 | 28914769 | 28914773 | 5 | + | 0.000 | 0.135 | 12.621 | |
| ENSG00000159023 | E029 | 58.0538842 | 1.119667e-03 | 6.881154e-02 | 2.223915e-01 | 1 | 28987431 | 28987447 | 17 | + | 1.787 | 1.742 | -0.154 |
| ENSG00000159023 | E030 | 142.1949153 | 3.471094e-04 | 1.655841e-05 | 3.252745e-04 | 1 | 28987448 | 28987497 | 50 | + | 2.192 | 2.103 | -0.296 |
| ENSG00000159023 | E031 | 129.3781510 | 4.113367e-04 | 2.224399e-07 | 7.567190e-06 | 1 | 28987498 | 28987510 | 13 | + | 2.165 | 2.041 | -0.416 |
| ENSG00000159023 | E032 | 258.0772948 | 3.949943e-04 | 4.280633e-11 | 3.273075e-09 | 1 | 28987511 | 28987610 | 100 | + | 2.459 | 2.345 | -0.379 |
| ENSG00000159023 | E033 | 475.4773184 | 2.599853e-04 | 1.043682e-16 | 1.987010e-14 | 1 | 28987611 | 28987905 | 295 | + | 2.718 | 2.614 | -0.344 |
| ENSG00000159023 | E034 | 1.2979604 | 1.901375e-01 | 6.481460e-01 | 1 | 28988763 | 28988829 | 67 | + | 0.271 | 0.402 | 0.815 | |
| ENSG00000159023 | E035 | 0.0000000 | 1 | 28989356 | 28989435 | 80 | + | ||||||
| ENSG00000159023 | E036 | 320.2209131 | 2.423890e-04 | 3.511193e-11 | 2.731477e-09 | 1 | 28993330 | 28993542 | 213 | + | 2.541 | 2.446 | -0.315 |
| ENSG00000159023 | E037 | 224.4662262 | 2.005993e-03 | 1.200998e-03 | 1.143899e-02 | 1 | 28997215 | 28997319 | 105 | + | 2.373 | 2.314 | -0.196 |
| ENSG00000159023 | E038 | 135.3359237 | 3.442027e-04 | 6.531337e-02 | 2.146021e-01 | 1 | 29011865 | 29011907 | 43 | + | 2.136 | 2.122 | -0.047 |
| ENSG00000159023 | E039 | 180.2331139 | 2.138465e-03 | 1.655367e-02 | 8.382040e-02 | 1 | 29015692 | 29015767 | 76 | + | 2.270 | 2.232 | -0.127 |
| ENSG00000159023 | E040 | 247.1400315 | 3.038709e-04 | 2.754017e-03 | 2.189380e-02 | 1 | 29018224 | 29018358 | 135 | + | 2.404 | 2.377 | -0.090 |
| ENSG00000159023 | E041 | 223.9851776 | 1.559087e-03 | 2.531280e-02 | 1.131652e-01 | 1 | 29018359 | 29018442 | 84 | + | 2.361 | 2.338 | -0.078 |
| ENSG00000159023 | E042 | 207.4546671 | 2.719774e-04 | 4.171692e-02 | 1.591924e-01 | 1 | 29030400 | 29030487 | 88 | + | 2.321 | 2.313 | -0.025 |
| ENSG00000159023 | E043 | 0.3040503 | 2.444117e-02 | 2.471142e-01 | 1 | 29031788 | 29031913 | 126 | + | 0.196 | 0.000 | -14.051 | |
| ENSG00000159023 | E044 | 264.0570006 | 3.911962e-03 | 7.454184e-02 | 2.338917e-01 | 1 | 29033093 | 29033245 | 153 | + | 2.428 | 2.413 | -0.051 |
| ENSG00000159023 | E045 | 0.3393995 | 2.469553e-02 | 2.459487e-01 | 1 | 29035006 | 29035283 | 278 | + | 0.196 | 0.000 | -14.047 | |
| ENSG00000159023 | E046 | 230.5430110 | 3.028711e-03 | 1.061996e-01 | 2.926973e-01 | 1 | 29035826 | 29035923 | 98 | + | 2.365 | 2.356 | -0.029 |
| ENSG00000159023 | E047 | 301.1341629 | 1.076327e-03 | 1.067470e-01 | 2.935678e-01 | 1 | 29039254 | 29039417 | 164 | + | 2.474 | 2.480 | 0.019 |
| ENSG00000159023 | E048 | 126.2588994 | 3.340749e-03 | 5.016155e-01 | 7.019559e-01 | 1 | 29039418 | 29039426 | 9 | + | 2.092 | 2.111 | 0.063 |
| ENSG00000159023 | E049 | 98.9636221 | 6.890067e-03 | 6.521917e-01 | 8.048455e-01 | 1 | 29053104 | 29053106 | 3 | + | 1.985 | 2.011 | 0.086 |
| ENSG00000159023 | E050 | 201.5028074 | 1.080526e-03 | 2.706167e-01 | 5.105543e-01 | 1 | 29053107 | 29053163 | 57 | + | 2.296 | 2.310 | 0.045 |
| ENSG00000159023 | E051 | 324.6586379 | 2.654175e-04 | 5.107376e-03 | 3.518661e-02 | 1 | 29053164 | 29053312 | 149 | + | 2.515 | 2.502 | -0.045 |
| ENSG00000159023 | E052 | 6.6766187 | 2.920342e-01 | 1.187241e-01 | 3.137677e-01 | 1 | 29053313 | 29054514 | 1202 | + | 0.998 | 0.671 | -1.280 |
| ENSG00000159023 | E053 | 23.6493413 | 2.065400e-02 | 8.488766e-01 | 9.242902e-01 | 1 | 29058589 | 29058603 | 15 | + | 1.369 | 1.426 | 0.200 |
| ENSG00000159023 | E054 | 32.7586761 | 7.475653e-03 | 9.803940e-01 | 9.919594e-01 | 1 | 29058604 | 29058645 | 42 | + | 1.512 | 1.555 | 0.147 |
| ENSG00000159023 | E055 | 6.1111293 | 9.676703e-02 | 6.603559e-01 | 8.101750e-01 | 1 | 29058811 | 29058852 | 42 | + | 0.886 | 0.814 | -0.280 |
| ENSG00000159023 | E056 | 190.1491832 | 1.590783e-03 | 1.818125e-01 | 4.063800e-01 | 1 | 29060422 | 29060484 | 63 | + | 2.274 | 2.277 | 0.011 |
| ENSG00000159023 | E057 | 1.5539852 | 1.245010e-02 | 6.976587e-01 | 8.340091e-01 | 1 | 29064957 | 29064981 | 25 | + | 0.433 | 0.391 | -0.224 |
| ENSG00000159023 | E058 | 433.4183383 | 6.380693e-04 | 2.716964e-03 | 2.166844e-02 | 1 | 29064982 | 29065158 | 177 | + | 2.642 | 2.625 | -0.056 |
| ENSG00000159023 | E059 | 0.3206185 | 2.744240e-02 | 2.470117e-01 | 1 | 29065159 | 29065683 | 525 | + | 0.196 | 0.000 | -13.988 | |
| ENSG00000159023 | E060 | 0.1779838 | 3.668788e-02 | 5.631832e-01 | 1 | 29065684 | 29065825 | 142 | + | 0.109 | 0.000 | -12.834 | |
| ENSG00000159023 | E061 | 0.1779838 | 3.668788e-02 | 5.631832e-01 | 1 | 29065826 | 29065950 | 125 | + | 0.109 | 0.000 | -12.834 | |
| ENSG00000159023 | E062 | 1.1472137 | 1.435378e-02 | 8.595094e-01 | 1 | 29068733 | 29068768 | 36 | + | 0.330 | 0.322 | -0.052 | |
| ENSG00000159023 | E063 | 0.7310763 | 2.092788e-01 | 8.632127e-01 | 1 | 29068769 | 29068783 | 15 | + | 0.198 | 0.242 | 0.370 | |
| ENSG00000159023 | E064 | 0.3503582 | 4.224729e-02 | 9.111021e-01 | 1 | 29069166 | 29070363 | 1198 | + | 0.109 | 0.136 | 0.361 | |
| ENSG00000159023 | E065 | 0.0000000 | 1 | 29070364 | 29070385 | 22 | + | ||||||
| ENSG00000159023 | E066 | 0.0000000 | 1 | 29070386 | 29070390 | 5 | + | ||||||
| ENSG00000159023 | E067 | 0.8455639 | 3.149608e-01 | 8.310722e-01 | 1 | 29070391 | 29073093 | 2703 | + | 0.270 | 0.241 | -0.220 | |
| ENSG00000159023 | E068 | 0.4231520 | 8.803805e-02 | 5.152193e-01 | 1 | 29079441 | 29081664 | 2224 | + | 0.109 | 0.236 | 1.344 | |
| ENSG00000159023 | E069 | 0.0000000 | 1 | 29082466 | 29082757 | 292 | + | ||||||
| ENSG00000159023 | E070 | 0.0000000 | 1 | 29083897 | 29083994 | 98 | + | ||||||
| ENSG00000159023 | E071 | 0.3336024 | 2.444117e-02 | 1.628470e-01 | 1 | 29083995 | 29084122 | 128 | + | 0.000 | 0.238 | 13.733 | |
| ENSG00000159023 | E072 | 11.3138277 | 5.378415e-02 | 7.503550e-01 | 8.669530e-01 | 1 | 29096155 | 29096231 | 77 | + | 1.081 | 1.077 | -0.014 |
| ENSG00000159023 | E073 | 20.9011959 | 1.772562e-03 | 4.734476e-01 | 6.824337e-01 | 1 | 29096232 | 29096604 | 373 | + | 1.338 | 1.325 | -0.045 |
| ENSG00000159023 | E074 | 2.5097131 | 6.964902e-02 | 3.412344e-01 | 5.791960e-01 | 1 | 29096605 | 29097586 | 982 | + | 0.433 | 0.635 | 0.955 |
| ENSG00000159023 | E075 | 1.3734580 | 3.036512e-01 | 7.395137e-02 | 1 | 29097587 | 29097806 | 220 | + | 0.110 | 0.559 | 3.188 | |
| ENSG00000159023 | E076 | 401.4563838 | 3.603122e-03 | 2.247475e-02 | 1.041434e-01 | 1 | 29097807 | 29097935 | 129 | + | 2.615 | 2.582 | -0.110 |
| ENSG00000159023 | E077 | 389.8574132 | 4.066559e-03 | 6.307399e-02 | 2.095921e-01 | 1 | 29109336 | 29109437 | 102 | + | 2.597 | 2.575 | -0.071 |
| ENSG00000159023 | E078 | 0.6847684 | 1.872054e-02 | 3.891889e-01 | 1 | 29109438 | 29109738 | 301 | + | 0.268 | 0.136 | -1.221 | |
| ENSG00000159023 | E079 | 345.2733976 | 1.798448e-03 | 5.383301e-02 | 1.886950e-01 | 1 | 29112368 | 29112448 | 81 | + | 2.538 | 2.530 | -0.030 |
| ENSG00000159023 | E080 | 18.3311254 | 2.196711e-01 | 9.081132e-01 | 9.562100e-01 | 1 | 29112449 | 29114611 | 2163 | + | 1.224 | 1.346 | 0.426 |
| ENSG00000159023 | E081 | 343.0384666 | 8.901982e-04 | 4.138822e-01 | 6.388946e-01 | 1 | 29115699 | 29115803 | 105 | + | 2.522 | 2.546 | 0.080 |
| ENSG00000159023 | E082 | 536.5256931 | 1.312512e-04 | 2.049474e-01 | 4.358443e-01 | 1 | 29116819 | 29117146 | 328 | + | 2.696 | 2.760 | 0.213 |
| ENSG00000159023 | E083 | 1108.0357566 | 8.934258e-05 | 3.274437e-03 | 2.503939e-02 | 1 | 29117147 | 29117866 | 720 | + | 3.006 | 3.082 | 0.253 |
| ENSG00000159023 | E084 | 2419.3261128 | 4.899819e-03 | 5.129748e-11 | 3.852938e-09 | 1 | 29117867 | 29121223 | 3357 | + | 3.264 | 3.493 | 0.761 |