Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000122218
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000368069 | ENSG00000122218 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | COPA | protein_coding | protein_coding | 72.33282 | 62.8101 | 73.60129 | 16.48273 | 3.317729 | 0.228701 | 11.187920 | 10.547713 | 10.782651 | 3.9027008 | 1.7825204 | 0.03175191 | 0.15375000 | 0.15886667 | 0.14596667 | -0.01290000 | 9.444550e-01 | 7.928887e-41 | FALSE | TRUE |
| ENST00000545284 | ENSG00000122218 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | COPA | protein_coding | retained_intron | 72.33282 | 62.8101 | 73.60129 | 16.48273 | 3.317729 | 0.228701 | 7.091427 | 9.063354 | 2.148779 | 2.8123617 | 1.2255643 | -2.07142009 | 0.09652500 | 0.13940000 | 0.02876667 | -0.11063333 | 5.019973e-01 | 7.928887e-41 | FALSE | FALSE |
| ENST00000647899 | ENSG00000122218 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | COPA | protein_coding | protein_coding | 72.33282 | 62.8101 | 73.60129 | 16.48273 | 3.317729 | 0.228701 | 4.182075 | 0.000000 | 10.054033 | 0.0000000 | 0.9274024 | 9.97499280 | 0.05725417 | 0.00000000 | 0.13600000 | 0.13600000 | 7.928887e-41 | 7.928887e-41 | FALSE | TRUE |
| ENST00000648280 | ENSG00000122218 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | COPA | protein_coding | protein_coding | 72.33282 | 62.8101 | 73.60129 | 16.48273 | 3.317729 | 0.228701 | 5.461514 | 4.964698 | 0.000000 | 1.5772139 | 0.0000000 | -8.95846505 | 0.07382917 | 0.07886667 | 0.00000000 | -0.07886667 | 2.690366e-24 | 7.928887e-41 | FALSE | TRUE |
| ENST00000648501 | ENSG00000122218 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | COPA | protein_coding | nonsense_mediated_decay | 72.33282 | 62.8101 | 73.60129 | 16.48273 | 3.317729 | 0.228701 | 9.649368 | 9.533518 | 12.747386 | 2.3784676 | 0.8541736 | 0.41873960 | 0.13545417 | 0.15280000 | 0.17333333 | 0.02053333 | 7.513995e-01 | 7.928887e-41 | FALSE | TRUE |
| ENST00000648805 | ENSG00000122218 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | COPA | protein_coding | nonsense_mediated_decay | 72.33282 | 62.8101 | 73.60129 | 16.48273 | 3.317729 | 0.228701 | 8.176714 | 6.327630 | 10.004858 | 2.1052426 | 1.1337308 | 0.66012649 | 0.11208333 | 0.09736667 | 0.13536667 | 0.03800000 | 4.096450e-01 | 7.928887e-41 | FALSE | TRUE |
| ENST00000649676 | ENSG00000122218 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | COPA | protein_coding | protein_coding | 72.33282 | 62.8101 | 73.60129 | 16.48273 | 3.317729 | 0.228701 | 9.579691 | 10.630540 | 3.735891 | 3.1761795 | 1.0908864 | -1.50619032 | 0.13194167 | 0.16576667 | 0.04970000 | -0.11606667 | 1.641499e-02 | 7.928887e-41 | FALSE | TRUE |
| ENST00000649787 | ENSG00000122218 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | COPA | protein_coding | protein_coding | 72.33282 | 62.8101 | 73.60129 | 16.48273 | 3.317729 | 0.228701 | 7.351247 | 4.647764 | 12.272599 | 0.8621417 | 1.2661263 | 1.39890645 | 0.10310833 | 0.08033333 | 0.16900000 | 0.08866667 | 2.054125e-01 | 7.928887e-41 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000122218 | E001 | 3.1578335 | 0.0083540051 | 7.201090e-01 | 8.482598e-01 | 1 | 160288594 | 160288658 | 65 | - | 0.580 | 0.638 | 0.254 |
| ENSG00000122218 | E002 | 3.6530392 | 0.0261022052 | 8.843896e-01 | 9.436516e-01 | 1 | 160288659 | 160288685 | 27 | - | 0.646 | 0.671 | 0.105 |
| ENSG00000122218 | E003 | 41.9335047 | 0.0118798464 | 8.524935e-01 | 9.264680e-01 | 1 | 160288686 | 160289200 | 515 | - | 1.620 | 1.640 | 0.068 |
| ENSG00000122218 | E004 | 25.5893331 | 0.0075452482 | 5.866770e-01 | 7.613905e-01 | 1 | 160289201 | 160289272 | 72 | - | 1.398 | 1.447 | 0.169 |
| ENSG00000122218 | E005 | 23.6444769 | 0.0019236932 | 4.175021e-02 | 1.592754e-01 | 1 | 160289273 | 160289290 | 18 | - | 1.308 | 1.459 | 0.523 |
| ENSG00000122218 | E006 | 20.6413343 | 0.0017634494 | 2.463576e-02 | 1.110781e-01 | 1 | 160289291 | 160289292 | 2 | - | 1.235 | 1.411 | 0.611 |
| ENSG00000122218 | E007 | 20.3973835 | 0.0017751505 | 9.103893e-03 | 5.428924e-02 | 1 | 160289293 | 160289294 | 2 | - | 1.211 | 1.416 | 0.717 |
| ENSG00000122218 | E008 | 21.0647760 | 0.0016886371 | 5.896835e-03 | 3.923745e-02 | 1 | 160289295 | 160289300 | 6 | - | 1.219 | 1.433 | 0.744 |
| ENSG00000122218 | E009 | 156.2588422 | 0.0053649288 | 1.844741e-05 | 3.568102e-04 | 1 | 160289301 | 160289353 | 53 | - | 2.076 | 2.286 | 0.700 |
| ENSG00000122218 | E010 | 492.5080579 | 0.0001477886 | 1.445582e-23 | 6.327143e-21 | 1 | 160289354 | 160289614 | 261 | - | 2.595 | 2.765 | 0.567 |
| ENSG00000122218 | E011 | 172.7061302 | 0.0003689494 | 1.322677e-11 | 1.114191e-09 | 1 | 160289615 | 160289626 | 12 | - | 2.129 | 2.322 | 0.646 |
| ENSG00000122218 | E012 | 395.2953502 | 0.0001746545 | 1.925341e-17 | 4.031655e-15 | 1 | 160289627 | 160289780 | 154 | - | 2.505 | 2.666 | 0.537 |
| ENSG00000122218 | E013 | 173.5071308 | 0.0003046875 | 2.165947e-11 | 1.761627e-09 | 1 | 160289781 | 160289795 | 15 | - | 2.128 | 2.319 | 0.636 |
| ENSG00000122218 | E014 | 802.7009522 | 0.0001117307 | 3.198303e-18 | 7.533222e-16 | 1 | 160289796 | 160290216 | 421 | - | 2.837 | 2.954 | 0.389 |
| ENSG00000122218 | E015 | 6.6667462 | 0.3307378104 | 5.798897e-01 | 7.571317e-01 | 1 | 160290217 | 160290491 | 275 | - | 0.751 | 0.988 | 0.911 |
| ENSG00000122218 | E016 | 575.9400415 | 0.0004121315 | 8.707989e-08 | 3.279700e-06 | 1 | 160290492 | 160290686 | 195 | - | 2.705 | 2.803 | 0.326 |
| ENSG00000122218 | E017 | 2.5920605 | 0.0776104681 | 5.406673e-01 | 7.295055e-01 | 1 | 160291245 | 160291334 | 90 | - | 0.502 | 0.604 | 0.471 |
| ENSG00000122218 | E018 | 518.8763416 | 0.0001250738 | 2.465588e-06 | 6.272861e-05 | 1 | 160291335 | 160291496 | 162 | - | 2.669 | 2.747 | 0.261 |
| ENSG00000122218 | E019 | 412.0319675 | 0.0006834635 | 4.804440e-03 | 3.355634e-02 | 1 | 160291819 | 160291929 | 111 | - | 2.575 | 2.642 | 0.223 |
| ENSG00000122218 | E020 | 505.0762110 | 0.0008565874 | 3.864754e-03 | 2.838895e-02 | 1 | 160292012 | 160292198 | 187 | - | 2.662 | 2.732 | 0.232 |
| ENSG00000122218 | E021 | 364.7557418 | 0.0020495303 | 8.744750e-03 | 5.268785e-02 | 1 | 160292484 | 160292560 | 77 | - | 2.516 | 2.601 | 0.282 |
| ENSG00000122218 | E022 | 335.6561373 | 0.0004642636 | 8.556070e-03 | 5.186014e-02 | 1 | 160292561 | 160292620 | 60 | - | 2.491 | 2.552 | 0.203 |
| ENSG00000122218 | E023 | 358.3455543 | 0.0001879854 | 6.771352e-04 | 7.243845e-03 | 1 | 160293166 | 160293234 | 69 | - | 2.515 | 2.584 | 0.228 |
| ENSG00000122218 | E024 | 387.3312501 | 0.0006585339 | 1.333605e-05 | 2.692626e-04 | 1 | 160293386 | 160293463 | 78 | - | 2.533 | 2.630 | 0.323 |
| ENSG00000122218 | E025 | 8.6397025 | 0.1012564805 | 2.614554e-01 | 5.005427e-01 | 1 | 160293706 | 160294483 | 778 | - | 0.875 | 1.074 | 0.742 |
| ENSG00000122218 | E026 | 461.6894143 | 0.0028521777 | 5.616325e-02 | 1.940078e-01 | 1 | 160294484 | 160294593 | 110 | - | 2.625 | 2.695 | 0.236 |
| ENSG00000122218 | E027 | 331.9684662 | 0.0033995409 | 1.568650e-01 | 3.720674e-01 | 1 | 160294768 | 160294802 | 35 | - | 2.488 | 2.546 | 0.195 |
| ENSG00000122218 | E028 | 239.8615213 | 0.0020851330 | 2.424086e-01 | 4.792270e-01 | 1 | 160294803 | 160294806 | 4 | - | 2.353 | 2.396 | 0.142 |
| ENSG00000122218 | E029 | 355.5212528 | 0.0009870119 | 5.570709e-01 | 7.411809e-01 | 1 | 160294807 | 160294857 | 51 | - | 2.536 | 2.554 | 0.060 |
| ENSG00000122218 | E030 | 487.6789466 | 0.0002065008 | 1.501728e-01 | 3.626243e-01 | 1 | 160295736 | 160295859 | 124 | - | 2.667 | 2.695 | 0.092 |
| ENSG00000122218 | E031 | 2.6909754 | 0.3850117127 | 5.181587e-01 | 7.137600e-01 | 1 | 160295860 | 160296060 | 201 | - | 0.640 | 0.481 | -0.731 |
| ENSG00000122218 | E032 | 410.2050510 | 0.0009093196 | 8.828364e-01 | 9.427850e-01 | 1 | 160296061 | 160296149 | 89 | - | 2.605 | 2.614 | 0.027 |
| ENSG00000122218 | E033 | 425.4543281 | 0.0014706036 | 9.315713e-01 | 9.678997e-01 | 1 | 160297343 | 160297438 | 96 | - | 2.621 | 2.629 | 0.025 |
| ENSG00000122218 | E034 | 587.4194078 | 0.0001387481 | 8.781899e-02 | 2.596655e-01 | 1 | 160297556 | 160297745 | 190 | - | 2.775 | 2.751 | -0.079 |
| ENSG00000122218 | E035 | 5.4507833 | 0.0061423735 | 9.731292e-01 | 9.885256e-01 | 1 | 160297746 | 160298149 | 404 | - | 0.799 | 0.803 | 0.017 |
| ENSG00000122218 | E036 | 413.4296896 | 0.0001351901 | 6.919460e-01 | 8.303010e-01 | 1 | 160298845 | 160298931 | 87 | - | 2.614 | 2.609 | -0.017 |
| ENSG00000122218 | E037 | 345.7811980 | 0.0002960349 | 2.360937e-01 | 4.720346e-01 | 1 | 160298932 | 160298991 | 60 | - | 2.546 | 2.524 | -0.073 |
| ENSG00000122218 | E038 | 6.6100162 | 0.1130450217 | 5.339281e-01 | 7.248584e-01 | 1 | 160298992 | 160299101 | 110 | - | 0.933 | 0.807 | -0.484 |
| ENSG00000122218 | E039 | 326.9484290 | 0.0003132473 | 1.728132e-01 | 3.942307e-01 | 1 | 160299102 | 160299140 | 39 | - | 2.522 | 2.495 | -0.088 |
| ENSG00000122218 | E040 | 461.1407085 | 0.0001783669 | 9.990096e-02 | 2.815614e-01 | 1 | 160299141 | 160299264 | 124 | - | 2.672 | 2.646 | -0.088 |
| ENSG00000122218 | E041 | 1.8231797 | 0.4691162726 | 7.373651e-01 | 8.588466e-01 | 1 | 160299265 | 160299279 | 15 | - | 0.511 | 0.369 | -0.743 |
| ENSG00000122218 | E042 | 2.2415300 | 0.0411871404 | 3.995729e-01 | 6.279420e-01 | 1 | 160305231 | 160305432 | 202 | - | 0.581 | 0.426 | -0.753 |
| ENSG00000122218 | E043 | 498.7184144 | 0.0013071271 | 9.489791e-03 | 5.591897e-02 | 1 | 160305433 | 160305571 | 139 | - | 2.724 | 2.666 | -0.193 |
| ENSG00000122218 | E044 | 13.3158240 | 0.0036224514 | 5.643798e-01 | 7.463491e-01 | 1 | 160305572 | 160305598 | 27 | - | 1.168 | 1.116 | -0.186 |
| ENSG00000122218 | E045 | 414.4992074 | 0.0013861739 | 1.175661e-03 | 1.124442e-02 | 1 | 160305688 | 160305773 | 86 | - | 2.652 | 2.574 | -0.260 |
| ENSG00000122218 | E046 | 4.8629543 | 0.1143011607 | 9.414539e-01 | 9.729413e-01 | 1 | 160305774 | 160305924 | 151 | - | 0.777 | 0.756 | -0.085 |
| ENSG00000122218 | E047 | 422.9899772 | 0.0002528602 | 2.383823e-03 | 1.958719e-02 | 1 | 160306354 | 160306454 | 101 | - | 2.649 | 2.594 | -0.182 |
| ENSG00000122218 | E048 | 265.8194493 | 0.0001942591 | 6.727534e-03 | 4.335167e-02 | 1 | 160306455 | 160306493 | 39 | - | 2.448 | 2.389 | -0.198 |
| ENSG00000122218 | E049 | 332.9578072 | 0.0001650702 | 5.349262e-04 | 5.992267e-03 | 1 | 160307163 | 160307245 | 83 | - | 2.549 | 2.481 | -0.226 |
| ENSG00000122218 | E050 | 9.7347088 | 0.2741362486 | 2.311279e-01 | 4.664640e-01 | 1 | 160308180 | 160308929 | 750 | - | 1.144 | 0.867 | -1.022 |
| ENSG00000122218 | E051 | 2.9695696 | 0.1009847967 | 5.900761e-01 | 7.638075e-01 | 1 | 160308930 | 160309100 | 171 | - | 0.543 | 0.642 | 0.443 |
| ENSG00000122218 | E052 | 327.6559017 | 0.0001646864 | 4.742066e-05 | 7.951341e-04 | 1 | 160309101 | 160309176 | 76 | - | 2.547 | 2.467 | -0.270 |
| ENSG00000122218 | E053 | 6.4604869 | 0.1112466343 | 8.082513e-01 | 9.011668e-01 | 1 | 160309177 | 160309781 | 605 | - | 0.899 | 0.843 | -0.214 |
| ENSG00000122218 | E054 | 0.6294705 | 0.0275405629 | 3.486617e-01 | 1 | 160309782 | 160309808 | 27 | - | 0.287 | 0.125 | -1.488 | |
| ENSG00000122218 | E055 | 3.7387421 | 0.2013127991 | 3.071375e-01 | 5.477517e-01 | 1 | 160309809 | 160310191 | 383 | - | 0.785 | 0.519 | -1.143 |
| ENSG00000122218 | E056 | 292.9283724 | 0.0002083635 | 7.592080e-05 | 1.187866e-03 | 1 | 160310192 | 160310258 | 67 | - | 2.501 | 2.417 | -0.281 |
| ENSG00000122218 | E057 | 14.5107922 | 0.2795988964 | 1.101790e-01 | 2.992886e-01 | 1 | 160310259 | 160311867 | 1609 | - | 1.339 | 0.945 | -1.416 |
| ENSG00000122218 | E058 | 434.0106260 | 0.0001652194 | 4.767454e-08 | 1.910390e-06 | 1 | 160311868 | 160312018 | 151 | - | 2.677 | 2.581 | -0.319 |
| ENSG00000122218 | E059 | 310.5253568 | 0.0002289836 | 5.694101e-08 | 2.240995e-06 | 1 | 160313085 | 160313167 | 83 | - | 2.540 | 2.426 | -0.378 |
| ENSG00000122218 | E060 | 384.6457458 | 0.0001516097 | 2.113888e-09 | 1.158396e-07 | 1 | 160313990 | 160314125 | 136 | - | 2.631 | 2.520 | -0.370 |
| ENSG00000122218 | E061 | 339.1345508 | 0.0002398447 | 1.017311e-03 | 1.004026e-02 | 1 | 160323431 | 160323530 | 100 | - | 2.557 | 2.491 | -0.217 |
| ENSG00000122218 | E062 | 218.9839518 | 0.0002599594 | 5.665873e-03 | 3.806949e-02 | 1 | 160325543 | 160325568 | 26 | - | 2.369 | 2.302 | -0.225 |
| ENSG00000122218 | E063 | 336.9812968 | 0.0001447606 | 8.744981e-09 | 4.164607e-07 | 1 | 160325569 | 160325652 | 84 | - | 2.575 | 2.462 | -0.377 |
| ENSG00000122218 | E064 | 2.8593608 | 0.1719852707 | 2.756656e-01 | 5.157488e-01 | 1 | 160325653 | 160325919 | 267 | - | 0.698 | 0.468 | -1.044 |
| ENSG00000122218 | E065 | 358.6719218 | 0.0001717074 | 4.547378e-11 | 3.459899e-09 | 1 | 160332448 | 160332557 | 110 | - | 2.607 | 2.480 | -0.424 |
| ENSG00000122218 | E066 | 24.8019249 | 0.0406680863 | 2.912681e-03 | 2.287671e-02 | 1 | 160332558 | 160333461 | 904 | - | 1.553 | 1.180 | -1.299 |
| ENSG00000122218 | E067 | 15.0115647 | 0.0546594542 | 1.081558e-01 | 2.959626e-01 | 1 | 160333462 | 160333602 | 141 | - | 1.305 | 1.057 | -0.881 |
| ENSG00000122218 | E068 | 324.6676422 | 0.0001592896 | 6.705196e-12 | 5.961762e-10 | 1 | 160333603 | 160333679 | 77 | - | 2.569 | 2.431 | -0.462 |
| ENSG00000122218 | E069 | 9.5076119 | 0.0746203396 | 3.085595e-02 | 1.299085e-01 | 1 | 160333680 | 160335241 | 1562 | - | 1.169 | 0.796 | -1.390 |
| ENSG00000122218 | E070 | 280.1805085 | 0.0002169009 | 2.834578e-12 | 2.705882e-10 | 1 | 160335242 | 160335322 | 81 | - | 2.512 | 2.358 | -0.512 |
| ENSG00000122218 | E071 | 6.4969648 | 0.2904244475 | 4.458097e-01 | 6.626470e-01 | 1 | 160336749 | 160339436 | 2688 | - | 0.778 | 0.957 | 0.690 |
| ENSG00000122218 | E072 | 2.5113784 | 0.0666943748 | 7.108932e-01 | 8.423823e-01 | 1 | 160339437 | 160339908 | 472 | - | 0.505 | 0.565 | 0.281 |
| ENSG00000122218 | E073 | 259.1112152 | 0.0002109258 | 3.809539e-08 | 1.563808e-06 | 1 | 160339909 | 160339982 | 74 | - | 2.466 | 2.342 | -0.415 |
| ENSG00000122218 | E074 | 0.9818539 | 0.0210834516 | 9.426724e-01 | 1 | 160339983 | 160340180 | 198 | - | 0.287 | 0.301 | 0.096 | |
| ENSG00000122218 | E075 | 292.8623379 | 0.0003183776 | 1.009040e-08 | 4.736268e-07 | 1 | 160340181 | 160340294 | 114 | - | 2.521 | 2.394 | -0.421 |
| ENSG00000122218 | E076 | 204.9456178 | 0.0002695754 | 1.174980e-05 | 2.409014e-04 | 1 | 160343131 | 160343566 | 436 | - | 2.359 | 2.247 | -0.373 |