Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000163539
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000480013 | ENSG00000163539 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CLASP2 | protein_coding | protein_coding | 17.54645 | 3.711994 | 28.77653 | 0.162994 | 0.5421996 | 2.951246 | 0.2968513 | 0.6955031 | 0.000000 | 0.3524020 | 0.00000000 | -6.140580 | 0.06639167 | 0.19136667 | 0.00000000 | -0.19136667 | 3.273278e-02 | 2.453125e-17 | FALSE | TRUE |
| ENST00000487553 | ENSG00000163539 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CLASP2 | protein_coding | protein_coding | 17.54645 | 3.711994 | 28.77653 | 0.162994 | 0.5421996 | 2.951246 | 1.0518115 | 0.0000000 | 2.288796 | 0.0000000 | 0.07748018 | 7.844734 | 0.05027500 | 0.00000000 | 0.07956667 | 0.07956667 | 3.853217e-09 | 2.453125e-17 | FALSE | TRUE |
| ENST00000494261 | ENSG00000163539 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CLASP2 | protein_coding | retained_intron | 17.54645 | 3.711994 | 28.77653 | 0.162994 | 0.5421996 | 2.951246 | 1.1896312 | 0.1756028 | 2.221644 | 0.1466999 | 0.07606801 | 3.587816 | 0.07145417 | 0.04526667 | 0.07716667 | 0.03190000 | 5.350074e-01 | 2.453125e-17 | FALSE | FALSE |
| MSTRG.22689.1 | ENSG00000163539 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CLASP2 | protein_coding | 17.54645 | 3.711994 | 28.77653 | 0.162994 | 0.5421996 | 2.951246 | 1.7921782 | 0.7891004 | 1.820652 | 0.3314898 | 0.92814227 | 1.195909 | 0.14462500 | 0.21303333 | 0.06323333 | -0.14980000 | 5.819189e-01 | 2.453125e-17 | FALSE | TRUE | |
| MSTRG.22689.10 | ENSG00000163539 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CLASP2 | protein_coding | 17.54645 | 3.711994 | 28.77653 | 0.162994 | 0.5421996 | 2.951246 | 0.4499719 | 0.4297430 | 0.000000 | 0.2202632 | 0.00000000 | -5.458589 | 0.07425000 | 0.11093333 | 0.00000000 | -0.11093333 | 1.443155e-02 | 2.453125e-17 | FALSE | TRUE | |
| MSTRG.22689.12 | ENSG00000163539 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CLASP2 | protein_coding | 17.54645 | 3.711994 | 28.77653 | 0.162994 | 0.5421996 | 2.951246 | 2.5898340 | 0.0000000 | 4.939945 | 0.0000000 | 0.26136883 | 8.951269 | 0.08604167 | 0.00000000 | 0.17143333 | 0.17143333 | 2.453125e-17 | 2.453125e-17 | FALSE | TRUE | |
| MSTRG.22689.9 | ENSG00000163539 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CLASP2 | protein_coding | 17.54645 | 3.711994 | 28.77653 | 0.162994 | 0.5421996 | 2.951246 | 7.6654268 | 1.0308498 | 12.702931 | 0.5353408 | 0.61181128 | 3.610463 | 0.34744583 | 0.28190000 | 0.44203333 | 0.16013333 | 7.348357e-01 | 2.453125e-17 | 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_2hB | HEK293_OSMI2_2hA | log2fold_HEK293_OSMI2_2hA_HEK293_TMG_2hB |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000163539 | E001 | 0.0000000 | 3 | 33496245 | 33496248 | 4 | - | ||||||
| ENSG00000163539 | E002 | 25.9432089 | 0.0366792859 | 6.800112e-03 | 2.070327e-02 | 3 | 33496249 | 33496992 | 744 | - | 1.215 | 1.585 | 1.283 |
| ENSG00000163539 | E003 | 32.2436366 | 0.0246603762 | 1.367559e-08 | 1.643596e-07 | 3 | 33496993 | 33497133 | 141 | - | 1.218 | 1.832 | 2.110 |
| ENSG00000163539 | E004 | 148.3826726 | 0.0315997767 | 1.173329e-06 | 9.603546e-06 | 3 | 33497134 | 33497754 | 621 | - | 1.907 | 2.414 | 1.696 |
| ENSG00000163539 | E005 | 179.0579037 | 0.0225116844 | 2.079255e-06 | 1.611540e-05 | 3 | 33497755 | 33498134 | 380 | - | 2.016 | 2.440 | 1.417 |
| ENSG00000163539 | E006 | 149.7161286 | 0.0003363024 | 3.787924e-26 | 4.559154e-24 | 3 | 33498135 | 33498466 | 332 | - | 1.947 | 2.348 | 1.345 |
| ENSG00000163539 | E007 | 64.7298118 | 0.0004053225 | 1.451903e-04 | 7.263233e-04 | 3 | 33498467 | 33498512 | 46 | - | 1.624 | 1.874 | 0.844 |
| ENSG00000163539 | E008 | 92.5053950 | 0.0003076624 | 3.956384e-04 | 1.757715e-03 | 3 | 33498513 | 33498583 | 71 | - | 1.789 | 1.997 | 0.699 |
| ENSG00000163539 | E009 | 122.5646304 | 0.0003503731 | 3.278177e-03 | 1.108641e-02 | 3 | 33498584 | 33498717 | 134 | - | 1.919 | 2.084 | 0.555 |
| ENSG00000163539 | E010 | 104.6350637 | 0.0039227361 | 1.699518e-01 | 2.881434e-01 | 3 | 33501652 | 33501768 | 117 | - | 1.860 | 1.978 | 0.397 |
| ENSG00000163539 | E011 | 9.6430438 | 0.0018139440 | 1.571716e-01 | 2.713319e-01 | 3 | 33501769 | 33505451 | 3683 | - | 0.860 | 1.080 | 0.819 |
| ENSG00000163539 | E012 | 127.1056850 | 0.0002593054 | 2.076874e-01 | 3.357004e-01 | 3 | 33510558 | 33510764 | 207 | - | 1.947 | 2.043 | 0.323 |
| ENSG00000163539 | E013 | 0.1472490 | 0.0424776957 | 9.270995e-01 | 3 | 33514580 | 33514679 | 100 | - | 0.051 | 0.000 | -8.454 | |
| ENSG00000163539 | E014 | 106.3417669 | 0.0022280170 | 3.404146e-01 | 4.843776e-01 | 3 | 33516023 | 33516151 | 129 | - | 1.872 | 1.963 | 0.304 |
| ENSG00000163539 | E015 | 160.9825780 | 0.0002463397 | 3.043123e-01 | 4.463261e-01 | 3 | 33516981 | 33517174 | 194 | - | 2.065 | 2.069 | 0.012 |
| ENSG00000163539 | E016 | 139.8264339 | 0.0041316657 | 6.420986e-01 | 7.549678e-01 | 3 | 33535233 | 33535372 | 140 | - | 2.001 | 2.020 | 0.063 |
| ENSG00000163539 | E017 | 92.8061625 | 0.0004100714 | 7.669153e-01 | 8.492755e-01 | 3 | 33535373 | 33535461 | 89 | - | 1.825 | 1.853 | 0.096 |
| ENSG00000163539 | E018 | 105.6407079 | 0.0003317047 | 6.863620e-01 | 7.888926e-01 | 3 | 33538789 | 33538922 | 134 | - | 1.878 | 1.902 | 0.081 |
| ENSG00000163539 | E019 | 60.4134108 | 0.0006911578 | 8.497990e-01 | 9.068024e-01 | 3 | 33538923 | 33538942 | 20 | - | 1.639 | 1.670 | 0.105 |
| ENSG00000163539 | E020 | 112.8746525 | 0.0017315643 | 1.829085e-03 | 6.693092e-03 | 3 | 33543433 | 33543539 | 107 | - | 1.929 | 1.805 | -0.418 |
| ENSG00000163539 | E021 | 114.4328676 | 0.0002987617 | 1.869072e-02 | 4.865613e-02 | 3 | 33544698 | 33544841 | 144 | - | 1.928 | 1.859 | -0.235 |
| ENSG00000163539 | E022 | 8.0929855 | 0.0029499974 | 8.656210e-01 | 9.174432e-01 | 3 | 33544842 | 33545111 | 270 | - | 0.829 | 0.841 | 0.047 |
| ENSG00000163539 | E023 | 83.9982744 | 0.0053511869 | 1.693242e-01 | 2.873056e-01 | 3 | 33551252 | 33551395 | 144 | - | 1.792 | 1.744 | -0.163 |
| ENSG00000163539 | E024 | 3.6859800 | 0.0043831819 | 1.331404e-02 | 3.665130e-02 | 3 | 33558336 | 33559124 | 789 | - | 0.458 | 0.891 | 1.857 |
| ENSG00000163539 | E025 | 4.2823524 | 0.0038975927 | 2.937602e-01 | 4.348083e-01 | 3 | 33559125 | 33559175 | 51 | - | 0.574 | 0.784 | 0.888 |
| ENSG00000163539 | E026 | 64.4779542 | 0.0005509942 | 7.631067e-02 | 1.535967e-01 | 3 | 33559307 | 33559385 | 79 | - | 1.682 | 1.611 | -0.240 |
| ENSG00000163539 | E027 | 61.3960257 | 0.0004099086 | 5.181597e-01 | 6.524288e-01 | 3 | 33560808 | 33560971 | 164 | - | 1.652 | 1.654 | 0.008 |
| ENSG00000163539 | E028 | 0.0000000 | 3 | 33563964 | 33563966 | 3 | - | ||||||
| ENSG00000163539 | E029 | 4.5299739 | 0.1860988300 | 3.217350e-01 | 4.649787e-01 | 3 | 33566732 | 33566734 | 3 | - | 0.559 | 0.892 | 1.373 |
| ENSG00000163539 | E030 | 8.7265775 | 0.0023316266 | 1.539529e-01 | 2.670505e-01 | 3 | 33570727 | 33570730 | 4 | - | 0.821 | 1.048 | 0.856 |
| ENSG00000163539 | E031 | 35.7232376 | 0.0005654469 | 3.270310e-01 | 4.704785e-01 | 3 | 33570731 | 33570790 | 60 | - | 1.404 | 1.521 | 0.404 |
| ENSG00000163539 | E032 | 55.4509561 | 0.0004240982 | 5.412198e-01 | 6.722473e-01 | 3 | 33573110 | 33573169 | 60 | - | 1.608 | 1.611 | 0.009 |
| ENSG00000163539 | E033 | 116.3430095 | 0.0002637097 | 8.745870e-02 | 1.712837e-01 | 3 | 33573170 | 33573354 | 185 | - | 1.930 | 1.893 | -0.123 |
| ENSG00000163539 | E034 | 0.0000000 | 3 | 33574473 | 33574496 | 24 | - | ||||||
| ENSG00000163539 | E035 | 98.8558654 | 0.0002878105 | 1.812818e-03 | 6.639851e-03 | 3 | 33576169 | 33576275 | 107 | - | 1.872 | 1.749 | -0.414 |
| ENSG00000163539 | E036 | 0.2966881 | 0.0290785164 | 1.000000e+00 | 3 | 33576276 | 33576421 | 146 | - | 0.097 | 0.000 | -9.454 | |
| ENSG00000163539 | E037 | 0.0000000 | 3 | 33577202 | 33577264 | 63 | - | ||||||
| ENSG00000163539 | E038 | 104.8456645 | 0.0006589264 | 9.035458e-05 | 4.767150e-04 | 3 | 33581821 | 33581928 | 108 | - | 1.903 | 1.736 | -0.566 |
| ENSG00000163539 | E039 | 114.9349697 | 0.0009713024 | 9.296724e-03 | 2.702492e-02 | 3 | 33584750 | 33584920 | 171 | - | 1.935 | 1.848 | -0.292 |
| ENSG00000163539 | E040 | 0.0000000 | 3 | 33588705 | 33588731 | 27 | - | ||||||
| ENSG00000163539 | E041 | 0.0000000 | 3 | 33592213 | 33592239 | 27 | - | ||||||
| ENSG00000163539 | E042 | 83.8795618 | 0.0011457484 | 2.888652e-03 | 9.936747e-03 | 3 | 33592395 | 33592496 | 102 | - | 1.805 | 1.670 | -0.457 |
| ENSG00000163539 | E043 | 3.2612655 | 0.0050303973 | 1.938492e-02 | 5.016950e-02 | 3 | 33594951 | 33594968 | 18 | - | 0.574 | 0.000 | -12.914 |
| ENSG00000163539 | E044 | 3.4688924 | 0.0043139768 | 4.371214e-01 | 5.791449e-01 | 3 | 33596711 | 33596734 | 24 | - | 0.559 | 0.431 | -0.629 |
| ENSG00000163539 | E045 | 0.1472490 | 0.0424776957 | 9.270995e-01 | 3 | 33602413 | 33602442 | 30 | - | 0.051 | 0.000 | -8.454 | |
| ENSG00000163539 | E046 | 0.0000000 | 3 | 33602443 | 33602443 | 1 | - | ||||||
| ENSG00000163539 | E047 | 0.7437457 | 0.0153787590 | 7.063527e-01 | 8.044993e-01 | 3 | 33602444 | 33602589 | 146 | - | 0.176 | 0.266 | 0.761 |
| ENSG00000163539 | E048 | 1.5521227 | 0.0098130620 | 4.628260e-02 | 1.025533e-01 | 3 | 33602590 | 33602951 | 362 | - | 0.243 | 0.642 | 2.177 |
| ENSG00000163539 | E049 | 98.9429679 | 0.0019837140 | 3.422647e-02 | 8.019321e-02 | 3 | 33602952 | 33603125 | 174 | - | 1.868 | 1.793 | -0.254 |
| ENSG00000163539 | E050 | 75.9206563 | 0.0048862613 | 9.735632e-02 | 1.864372e-01 | 3 | 33604154 | 33604209 | 56 | - | 1.755 | 1.685 | -0.238 |
| ENSG00000163539 | E051 | 100.4215978 | 0.0065226112 | 9.107908e-02 | 1.768276e-01 | 3 | 33606591 | 33606758 | 168 | - | 1.873 | 1.804 | -0.232 |
| ENSG00000163539 | E052 | 70.5169507 | 0.0005853070 | 1.582423e-01 | 2.727751e-01 | 3 | 33607384 | 33607461 | 78 | - | 1.720 | 1.678 | -0.142 |
| ENSG00000163539 | E053 | 64.1895975 | 0.0027482845 | 1.621120e-01 | 2.778780e-01 | 3 | 33608567 | 33608626 | 60 | - | 1.681 | 1.629 | -0.177 |
| ENSG00000163539 | E054 | 45.4954464 | 0.0071513689 | 2.460723e-01 | 3.813420e-01 | 3 | 33612001 | 33612008 | 8 | - | 1.534 | 1.475 | -0.202 |
| ENSG00000163539 | E055 | 71.5046689 | 0.0026178977 | 1.368524e-01 | 2.437093e-01 | 3 | 33612009 | 33612071 | 63 | - | 1.725 | 1.671 | -0.184 |
| ENSG00000163539 | E056 | 84.0360271 | 0.0004955873 | 3.705246e-03 | 1.231228e-02 | 3 | 33619603 | 33619689 | 87 | - | 1.803 | 1.678 | -0.424 |
| ENSG00000163539 | E057 | 67.3436776 | 0.0016227476 | 6.438057e-04 | 2.693619e-03 | 3 | 33619690 | 33619738 | 49 | - | 1.716 | 1.522 | -0.660 |
| ENSG00000163539 | E058 | 50.2385356 | 0.0004934030 | 1.337943e-01 | 2.394271e-01 | 3 | 33622135 | 33622152 | 18 | - | 1.575 | 1.510 | -0.222 |
| ENSG00000163539 | E059 | 50.3084825 | 0.0005100546 | 4.035715e-02 | 9.167534e-02 | 3 | 33622153 | 33622186 | 34 | - | 1.582 | 1.475 | -0.368 |
| ENSG00000163539 | E060 | 60.6294725 | 0.0003944751 | 3.445271e-02 | 8.062704e-02 | 3 | 33622187 | 33622280 | 94 | - | 1.661 | 1.564 | -0.332 |
| ENSG00000163539 | E061 | 65.7596989 | 0.0003735216 | 3.808925e-03 | 1.260528e-02 | 3 | 33626988 | 33627080 | 93 | - | 1.701 | 1.553 | -0.501 |
| ENSG00000163539 | E062 | 52.2566643 | 0.0072415682 | 2.940418e-02 | 7.077917e-02 | 3 | 33632292 | 33632371 | 80 | - | 1.603 | 1.463 | -0.480 |
| ENSG00000163539 | E063 | 6.1822709 | 0.0035065938 | 4.153051e-01 | 5.586956e-01 | 3 | 33632372 | 33632374 | 3 | - | 0.750 | 0.643 | -0.446 |
| ENSG00000163539 | E064 | 0.4386386 | 0.1614793209 | 3.819625e-01 | 5.262206e-01 | 3 | 33644382 | 33644756 | 375 | - | 0.097 | 0.265 | 1.752 |
| ENSG00000163539 | E065 | 75.7531219 | 0.0004452533 | 1.662650e-03 | 6.162020e-03 | 3 | 33644757 | 33644903 | 147 | - | 1.762 | 1.611 | -0.512 |
| ENSG00000163539 | E066 | 0.0000000 | 3 | 33645003 | 33645281 | 279 | - | ||||||
| ENSG00000163539 | E067 | 2.5026562 | 0.0364192719 | 3.069966e-01 | 4.491665e-01 | 3 | 33645282 | 33645343 | 62 | - | 0.477 | 0.266 | -1.239 |
| ENSG00000163539 | E068 | 1.9176990 | 0.0073995085 | 4.837970e-01 | 6.218208e-01 | 3 | 33645344 | 33645503 | 160 | - | 0.398 | 0.267 | -0.823 |
| ENSG00000163539 | E069 | 0.5932625 | 0.1553999181 | 7.676892e-01 | 8.498692e-01 | 3 | 33658974 | 33659009 | 36 | - | 0.176 | 0.000 | -10.456 |
| ENSG00000163539 | E070 | 0.7427016 | 0.0156450523 | 5.255395e-01 | 6.588876e-01 | 3 | 33659010 | 33659441 | 432 | - | 0.211 | 0.000 | -10.776 |
| ENSG00000163539 | E071 | 0.2987644 | 0.0293399349 | 1.000000e+00 | 3 | 33659507 | 33659672 | 166 | - | 0.097 | 0.000 | -9.455 | |
| ENSG00000163539 | E072 | 68.4798441 | 0.0017958403 | 2.250617e-04 | 1.070615e-03 | 3 | 33663445 | 33663515 | 71 | - | 1.725 | 1.510 | -0.731 |
| ENSG00000163539 | E073 | 3.0183945 | 0.0053002171 | 1.432535e-02 | 3.896755e-02 | 3 | 33682979 | 33683604 | 626 | - | 0.398 | 0.841 | 1.985 |
| ENSG00000163539 | E074 | 91.2523645 | 0.0005457220 | 1.039064e-06 | 8.590741e-06 | 3 | 33684359 | 33684456 | 98 | - | 1.852 | 1.602 | -0.845 |
| ENSG00000163539 | E075 | 87.0341963 | 0.0008694676 | 9.991661e-09 | 1.232431e-07 | 3 | 33687060 | 33687135 | 76 | - | 1.839 | 1.510 | -1.115 |
| ENSG00000163539 | E076 | 78.8683935 | 0.0003466890 | 3.952914e-08 | 4.351858e-07 | 3 | 33688277 | 33688368 | 92 | - | 1.796 | 1.475 | -1.095 |
| ENSG00000163539 | E077 | 0.0000000 | 3 | 33689730 | 33689828 | 99 | - | ||||||
| ENSG00000163539 | E078 | 78.8175946 | 0.0003522795 | 1.442330e-04 | 7.219541e-04 | 3 | 33689829 | 33689932 | 104 | - | 1.784 | 1.593 | -0.649 |
| ENSG00000163539 | E079 | 62.2982435 | 0.0004320970 | 4.412302e-02 | 9.861018e-02 | 3 | 33696855 | 33696933 | 79 | - | 1.672 | 1.583 | -0.301 |
| ENSG00000163539 | E080 | 74.7924874 | 0.0013867443 | 8.234925e-06 | 5.577697e-05 | 3 | 33717808 | 33718356 | 549 | - | 1.770 | 1.510 | -0.883 |