Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000009307
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000261443 | ENSG00000009307 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CSDE1 | protein_coding | protein_coding | 275.8173 | 99.63576 | 467.1026 | 8.450501 | 13.03296 | 2.22889 | 4.645014 | 8.33299397 | 2.1301621 | 3.36444066 | 1.01211094 | -1.962845 | 0.04158750 | 0.0849666667 | 0.004466667 | -0.08050000 | 5.855942e-05 | 6.856575e-79 | FALSE | TRUE |
| ENST00000339438 | ENSG00000009307 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CSDE1 | protein_coding | protein_coding | 275.8173 | 99.63576 | 467.1026 | 8.450501 | 13.03296 | 2.22889 | 123.518634 | 62.47936701 | 182.7342704 | 5.44843989 | 6.09238694 | 1.548144 | 0.52108750 | 0.6352333333 | 0.391100000 | -0.24413333 | 2.378342e-02 | 6.856575e-79 | FALSE | TRUE |
| ENST00000525970 | ENSG00000009307 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CSDE1 | protein_coding | protein_coding | 275.8173 | 99.63576 | 467.1026 | 8.450501 | 13.03296 | 2.22889 | 28.120647 | 0.00000000 | 67.8702298 | 0.00000000 | 4.65937284 | 12.728776 | 0.06111250 | 0.0000000000 | 0.145333333 | 0.14533333 | 2.430729e-73 | 6.856575e-79 | FALSE | |
| ENST00000529046 | ENSG00000009307 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CSDE1 | protein_coding | protein_coding | 275.8173 | 99.63576 | 467.1026 | 8.450501 | 13.03296 | 2.22889 | 1.549932 | 6.10263084 | 0.4632958 | 3.29426608 | 0.08556470 | -3.690980 | 0.01359583 | 0.0602666667 | 0.001000000 | -0.05926667 | 2.764277e-01 | 6.856575e-79 | FALSE | TRUE |
| ENST00000534699 | ENSG00000009307 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CSDE1 | protein_coding | protein_coding | 275.8173 | 99.63576 | 467.1026 | 8.450501 | 13.03296 | 2.22889 | 18.231695 | 0.05218834 | 35.1742263 | 0.05218834 | 2.14198841 | 9.144069 | 0.05153333 | 0.0004666667 | 0.075566667 | 0.07510000 | 1.872178e-28 | 6.856575e-79 | FALSE | TRUE |
| ENST00000689631 | ENSG00000009307 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CSDE1 | protein_coding | retained_intron | 275.8173 | 99.63576 | 467.1026 | 8.450501 | 13.03296 | 2.22889 | 2.676818 | 9.26877336 | 0.1913650 | 9.06527705 | 0.06752247 | -5.526049 | 0.02335417 | 0.0811000000 | 0.000400000 | -0.08070000 | 4.991190e-01 | 6.856575e-79 | FALSE | TRUE |
| ENST00000692719 | ENSG00000009307 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CSDE1 | protein_coding | protein_coding | 275.8173 | 99.63576 | 467.1026 | 8.450501 | 13.03296 | 2.22889 | 1.572558 | 6.27324434 | 0.0000000 | 0.53398221 | 0.00000000 | -9.295366 | 0.01662500 | 0.0635333333 | 0.000000000 | -0.06353333 | 4.207752e-73 | 6.856575e-79 | FALSE | TRUE |
| MSTRG.1873.47 | ENSG00000009307 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | CSDE1 | protein_coding | 275.8173 | 99.63576 | 467.1026 | 8.450501 | 13.03296 | 2.22889 | 68.682075 | 0.19566753 | 133.4473337 | 0.10313296 | 4.42796521 | 9.341849 | 0.16804167 | 0.0018333333 | 0.285600000 | 0.28376667 | 6.856575e-79 | 6.856575e-79 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000009307 | E001 | 1.3318114 | 9.619733e-03 | 6.312717e-02 | 1.319249e-01 | 1 | 114716913 | 114716915 | 3 | - | 0.407 | 0.000 | -11.811 |
| ENSG00000009307 | E002 | 5.0925270 | 2.137581e-01 | 2.963752e-01 | 4.375713e-01 | 1 | 114716916 | 114716918 | 3 | - | 0.613 | 1.002 | 1.545 |
| ENSG00000009307 | E003 | 5.7922630 | 1.246519e-01 | 4.429043e-02 | 9.891531e-02 | 1 | 114716919 | 114716919 | 1 | - | 0.613 | 1.100 | 1.900 |
| ENSG00000009307 | E004 | 6.3824170 | 1.301026e-01 | 7.460408e-02 | 1.509008e-01 | 1 | 114716920 | 114716920 | 1 | - | 0.665 | 1.118 | 1.742 |
| ENSG00000009307 | E005 | 29.2502572 | 3.725097e-02 | 5.574268e-03 | 1.748689e-02 | 1 | 114716921 | 114716922 | 2 | - | 1.305 | 1.665 | 1.240 |
| ENSG00000009307 | E006 | 58.8273067 | 3.551748e-02 | 1.309244e-08 | 1.579623e-07 | 1 | 114716923 | 114716927 | 5 | - | 1.454 | 2.094 | 2.168 |
| ENSG00000009307 | E007 | 111.1588329 | 1.919502e-02 | 1.985181e-10 | 3.327610e-09 | 1 | 114716928 | 114716946 | 19 | - | 1.792 | 2.315 | 1.756 |
| ENSG00000009307 | E008 | 1344.3159977 | 1.682221e-02 | 2.256954e-16 | 9.301134e-15 | 1 | 114716947 | 114717294 | 348 | - | 2.847 | 3.406 | 1.858 |
| ENSG00000009307 | E009 | 396.3231205 | 1.012954e-02 | 1.163042e-23 | 1.110029e-21 | 1 | 114717295 | 114717304 | 10 | - | 2.318 | 2.879 | 1.868 |
| ENSG00000009307 | E010 | 338.1933379 | 8.991644e-03 | 5.558211e-27 | 7.163173e-25 | 1 | 114717305 | 114717311 | 7 | - | 2.242 | 2.816 | 1.915 |
| ENSG00000009307 | E011 | 2339.6283577 | 3.792531e-03 | 1.204435e-41 | 4.647181e-39 | 1 | 114717312 | 114717801 | 490 | - | 3.156 | 3.583 | 1.420 |
| ENSG00000009307 | E012 | 1275.8602245 | 1.622187e-03 | 1.860192e-35 | 4.686274e-33 | 1 | 114717802 | 114717956 | 155 | - | 2.953 | 3.245 | 0.970 |
| ENSG00000009307 | E013 | 2208.0588899 | 3.290656e-03 | 6.091882e-09 | 7.828045e-08 | 1 | 114717957 | 114718216 | 260 | - | 3.230 | 3.415 | 0.614 |
| ENSG00000009307 | E014 | 1970.4568317 | 2.185570e-03 | 1.001865e-07 | 1.016956e-06 | 1 | 114718613 | 114718745 | 133 | - | 3.194 | 3.339 | 0.485 |
| ENSG00000009307 | E015 | 38.8883459 | 2.766053e-03 | 1.688431e-02 | 4.467683e-02 | 1 | 114718746 | 114719578 | 833 | - | 1.576 | 1.417 | -0.543 |
| ENSG00000009307 | E016 | 2064.8469057 | 1.791400e-03 | 3.190469e-07 | 2.935182e-06 | 1 | 114719579 | 114719742 | 164 | - | 3.219 | 3.349 | 0.431 |
| ENSG00000009307 | E017 | 75.5919282 | 1.751792e-03 | 8.839730e-06 | 5.949557e-05 | 1 | 114719743 | 114720538 | 796 | - | 1.873 | 1.642 | -0.779 |
| ENSG00000009307 | E018 | 1318.1571412 | 1.279410e-03 | 3.690951e-04 | 1.654535e-03 | 1 | 114720539 | 114720566 | 28 | - | 3.036 | 3.128 | 0.306 |
| ENSG00000009307 | E019 | 1194.3903529 | 1.320809e-03 | 3.657003e-03 | 1.217422e-02 | 1 | 114720567 | 114720577 | 11 | - | 2.997 | 3.078 | 0.267 |
| ENSG00000009307 | E020 | 2572.7859567 | 1.061321e-03 | 6.131972e-02 | 1.288526e-01 | 1 | 114720578 | 114720717 | 140 | - | 3.338 | 3.388 | 0.166 |
| ENSG00000009307 | E021 | 9.0640652 | 4.043720e-03 | 6.145156e-01 | 7.329526e-01 | 1 | 114720718 | 114720737 | 20 | - | 0.968 | 0.922 | -0.174 |
| ENSG00000009307 | E022 | 2282.3550865 | 8.653592e-04 | 9.339664e-01 | 9.623890e-01 | 1 | 114723883 | 114724002 | 120 | - | 3.295 | 3.313 | 0.062 |
| ENSG00000009307 | E023 | 3.5387219 | 3.481499e-02 | 4.805513e-01 | 6.188162e-01 | 1 | 114724003 | 114724287 | 285 | - | 0.649 | 0.536 | -0.505 |
| ENSG00000009307 | E024 | 1.5135158 | 8.805737e-03 | 3.002926e-01 | 4.419566e-01 | 1 | 114724288 | 114724335 | 48 | - | 0.407 | 0.208 | -1.343 |
| ENSG00000009307 | E025 | 2244.1982179 | 2.822897e-04 | 8.340974e-01 | 8.960972e-01 | 1 | 114725221 | 114725333 | 113 | - | 3.289 | 3.303 | 0.050 |
| ENSG00000009307 | E026 | 2186.6114644 | 5.806318e-05 | 1.854284e-01 | 3.080371e-01 | 1 | 114726211 | 114726386 | 176 | - | 3.279 | 3.285 | 0.019 |
| ENSG00000009307 | E027 | 1756.5225816 | 8.233831e-04 | 1.153740e-04 | 5.926265e-04 | 1 | 114726983 | 114727087 | 105 | - | 3.198 | 3.147 | -0.170 |
| ENSG00000009307 | E028 | 1035.3911509 | 1.305580e-03 | 5.863796e-07 | 5.119492e-06 | 1 | 114727088 | 114727090 | 3 | - | 2.979 | 2.883 | -0.318 |
| ENSG00000009307 | E029 | 2105.4769944 | 2.236730e-03 | 9.848286e-04 | 3.907202e-03 | 1 | 114730258 | 114730402 | 145 | - | 3.280 | 3.213 | -0.223 |
| ENSG00000009307 | E030 | 924.8905846 | 4.148878e-03 | 2.119470e-01 | 3.408088e-01 | 1 | 114730403 | 114730422 | 20 | - | 2.914 | 2.887 | -0.090 |
| ENSG00000009307 | E031 | 5.5035588 | 8.187326e-03 | 9.809106e-01 | 9.920699e-01 | 1 | 114730423 | 114730507 | 85 | - | 0.753 | 0.772 | 0.074 |
| ENSG00000009307 | E032 | 947.1973469 | 4.220129e-03 | 4.030638e-01 | 5.468605e-01 | 1 | 114730508 | 114730528 | 21 | - | 2.921 | 2.907 | -0.046 |
| ENSG00000009307 | E033 | 1130.4350748 | 3.635663e-03 | 1.155779e-01 | 2.136684e-01 | 1 | 114730529 | 114730568 | 40 | - | 3.003 | 2.966 | -0.122 |
| ENSG00000009307 | E034 | 1353.3571752 | 2.500149e-03 | 9.838506e-03 | 2.836776e-02 | 1 | 114730569 | 114730648 | 80 | - | 3.086 | 3.030 | -0.184 |
| ENSG00000009307 | E035 | 3.1367168 | 4.915198e-03 | 1.162380e-01 | 2.145998e-01 | 1 | 114730649 | 114730839 | 191 | - | 0.632 | 0.347 | -1.421 |
| ENSG00000009307 | E036 | 4.9643330 | 4.786372e-03 | 4.848885e-01 | 6.228264e-01 | 1 | 114731404 | 114732603 | 1200 | - | 0.697 | 0.814 | 0.473 |
| ENSG00000009307 | E037 | 2244.6985395 | 4.687279e-04 | 2.498125e-17 | 1.156272e-15 | 1 | 114732604 | 114732816 | 213 | - | 3.315 | 3.214 | -0.336 |
| ENSG00000009307 | E038 | 7.0277673 | 4.741268e-02 | 3.194201e-01 | 4.625087e-01 | 1 | 114732817 | 114732868 | 52 | - | 0.792 | 0.960 | 0.644 |
| ENSG00000009307 | E039 | 1628.5263862 | 1.239708e-03 | 1.835762e-10 | 3.095227e-09 | 1 | 114733732 | 114733857 | 126 | - | 3.179 | 3.065 | -0.378 |
| ENSG00000009307 | E040 | 1529.9443091 | 3.708163e-03 | 5.965370e-05 | 3.297314e-04 | 1 | 114733989 | 114734117 | 129 | - | 3.152 | 3.037 | -0.382 |
| ENSG00000009307 | E041 | 4.4896447 | 7.421054e-03 | 2.002792e-01 | 3.265651e-01 | 1 | 114734118 | 114734441 | 324 | - | 0.740 | 0.538 | -0.876 |
| ENSG00000009307 | E042 | 1160.5531292 | 8.257041e-03 | 1.179058e-03 | 4.570302e-03 | 1 | 114734442 | 114734523 | 82 | - | 3.036 | 2.899 | -0.456 |
| ENSG00000009307 | E043 | 1349.5989172 | 7.659595e-03 | 3.478068e-05 | 2.034645e-04 | 1 | 114736758 | 114736855 | 98 | - | 3.108 | 2.937 | -0.568 |
| ENSG00000009307 | E044 | 2.5529175 | 7.449885e-03 | 6.103079e-01 | 7.296356e-01 | 1 | 114736856 | 114737470 | 615 | - | 0.534 | 0.453 | -0.397 |
| ENSG00000009307 | E045 | 124.1331780 | 2.511759e-03 | 1.540712e-04 | 7.652341e-04 | 1 | 114737471 | 114737563 | 93 | - | 2.073 | 1.913 | -0.536 |
| ENSG00000009307 | E046 | 1044.0393934 | 3.314287e-03 | 2.925351e-11 | 5.644724e-10 | 1 | 114737963 | 114737987 | 25 | - | 3.002 | 2.805 | -0.654 |
| ENSG00000009307 | E047 | 851.1605500 | 2.279538e-03 | 2.412683e-10 | 3.984619e-09 | 1 | 114737988 | 114738004 | 17 | - | 2.907 | 2.743 | -0.544 |
| ENSG00000009307 | E048 | 1223.1818149 | 8.483707e-03 | 5.520556e-05 | 3.077005e-04 | 1 | 114738005 | 114738072 | 68 | - | 3.066 | 2.892 | -0.580 |
| ENSG00000009307 | E049 | 1050.0344781 | 8.984711e-03 | 1.752054e-06 | 1.380245e-05 | 1 | 114739692 | 114739725 | 34 | - | 3.008 | 2.788 | -0.730 |
| ENSG00000009307 | E050 | 972.3642017 | 6.552785e-03 | 1.942122e-07 | 1.865483e-06 | 1 | 114739726 | 114739752 | 27 | - | 2.973 | 2.764 | -0.695 |
| ENSG00000009307 | E051 | 1668.8021186 | 9.135323e-03 | 6.442417e-07 | 5.573553e-06 | 1 | 114739753 | 114739869 | 117 | - | 3.210 | 2.984 | -0.751 |
| ENSG00000009307 | E052 | 978.3168278 | 6.731750e-03 | 8.450832e-09 | 1.055641e-07 | 1 | 114739870 | 114739890 | 21 | - | 2.980 | 2.743 | -0.786 |
| ENSG00000009307 | E053 | 2.1528738 | 6.747618e-03 | 9.063517e-01 | 9.444908e-01 | 1 | 114739891 | 114739922 | 32 | - | 0.462 | 0.453 | -0.048 |
| ENSG00000009307 | E054 | 11.2264523 | 1.537141e-03 | 1.061102e-01 | 1.997759e-01 | 1 | 114741527 | 114741615 | 89 | - | 1.069 | 0.889 | -0.667 |
| ENSG00000009307 | E055 | 8.3572935 | 1.975129e-03 | 1.315214e-01 | 2.362571e-01 | 1 | 114741616 | 114741673 | 58 | - | 0.960 | 0.771 | -0.728 |
| ENSG00000009307 | E056 | 1.0360657 | 3.697172e-02 | 2.662797e-01 | 4.044537e-01 | 1 | 114745157 | 114745245 | 89 | - | 0.228 | 0.451 | 1.403 |
| ENSG00000009307 | E057 | 0.8942170 | 1.357548e-02 | 1.650186e-01 | 2.817262e-01 | 1 | 114746543 | 114746859 | 317 | - | 0.309 | 0.000 | -11.202 |
| ENSG00000009307 | E058 | 0.9048261 | 4.055075e-01 | 3.463419e-01 | 4.904899e-01 | 1 | 114748317 | 114748418 | 102 | - | 0.311 | 0.000 | -11.216 |
| ENSG00000009307 | E059 | 0.2966881 | 2.694368e-02 | 8.825530e-01 | 1 | 114749817 | 114749820 | 4 | - | 0.129 | 0.000 | -9.617 | |
| ENSG00000009307 | E060 | 1017.5077582 | 5.838653e-03 | 9.255453e-10 | 1.380644e-08 | 1 | 114749821 | 114749904 | 84 | - | 2.997 | 2.760 | -0.786 |
| ENSG00000009307 | E061 | 793.1549200 | 6.769811e-03 | 8.982135e-06 | 6.036534e-05 | 1 | 114749905 | 114749973 | 69 | - | 2.879 | 2.697 | -0.607 |
| ENSG00000009307 | E062 | 1560.3067899 | 1.197294e-02 | 3.639239e-06 | 2.674332e-05 | 1 | 114749974 | 114750148 | 175 | - | 3.183 | 2.944 | -0.796 |
| ENSG00000009307 | E063 | 985.2269417 | 1.001201e-02 | 1.280538e-07 | 1.274129e-06 | 1 | 114750149 | 114750207 | 59 | - | 2.987 | 2.727 | -0.865 |
| ENSG00000009307 | E064 | 0.9704895 | 9.660502e-02 | 7.561021e-01 | 8.412619e-01 | 1 | 114752837 | 114752937 | 101 | - | 0.271 | 0.209 | -0.488 |
| ENSG00000009307 | E065 | 1.9574529 | 7.157216e-03 | 1.518512e-01 | 2.641886e-01 | 1 | 114756182 | 114756319 | 138 | - | 0.488 | 0.208 | -1.758 |
| ENSG00000009307 | E066 | 7.1447453 | 2.294243e-03 | 1.830338e-01 | 3.049898e-01 | 1 | 114756777 | 114756888 | 112 | - | 0.898 | 0.723 | -0.688 |
| ENSG00000009307 | E067 | 1.3684568 | 1.321933e-01 | 4.527593e-01 | 5.935775e-01 | 1 | 114757830 | 114757924 | 95 | - | 0.377 | 0.208 | -1.172 |
| ENSG00000009307 | E068 | 716.5036940 | 1.213737e-02 | 2.036239e-07 | 1.948477e-06 | 1 | 114757925 | 114758027 | 103 | - | 2.852 | 2.567 | -0.950 |
| ENSG00000009307 | E069 | 0.1515154 | 4.343565e-02 | 1.000000e+00 | 1 | 114758576 | 114758676 | 101 | - | 0.069 | 0.000 | -8.618 |