Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000104408
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000519030 | ENSG00000104408 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | EIF3E | protein_coding | protein_coding | 275.7603 | 60.53963 | 492.032 | 11.20044 | 17.84429 | 3.022591 | 52.155998 | 17.325593 | 72.38456 | 4.666312 | 2.032806 | 2.062144 | 0.2138333 | 0.27690000 | 0.1473667 | -0.129533333 | 0.03463544 | 3.874696e-07 | FALSE | TRUE |
| ENST00000676698 | ENSG00000104408 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | EIF3E | protein_coding | protein_coding | 275.7603 | 60.53963 | 492.032 | 11.20044 | 17.84429 | 3.022591 | 114.946871 | 22.903594 | 207.95765 | 5.111909 | 6.295709 | 3.182083 | 0.3833417 | 0.37243333 | 0.4230000 | 0.050566667 | 0.67193846 | 3.874696e-07 | FALSE | TRUE |
| ENST00000676706 | ENSG00000104408 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | EIF3E | protein_coding | nonsense_mediated_decay | 275.7603 | 60.53963 | 492.032 | 11.20044 | 17.84429 | 3.022591 | 9.328537 | 3.374392 | 21.36159 | 2.257419 | 1.658103 | 2.658725 | 0.0508750 | 0.04693333 | 0.0434000 | -0.003533333 | 0.91174296 | 3.874696e-07 | FALSE | TRUE |
| ENST00000677590 | ENSG00000104408 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | EIF3E | protein_coding | processed_transcript | 275.7603 | 60.53963 | 492.032 | 11.20044 | 17.84429 | 3.022591 | 61.920409 | 9.044508 | 122.61404 | 1.098835 | 2.934286 | 3.759462 | 0.1959083 | 0.15633333 | 0.2494333 | 0.093100000 | 0.13403075 | 3.874696e-07 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000104408 | E001 | 1.6190741 | 2.099023e-01 | 2.913361e-02 | 1.247556e-01 | 8 | 108162787 | 108165423 | 2637 | - | 0.219 | 0.698 | 2.602 |
| ENSG00000104408 | E002 | 0.1779838 | 3.610356e-02 | 9.046812e-01 | 8 | 108192706 | 108192791 | 86 | - | 0.053 | 0.000 | -10.098 | |
| ENSG00000104408 | E003 | 0.8048655 | 1.950655e-02 | 5.566447e-01 | 8 | 108200551 | 108201207 | 657 | - | 0.217 | 0.000 | -12.683 | |
| ENSG00000104408 | E004 | 0.0000000 | 8 | 108201208 | 108201215 | 8 | - | ||||||
| ENSG00000104408 | E005 | 3.2864545 | 7.371364e-03 | 4.458258e-01 | 6.626492e-01 | 8 | 108201216 | 108201402 | 187 | - | 0.487 | 0.626 | 0.639 |
| ENSG00000104408 | E006 | 7.8462773 | 4.204034e-03 | 4.924761e-01 | 6.956744e-01 | 8 | 108201403 | 108201731 | 329 | - | 0.817 | 0.701 | -0.466 |
| ENSG00000104408 | E007 | 2.7487625 | 8.787742e-03 | 8.054498e-01 | 8.993569e-01 | 8 | 108201732 | 108201739 | 8 | - | 0.469 | 0.416 | -0.272 |
| ENSG00000104408 | E008 | 2.7487625 | 8.787742e-03 | 8.054498e-01 | 8.993569e-01 | 8 | 108201740 | 108201742 | 3 | - | 0.469 | 0.416 | -0.272 |
| ENSG00000104408 | E009 | 3.8915842 | 6.697839e-03 | 4.511716e-03 | 3.199670e-02 | 8 | 108201743 | 108201744 | 2 | - | 0.469 | 0.916 | 1.898 |
| ENSG00000104408 | E010 | 4.0695680 | 6.562200e-03 | 6.300685e-03 | 4.120620e-02 | 8 | 108201745 | 108201758 | 14 | - | 0.487 | 0.916 | 1.805 |
| ENSG00000104408 | E011 | 34.8835086 | 1.024407e-03 | 2.524284e-04 | 3.246112e-03 | 8 | 108201759 | 108201776 | 18 | - | 1.359 | 1.623 | 0.908 |
| ENSG00000104408 | E012 | 105.1769264 | 4.586629e-03 | 1.629005e-01 | 3.810972e-01 | 8 | 108201777 | 108201792 | 16 | - | 1.863 | 1.942 | 0.266 |
| ENSG00000104408 | E013 | 107.9986550 | 5.405778e-03 | 1.122689e-01 | 3.029208e-01 | 8 | 108201793 | 108201793 | 1 | - | 1.871 | 1.964 | 0.312 |
| ENSG00000104408 | E014 | 202.9715132 | 2.347282e-04 | 1.609146e-09 | 9.024771e-08 | 8 | 108201794 | 108201812 | 19 | - | 2.123 | 2.316 | 0.645 |
| ENSG00000104408 | E015 | 265.4196256 | 1.812189e-04 | 3.068282e-08 | 1.287533e-06 | 8 | 108201813 | 108201822 | 10 | - | 2.245 | 2.403 | 0.526 |
| ENSG00000104408 | E016 | 265.9907615 | 1.833763e-04 | 8.977945e-09 | 4.267175e-07 | 8 | 108201823 | 108201826 | 4 | - | 2.245 | 2.408 | 0.544 |
| ENSG00000104408 | E017 | 328.6235963 | 1.764086e-04 | 1.857850e-09 | 1.029718e-07 | 8 | 108201827 | 108201853 | 27 | - | 2.338 | 2.492 | 0.516 |
| ENSG00000104408 | E018 | 313.0720423 | 1.853258e-04 | 1.213433e-09 | 6.980653e-08 | 8 | 108201854 | 108201855 | 2 | - | 2.315 | 2.475 | 0.534 |
| ENSG00000104408 | E019 | 416.2296792 | 1.293234e-04 | 1.645345e-08 | 7.358900e-07 | 8 | 108201856 | 108201869 | 14 | - | 2.444 | 2.574 | 0.433 |
| ENSG00000104408 | E020 | 352.0260361 | 1.536794e-04 | 1.223975e-11 | 1.038776e-09 | 8 | 108201870 | 108201873 | 4 | - | 2.365 | 2.532 | 0.557 |
| ENSG00000104408 | E021 | 338.8458026 | 1.908537e-04 | 1.147172e-08 | 5.304006e-07 | 8 | 108201874 | 108201877 | 4 | - | 2.353 | 2.499 | 0.485 |
| ENSG00000104408 | E022 | 393.0258149 | 6.825953e-04 | 1.676800e-05 | 3.287284e-04 | 8 | 108201878 | 108201881 | 4 | - | 2.423 | 2.536 | 0.376 |
| ENSG00000104408 | E023 | 392.1040606 | 6.675547e-04 | 1.961492e-05 | 3.763065e-04 | 8 | 108201882 | 108201882 | 1 | - | 2.423 | 2.534 | 0.372 |
| ENSG00000104408 | E024 | 525.7062326 | 1.594385e-04 | 1.255424e-10 | 8.716266e-09 | 8 | 108201883 | 108201909 | 27 | - | 2.545 | 2.679 | 0.444 |
| ENSG00000104408 | E025 | 597.3566136 | 1.433059e-04 | 1.931734e-07 | 6.685406e-06 | 8 | 108201910 | 108201923 | 14 | - | 2.606 | 2.708 | 0.340 |
| ENSG00000104408 | E026 | 13.0821688 | 2.845749e-03 | 2.552639e-02 | 1.138258e-01 | 8 | 108201924 | 108202982 | 1059 | - | 0.961 | 1.212 | 0.907 |
| ENSG00000104408 | E027 | 580.4528545 | 4.085915e-04 | 1.453831e-05 | 2.899518e-04 | 8 | 108202983 | 108202989 | 7 | - | 2.595 | 2.687 | 0.307 |
| ENSG00000104408 | E028 | 1624.2759339 | 7.467506e-05 | 5.093057e-02 | 1.818813e-01 | 8 | 108202990 | 108203117 | 128 | - | 3.052 | 3.074 | 0.075 |
| ENSG00000104408 | E029 | 8.5998388 | 3.882517e-03 | 7.890271e-01 | 8.898943e-01 | 8 | 108203118 | 108203144 | 27 | - | 0.834 | 0.871 | 0.144 |
| ENSG00000104408 | E030 | 11.9320358 | 2.749282e-03 | 1.734326e-02 | 8.669739e-02 | 8 | 108203145 | 108203400 | 256 | - | 0.916 | 1.190 | 1.000 |
| ENSG00000104408 | E031 | 1581.7692479 | 8.521720e-05 | 8.130947e-01 | 9.040934e-01 | 8 | 108203401 | 108203469 | 69 | - | 3.043 | 3.038 | -0.018 |
| ENSG00000104408 | E032 | 1247.4509282 | 1.214615e-04 | 3.690724e-02 | 1.467021e-01 | 8 | 108203470 | 108203503 | 34 | - | 2.944 | 2.910 | -0.114 |
| ENSG00000104408 | E033 | 1865.4738553 | 6.849600e-05 | 2.824456e-04 | 3.552493e-03 | 8 | 108214607 | 108214716 | 110 | - | 3.121 | 3.074 | -0.156 |
| ENSG00000104408 | E034 | 1495.8270655 | 1.116689e-04 | 4.413742e-02 | 1.654324e-01 | 8 | 108216412 | 108216475 | 64 | - | 3.023 | 2.993 | -0.101 |
| ENSG00000104408 | E035 | 1201.2413881 | 5.150887e-04 | 2.239655e-02 | 1.038884e-01 | 8 | 108216476 | 108216513 | 38 | - | 2.930 | 2.885 | -0.147 |
| ENSG00000104408 | E036 | 7.5807167 | 8.547958e-03 | 8.382302e-01 | 9.184572e-01 | 8 | 108216514 | 108217092 | 579 | - | 0.800 | 0.765 | -0.138 |
| ENSG00000104408 | E037 | 2076.9591792 | 9.622401e-04 | 6.931522e-03 | 4.432473e-02 | 8 | 108217334 | 108217460 | 127 | - | 3.168 | 3.114 | -0.180 |
| ENSG00000104408 | E038 | 4.7946252 | 2.031172e-02 | 1.499127e-01 | 3.621684e-01 | 8 | 108217461 | 108217921 | 461 | - | 0.586 | 0.823 | 0.987 |
| ENSG00000104408 | E039 | 1.5533880 | 1.232384e-02 | 1.827883e-01 | 4.076206e-01 | 8 | 108219750 | 108219830 | 81 | - | 0.360 | 0.000 | -13.882 |
| ENSG00000104408 | E040 | 2.8392922 | 7.672906e-03 | 7.356926e-01 | 8.577339e-01 | 8 | 108221488 | 108221603 | 116 | - | 0.468 | 0.533 | 0.315 |
| ENSG00000104408 | E041 | 1.0269444 | 3.706549e-01 | 7.514469e-01 | 8 | 108225712 | 108225833 | 122 | - | 0.221 | 0.258 | 0.290 | |
| ENSG00000104408 | E042 | 3.9203873 | 8.529861e-03 | 1.082502e-01 | 2.961143e-01 | 8 | 108226483 | 108227794 | 1312 | - | 0.613 | 0.256 | -1.946 |
| ENSG00000104408 | E043 | 0.8018448 | 2.089669e-02 | 1.511663e-01 | 8 | 108227795 | 108228176 | 382 | - | 0.143 | 0.416 | 2.049 | |
| ENSG00000104408 | E044 | 4.2170267 | 8.336589e-03 | 3.406940e-01 | 5.786520e-01 | 8 | 108228177 | 108228266 | 90 | - | 0.613 | 0.417 | -0.947 |
| ENSG00000104408 | E045 | 1400.3552900 | 8.150136e-04 | 7.059391e-05 | 1.117702e-03 | 8 | 108228267 | 108228314 | 48 | - | 3.001 | 2.917 | -0.278 |
| ENSG00000104408 | E046 | 1244.2352603 | 2.346058e-04 | 2.585790e-01 | 4.973922e-01 | 8 | 108228315 | 108228391 | 77 | - | 2.941 | 2.920 | -0.071 |
| ENSG00000104408 | E047 | 1443.2381239 | 3.457756e-04 | 1.994353e-01 | 4.290262e-01 | 8 | 108229070 | 108229195 | 126 | - | 3.001 | 3.019 | 0.059 |
| ENSG00000104408 | E048 | 8.6226181 | 3.147070e-02 | 5.407017e-01 | 7.295215e-01 | 8 | 108229196 | 108230121 | 926 | - | 0.833 | 0.918 | 0.326 |
| ENSG00000104408 | E049 | 3.8131018 | 6.667830e-03 | 1.213079e-01 | 3.179374e-01 | 8 | 108230122 | 108230513 | 392 | - | 0.599 | 0.256 | -1.886 |
| ENSG00000104408 | E050 | 5.8201191 | 4.610690e-03 | 1.135307e-01 | 3.050309e-01 | 8 | 108230514 | 108230724 | 211 | - | 0.732 | 0.417 | -1.450 |
| ENSG00000104408 | E051 | 68.3463455 | 1.741243e-03 | 2.631714e-05 | 4.817046e-04 | 8 | 108230725 | 108231806 | 1082 | - | 1.719 | 1.400 | -1.089 |
| ENSG00000104408 | E052 | 130.1556143 | 4.170078e-04 | 1.364078e-13 | 1.653475e-11 | 8 | 108231807 | 108233393 | 1587 | - | 2.004 | 1.580 | -1.431 |
| ENSG00000104408 | E053 | 73.2108849 | 6.532028e-04 | 1.507348e-02 | 7.835875e-02 | 8 | 108233394 | 108233672 | 279 | - | 1.695 | 1.826 | 0.445 |
| ENSG00000104408 | E054 | 0.8136113 | 3.326703e-02 | 6.883401e-01 | 8 | 108234284 | 108234871 | 588 | - | 0.181 | 0.257 | 0.638 | |
| ENSG00000104408 | E055 | 4.1672502 | 6.479478e-03 | 8.230507e-02 | 2.493007e-01 | 8 | 108234872 | 108234997 | 126 | - | 0.539 | 0.822 | 1.198 |
| ENSG00000104408 | E056 | 1170.4105427 | 1.105774e-04 | 3.203283e-01 | 5.599958e-01 | 8 | 108234998 | 108235053 | 56 | - | 2.911 | 2.924 | 0.043 |
| ENSG00000104408 | E057 | 1391.3194875 | 2.496566e-04 | 1.946270e-01 | 4.228616e-01 | 8 | 108235054 | 108235097 | 44 | - | 2.991 | 2.969 | -0.075 |
| ENSG00000104408 | E058 | 1176.0491635 | 1.129321e-04 | 2.411591e-01 | 4.779009e-01 | 8 | 108235098 | 108235102 | 5 | - | 2.918 | 2.898 | -0.068 |
| ENSG00000104408 | E059 | 1116.5934953 | 8.173926e-05 | 4.378990e-02 | 1.645724e-01 | 8 | 108236161 | 108236162 | 2 | - | 2.897 | 2.864 | -0.113 |
| ENSG00000104408 | E060 | 1343.3841071 | 6.547818e-05 | 7.092994e-03 | 4.504351e-02 | 8 | 108236163 | 108236203 | 41 | - | 2.978 | 2.937 | -0.136 |
| ENSG00000104408 | E061 | 4.3588535 | 6.200625e-03 | 8.765867e-01 | 9.394814e-01 | 8 | 108236204 | 108236907 | 704 | - | 0.599 | 0.625 | 0.114 |
| ENSG00000104408 | E062 | 2016.2847935 | 5.840430e-05 | 8.468039e-05 | 1.301654e-03 | 8 | 108239958 | 108240075 | 118 | - | 3.155 | 3.106 | -0.161 |
| ENSG00000104408 | E063 | 7.2298068 | 4.934070e-03 | 6.379319e-01 | 7.956836e-01 | 8 | 108240076 | 108240098 | 23 | - | 0.782 | 0.701 | -0.327 |
| ENSG00000104408 | E064 | 7.4379374 | 1.549013e-02 | 1.554220e-02 | 8.012819e-02 | 8 | 108240099 | 108241798 | 1700 | - | 0.722 | 1.060 | 1.293 |
| ENSG00000104408 | E065 | 1383.9066577 | 7.519248e-05 | 2.913141e-07 | 9.602452e-06 | 8 | 108241799 | 108241885 | 87 | - | 2.995 | 2.918 | -0.255 |
| ENSG00000104408 | E066 | 663.8750378 | 4.903713e-04 | 3.378097e-05 | 5.969651e-04 | 8 | 108241886 | 108241892 | 7 | - | 2.679 | 2.579 | -0.333 |
| ENSG00000104408 | E067 | 687.8541349 | 1.443073e-04 | 4.363607e-06 | 1.023113e-04 | 8 | 108241893 | 108241913 | 21 | - | 2.694 | 2.596 | -0.328 |
| ENSG00000104408 | E068 | 2.5593721 | 8.319996e-03 | 7.711445e-02 | 2.390313e-01 | 8 | 108241914 | 108242111 | 198 | - | 0.384 | 0.701 | 1.499 |
| ENSG00000104408 | E069 | 4.0347664 | 7.520741e-03 | 1.495550e-03 | 1.358756e-02 | 8 | 108242112 | 108242256 | 145 | - | 0.468 | 0.957 | 2.053 |
| ENSG00000104408 | E070 | 3.3203757 | 1.456651e-01 | 6.442833e-02 | 2.126322e-01 | 8 | 108242257 | 108242346 | 90 | - | 0.431 | 0.827 | 1.751 |
| ENSG00000104408 | E071 | 9.1106920 | 1.248463e-01 | 6.036593e-04 | 6.611327e-03 | 8 | 108242347 | 108243292 | 946 | - | 0.688 | 1.354 | 2.475 |
| ENSG00000104408 | E072 | 7.1180093 | 4.365504e-03 | 2.546987e-02 | 1.136700e-01 | 8 | 108243293 | 108243463 | 171 | - | 0.722 | 1.027 | 1.178 |
| ENSG00000104408 | E073 | 29.1209756 | 2.298469e-01 | 1.928219e-02 | 9.344672e-02 | 8 | 108243464 | 108248469 | 5006 | - | 1.142 | 1.821 | 2.343 |
| ENSG00000104408 | E074 | 2.8559778 | 2.512918e-02 | 8.158673e-01 | 9.057947e-01 | 8 | 108248470 | 108248612 | 143 | - | 0.470 | 0.417 | -0.272 |
| ENSG00000104408 | E075 | 810.2919189 | 4.932556e-04 | 5.517974e-02 | 1.917336e-01 | 8 | 108248613 | 108248802 | 190 | - | 2.758 | 2.716 | -0.140 |
| ENSG00000104408 | E076 | 0.0000000 | 8 | 108268246 | 108268422 | 177 | - | ||||||
| ENSG00000104408 | E077 | 0.0000000 | 8 | 108303355 | 108308637 | 5283 | - | ||||||
| ENSG00000104408 | E078 | 0.0000000 | 8 | 108308638 | 108309021 | 384 | - | ||||||
| ENSG00000104408 | E079 | 0.0000000 | 8 | 108309022 | 108309335 | 314 | - | ||||||
| ENSG00000104408 | E080 | 0.0000000 | 8 | 108309336 | 108309463 | 128 | - | ||||||
| ENSG00000104408 | E081 | 0.0000000 | 8 | 108337365 | 108340395 | 3031 | - | ||||||
| ENSG00000104408 | E082 | 0.0000000 | 8 | 108355331 | 108355726 | 396 | - | ||||||
| ENSG00000104408 | E083 | 0.0000000 | 8 | 108380319 | 108383543 | 3225 | - | ||||||
| ENSG00000104408 | E084 | 0.0000000 | 8 | 108421997 | 108422089 | 93 | - | ||||||
| ENSG00000104408 | E085 | 0.0000000 | 8 | 108434373 | 108434487 | 115 | - | ||||||
| ENSG00000104408 | E086 | 0.0000000 | 8 | 108434488 | 108434493 | 6 | - | ||||||
| ENSG00000104408 | E087 | 0.0000000 | 8 | 108435154 | 108435333 | 180 | - | ||||||
| ENSG00000104408 | E088 | 0.0000000 | 8 | 108443365 | 108443369 | 5 | - | ||||||
| ENSG00000104408 | E089 | 0.1308682 | 3.264919e-02 | 5.628714e-02 | 8 | 108443370 | 108443496 | 127 | - | 0.000 | 0.256 | 12.395 |