Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000177731
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000327031 | ENSG00000177731 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | FLII | protein_coding | protein_coding | 88.75624 | 133.5449 | 57.10423 | 8.175034 | 0.6107542 | -1.225511 | 28.887463 | 38.758431 | 19.3281834 | 3.1583352 | 1.8070745 | -1.0034301 | 0.33062500 | 0.29556667 | 0.337933333 | 0.04236667 | 7.513372e-01 | 1.467924e-19 | FALSE | TRUE |
| ENST00000474265 | ENSG00000177731 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | FLII | protein_coding | retained_intron | 88.75624 | 133.5449 | 57.10423 | 8.175034 | 0.6107542 | -1.225511 | 9.113473 | 14.685278 | 5.2491661 | 5.4463528 | 0.4900719 | -1.4824467 | 0.09849583 | 0.10613333 | 0.091966667 | -0.01416667 | 9.856908e-01 | 1.467924e-19 | FALSE | FALSE |
| ENST00000493600 | ENSG00000177731 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | FLII | protein_coding | retained_intron | 88.75624 | 133.5449 | 57.10423 | 8.175034 | 0.6107542 | -1.225511 | 5.939515 | 3.873289 | 5.5002395 | 0.6014463 | 0.4553839 | 0.5048360 | 0.07757917 | 0.02876667 | 0.096400000 | 0.06763333 | 6.335464e-09 | 1.467924e-19 | TRUE | FALSE |
| ENST00000580453 | ENSG00000177731 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | FLII | protein_coding | retained_intron | 88.75624 | 133.5449 | 57.10423 | 8.175034 | 0.6107542 | -1.225511 | 4.043572 | 10.380462 | 0.2613440 | 2.3117832 | 0.1413794 | -5.2589932 | 0.03645000 | 0.07696667 | 0.004633333 | -0.07233333 | 3.837548e-03 | 1.467924e-19 | FALSE | FALSE |
| ENST00000581858 | ENSG00000177731 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | FLII | protein_coding | nonsense_mediated_decay | 88.75624 | 133.5449 | 57.10423 | 8.175034 | 0.6107542 | -1.225511 | 7.095136 | 24.081437 | 0.1626951 | 5.5648497 | 0.1626951 | -7.1241494 | 0.05589583 | 0.17633333 | 0.002900000 | -0.17343333 | 1.023586e-03 | 1.467924e-19 | FALSE | |
| MSTRG.13791.7 | ENSG00000177731 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | FLII | protein_coding | 88.75624 | 133.5449 | 57.10423 | 8.175034 | 0.6107542 | -1.225511 | 20.196018 | 30.347684 | 15.4619739 | 3.2121848 | 1.7043003 | -0.9724045 | 0.23188750 | 0.23063333 | 0.271366667 | 0.04073333 | 7.485448e-01 | 1.467924e-19 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000177731 | E001 | 1.6219638 | 0.0084283444 | 9.872199e-01 | 9.960687e-01 | 17 | 18244815 | 18244835 | 21 | - | 0.395 | 0.397 | 0.011 |
| ENSG00000177731 | E002 | 6.0104027 | 0.0575047693 | 1.193529e-02 | 3.337671e-02 | 17 | 18244836 | 18244840 | 5 | - | 0.395 | 0.898 | 2.216 |
| ENSG00000177731 | E003 | 69.1682797 | 0.0154596647 | 1.690792e-03 | 6.253717e-03 | 17 | 18244841 | 18244876 | 36 | - | 1.586 | 1.849 | 0.891 |
| ENSG00000177731 | E004 | 239.0308554 | 0.0082124448 | 2.099359e-09 | 2.927620e-08 | 17 | 18244877 | 18244921 | 45 | - | 2.054 | 2.393 | 1.131 |
| ENSG00000177731 | E005 | 259.3428292 | 0.0082136697 | 5.382844e-09 | 6.982443e-08 | 17 | 18244922 | 18244941 | 20 | - | 2.101 | 2.426 | 1.086 |
| ENSG00000177731 | E006 | 523.5263805 | 0.0037581410 | 4.468976e-13 | 1.161045e-11 | 17 | 18244942 | 18245058 | 117 | - | 2.450 | 2.721 | 0.906 |
| ENSG00000177731 | E007 | 634.6903050 | 0.0013488914 | 9.290654e-26 | 1.091865e-23 | 17 | 18245059 | 18245228 | 170 | - | 2.530 | 2.804 | 0.914 |
| ENSG00000177731 | E008 | 176.3407676 | 0.0010425297 | 1.104847e-16 | 4.722696e-15 | 17 | 18245229 | 18245229 | 1 | - | 1.933 | 2.252 | 1.070 |
| ENSG00000177731 | E009 | 197.0612369 | 0.0011829100 | 1.772338e-17 | 8.413033e-16 | 17 | 18245230 | 18245237 | 8 | - | 1.982 | 2.301 | 1.065 |
| ENSG00000177731 | E010 | 220.1874856 | 0.0002187516 | 5.763823e-23 | 5.092999e-21 | 17 | 18245238 | 18245245 | 8 | - | 2.035 | 2.347 | 1.044 |
| ENSG00000177731 | E011 | 362.6016757 | 0.0014753791 | 8.773936e-16 | 3.341097e-14 | 17 | 18245246 | 18245272 | 27 | - | 2.306 | 2.556 | 0.833 |
| ENSG00000177731 | E012 | 9.4614640 | 0.0072604426 | 4.433736e-04 | 1.941291e-03 | 17 | 18245273 | 18245350 | 78 | - | 1.213 | 0.831 | -1.408 |
| ENSG00000177731 | E013 | 8.2886581 | 0.0019953536 | 1.878487e-03 | 6.848202e-03 | 17 | 18245351 | 18245353 | 3 | - | 1.142 | 0.803 | -1.267 |
| ENSG00000177731 | E014 | 630.6004462 | 0.0027961876 | 3.755190e-06 | 2.750578e-05 | 17 | 18245354 | 18245419 | 66 | - | 2.627 | 2.780 | 0.511 |
| ENSG00000177731 | E015 | 14.0467869 | 0.0013005153 | 2.832327e-02 | 6.864919e-02 | 17 | 18245420 | 18245554 | 135 | - | 1.263 | 1.068 | -0.696 |
| ENSG00000177731 | E016 | 836.2915149 | 0.0048128392 | 1.355488e-01 | 2.418812e-01 | 17 | 18245555 | 18245660 | 106 | - | 2.818 | 2.884 | 0.222 |
| ENSG00000177731 | E017 | 39.4585770 | 0.0013784203 | 1.123949e-13 | 3.169998e-12 | 17 | 18245661 | 18245743 | 83 | - | 1.815 | 1.394 | -1.437 |
| ENSG00000177731 | E018 | 844.0274490 | 0.0022674745 | 1.177537e-01 | 2.167232e-01 | 17 | 18245744 | 18245837 | 94 | - | 2.832 | 2.885 | 0.176 |
| ENSG00000177731 | E019 | 441.5364381 | 0.0021675706 | 1.258267e-01 | 2.283285e-01 | 17 | 18245838 | 18245850 | 13 | - | 2.549 | 2.605 | 0.186 |
| ENSG00000177731 | E020 | 31.5355708 | 0.0006408213 | 1.256457e-06 | 1.021728e-05 | 17 | 18245851 | 18245933 | 83 | - | 1.654 | 1.354 | -1.027 |
| ENSG00000177731 | E021 | 641.0475422 | 0.0014460526 | 9.768478e-03 | 2.819245e-02 | 17 | 18245934 | 18245989 | 56 | - | 2.697 | 2.770 | 0.243 |
| ENSG00000177731 | E022 | 596.8975369 | 0.0002218719 | 1.251919e-05 | 8.134599e-05 | 17 | 18245990 | 18246062 | 73 | - | 2.654 | 2.741 | 0.288 |
| ENSG00000177731 | E023 | 3.6749224 | 0.0170517758 | 2.984485e-07 | 2.763720e-06 | 17 | 18246111 | 18246152 | 42 | - | 1.038 | 0.268 | -3.533 |
| ENSG00000177731 | E024 | 3.2860527 | 0.0048405946 | 1.589017e-05 | 1.008322e-04 | 17 | 18246153 | 18246161 | 9 | - | 0.950 | 0.316 | -2.888 |
| ENSG00000177731 | E025 | 552.9714654 | 0.0001069988 | 1.637765e-06 | 1.298199e-05 | 17 | 18246162 | 18246222 | 61 | - | 2.615 | 2.708 | 0.310 |
| ENSG00000177731 | E026 | 17.3355476 | 0.0263608898 | 1.548320e-04 | 7.684690e-04 | 17 | 18246223 | 18246307 | 85 | - | 1.466 | 1.061 | -1.425 |
| ENSG00000177731 | E027 | 701.5840720 | 0.0001889915 | 3.872448e-08 | 4.269340e-07 | 17 | 18246308 | 18246462 | 155 | - | 2.714 | 2.813 | 0.330 |
| ENSG00000177731 | E028 | 3.2192408 | 0.0049378097 | 5.948501e-03 | 1.847268e-02 | 17 | 18246545 | 18246593 | 49 | - | 0.841 | 0.433 | -1.795 |
| ENSG00000177731 | E029 | 859.4548736 | 0.0003991752 | 1.696638e-05 | 1.069414e-04 | 17 | 18246594 | 18246828 | 235 | - | 2.817 | 2.898 | 0.268 |
| ENSG00000177731 | E030 | 656.3217898 | 0.0006342868 | 1.683717e-01 | 2.860675e-01 | 17 | 18246913 | 18247052 | 140 | - | 2.732 | 2.769 | 0.122 |
| ENSG00000177731 | E031 | 2.5690952 | 0.1002806966 | 7.892226e-01 | 8.650835e-01 | 17 | 18247053 | 18247125 | 73 | - | 0.474 | 0.546 | 0.346 |
| ENSG00000177731 | E032 | 279.7511399 | 0.0003648440 | 4.029568e-01 | 5.467623e-01 | 17 | 18247169 | 18247175 | 7 | - | 2.398 | 2.385 | -0.042 |
| ENSG00000177731 | E033 | 645.1043214 | 0.0018046907 | 9.631899e-01 | 9.807462e-01 | 17 | 18247176 | 18247357 | 182 | - | 2.745 | 2.755 | 0.035 |
| ENSG00000177731 | E034 | 4.9112256 | 0.0032509108 | 8.674632e-05 | 4.598290e-04 | 17 | 18247358 | 18247436 | 79 | - | 1.037 | 0.525 | -2.073 |
| ENSG00000177731 | E035 | 534.4757093 | 0.0034050294 | 2.149126e-01 | 3.443343e-01 | 17 | 18247657 | 18247848 | 192 | - | 2.631 | 2.685 | 0.182 |
| ENSG00000177731 | E036 | 456.5324073 | 0.0002426944 | 3.420800e-02 | 8.015985e-02 | 17 | 18247929 | 18248033 | 105 | - | 2.563 | 2.614 | 0.169 |
| ENSG00000177731 | E037 | 626.8209977 | 0.0011898458 | 2.938163e-01 | 4.348608e-01 | 17 | 18248550 | 18248721 | 172 | - | 2.714 | 2.749 | 0.115 |
| ENSG00000177731 | E038 | 2.3498124 | 0.0085894625 | 1.808135e-01 | 3.022179e-01 | 17 | 18248722 | 18248759 | 38 | - | 0.299 | 0.552 | 1.373 |
| ENSG00000177731 | E039 | 431.7118056 | 0.0002116989 | 2.618495e-02 | 6.432558e-02 | 17 | 18248800 | 18248883 | 84 | - | 2.604 | 2.569 | -0.118 |
| ENSG00000177731 | E040 | 420.2279639 | 0.0001513025 | 2.293011e-03 | 8.128666e-03 | 17 | 18249127 | 18249201 | 75 | - | 2.605 | 2.553 | -0.170 |
| ENSG00000177731 | E041 | 448.5621524 | 0.0002331066 | 2.211886e-06 | 1.704157e-05 | 17 | 18249326 | 18249408 | 83 | - | 2.654 | 2.571 | -0.275 |
| ENSG00000177731 | E042 | 665.4372839 | 0.0001457533 | 2.433449e-16 | 9.995871e-15 | 17 | 18250838 | 18251017 | 180 | - | 2.850 | 2.731 | -0.394 |
| ENSG00000177731 | E043 | 6.9707573 | 0.0024472654 | 4.361449e-05 | 2.492649e-04 | 17 | 18251018 | 18251264 | 247 | - | 1.142 | 0.666 | -1.822 |
| ENSG00000177731 | E044 | 467.3173248 | 0.0004165667 | 1.899199e-05 | 1.184116e-04 | 17 | 18251265 | 18251386 | 122 | - | 2.668 | 2.591 | -0.257 |
| ENSG00000177731 | E045 | 341.3982214 | 0.0038849324 | 7.612148e-02 | 1.533022e-01 | 17 | 18251387 | 18251477 | 91 | - | 2.520 | 2.463 | -0.189 |
| ENSG00000177731 | E046 | 417.0685880 | 0.0020806395 | 2.036877e-02 | 5.225969e-02 | 17 | 18251680 | 18251813 | 134 | - | 2.606 | 2.549 | -0.189 |
| ENSG00000177731 | E047 | 105.4191117 | 0.0024160296 | 2.628932e-01 | 4.007204e-01 | 17 | 18251814 | 18251816 | 3 | - | 2.000 | 1.959 | -0.137 |
| ENSG00000177731 | E048 | 242.0748593 | 0.0016881772 | 7.313660e-02 | 1.485352e-01 | 17 | 18251999 | 18252055 | 57 | - | 2.362 | 2.315 | -0.158 |
| ENSG00000177731 | E049 | 317.4384684 | 0.0009359793 | 3.087392e-04 | 1.415119e-03 | 17 | 18252056 | 18252114 | 59 | - | 2.505 | 2.421 | -0.281 |
| ENSG00000177731 | E050 | 271.1145024 | 0.0017006104 | 1.127160e-03 | 4.394944e-03 | 17 | 18252115 | 18252146 | 32 | - | 2.442 | 2.352 | -0.299 |
| ENSG00000177731 | E051 | 225.8121403 | 0.0037485940 | 1.185846e-02 | 3.319272e-02 | 17 | 18252472 | 18252492 | 21 | - | 2.364 | 2.275 | -0.296 |
| ENSG00000177731 | E052 | 354.4927354 | 0.0007307405 | 2.216349e-07 | 2.106460e-06 | 17 | 18252493 | 18252556 | 64 | - | 2.575 | 2.460 | -0.381 |
| ENSG00000177731 | E053 | 337.0089329 | 0.0002457483 | 1.370590e-05 | 8.819477e-05 | 17 | 18253301 | 18253356 | 56 | - | 2.532 | 2.445 | -0.290 |
| ENSG00000177731 | E054 | 366.3369449 | 0.0010861743 | 6.028774e-06 | 4.214202e-05 | 17 | 18253357 | 18253426 | 70 | - | 2.582 | 2.477 | -0.350 |
| ENSG00000177731 | E055 | 247.3391936 | 0.0016778953 | 1.321116e-04 | 6.680587e-04 | 17 | 18253427 | 18253458 | 32 | - | 2.415 | 2.305 | -0.365 |
| ENSG00000177731 | E056 | 4.4952874 | 0.0036174194 | 3.156772e-03 | 1.072719e-02 | 17 | 18253459 | 18253543 | 85 | - | 0.950 | 0.552 | -1.625 |
| ENSG00000177731 | E057 | 309.6772176 | 0.0023079364 | 5.704355e-04 | 2.423197e-03 | 17 | 18253544 | 18253598 | 55 | - | 2.506 | 2.406 | -0.331 |
| ENSG00000177731 | E058 | 352.9398354 | 0.0034291287 | 2.937553e-03 | 1.007989e-02 | 17 | 18253599 | 18253719 | 121 | - | 2.557 | 2.465 | -0.307 |
| ENSG00000177731 | E059 | 9.8425287 | 0.0035231062 | 3.483396e-12 | 7.824508e-11 | 17 | 18253720 | 18253886 | 167 | - | 1.385 | 0.666 | -2.679 |
| ENSG00000177731 | E060 | 10.6273491 | 0.0072613204 | 1.550883e-13 | 4.290452e-12 | 17 | 18253887 | 18254078 | 192 | - | 1.427 | 0.646 | -2.910 |
| ENSG00000177731 | E061 | 155.4651648 | 0.0025150658 | 1.958003e-02 | 5.058473e-02 | 17 | 18254079 | 18254096 | 18 | - | 2.196 | 2.114 | -0.274 |
| ENSG00000177731 | E062 | 277.8566656 | 0.0029684509 | 5.039452e-04 | 2.174934e-03 | 17 | 18254097 | 18254178 | 82 | - | 2.467 | 2.357 | -0.368 |
| ENSG00000177731 | E063 | 155.2379374 | 0.0002717966 | 7.275719e-06 | 4.988647e-05 | 17 | 18254179 | 18254182 | 4 | - | 2.229 | 2.098 | -0.436 |
| ENSG00000177731 | E064 | 263.1956166 | 0.0041541794 | 8.698036e-05 | 4.609020e-04 | 17 | 18254521 | 18254603 | 83 | - | 2.466 | 2.324 | -0.473 |
| ENSG00000177731 | E065 | 178.4241276 | 0.0084825949 | 1.819720e-03 | 6.662555e-03 | 17 | 18254604 | 18254619 | 16 | - | 2.306 | 2.153 | -0.510 |
| ENSG00000177731 | E066 | 272.2029767 | 0.0006075838 | 1.764200e-06 | 1.388774e-05 | 17 | 18254620 | 18254682 | 63 | - | 2.461 | 2.347 | -0.379 |
| ENSG00000177731 | E067 | 205.1325425 | 0.0002177678 | 4.488254e-08 | 4.885860e-07 | 17 | 18254769 | 18254790 | 22 | - | 2.356 | 2.218 | -0.463 |
| ENSG00000177731 | E068 | 276.0521855 | 0.0001599607 | 1.135745e-09 | 1.666384e-08 | 17 | 18254791 | 18254854 | 64 | - | 2.479 | 2.346 | -0.444 |
| ENSG00000177731 | E069 | 309.9079532 | 0.0015324270 | 8.414076e-08 | 8.669285e-07 | 17 | 18255183 | 18255263 | 81 | - | 2.536 | 2.393 | -0.476 |
| ENSG00000177731 | E070 | 0.9212829 | 0.0152800808 | 6.330418e-01 | 7.478152e-01 | 17 | 18256525 | 18256525 | 1 | - | 0.299 | 0.216 | -0.622 |
| ENSG00000177731 | E071 | 293.5606656 | 0.0016157252 | 1.999605e-06 | 1.555598e-05 | 17 | 18256526 | 18256597 | 72 | - | 2.501 | 2.372 | -0.431 |
| ENSG00000177731 | E072 | 5.9538455 | 0.0060268768 | 1.920713e-03 | 6.979565e-03 | 17 | 18256598 | 18256908 | 311 | - | 1.037 | 0.646 | -1.530 |
| ENSG00000177731 | E073 | 294.2689560 | 0.0050854683 | 1.029159e-03 | 4.059049e-03 | 17 | 18256909 | 18257019 | 111 | - | 2.498 | 2.377 | -0.404 |
| ENSG00000177731 | E074 | 0.5997190 | 0.1681502424 | 8.742854e-03 | 2.564221e-02 | 17 | 18257020 | 18257033 | 14 | - | 0.475 | 0.000 | -13.919 |
| ENSG00000177731 | E075 | 0.7406253 | 0.0155803148 | 1.043838e-03 | 4.110328e-03 | 17 | 18257034 | 18257123 | 90 | - | 0.541 | 0.000 | -14.237 |
| ENSG00000177731 | E076 | 0.2924217 | 0.0290785164 | 5.424930e-02 | 17 | 18257124 | 18257126 | 3 | - | 0.299 | 0.000 | -12.915 | |
| ENSG00000177731 | E077 | 1.2221382 | 0.0104795114 | 9.254665e-03 | 2.692035e-02 | 17 | 18257127 | 18257276 | 150 | - | 0.599 | 0.155 | -2.796 |
| ENSG00000177731 | E078 | 1.1050636 | 0.0188747022 | 8.564837e-01 | 9.112531e-01 | 17 | 18258447 | 18258627 | 181 | - | 0.299 | 0.269 | -0.205 |
| ENSG00000177731 | E079 | 188.4237649 | 0.0110588131 | 4.622380e-03 | 1.488115e-02 | 17 | 18258628 | 18258756 | 129 | - | 2.323 | 2.176 | -0.491 |