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_2hA | HEK293_TMG_2hB | EIF3E | protein_coding | protein_coding | 275.7603 | 98.65668 | 455.7216 | 13.42772 | 16.61238 | 2.20755 | 52.155998 | 26.137724 | 84.99575 | 4.423551 | 1.168936 | 1.7008751 | 0.2138333 | 0.2642 | 0.18700000 | -0.07720000 | 0.085681802 | 1.974471e-15 | FALSE | TRUE |
| ENST00000676698 | ENSG00000104408 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | EIF3E | protein_coding | protein_coding | 275.7603 | 98.65668 | 455.7216 | 13.42772 | 16.61238 | 2.20755 | 114.946871 | 33.085542 | 191.44304 | 1.191398 | 6.295530 | 2.5322818 | 0.3833417 | 0.3438 | 0.42020000 | 0.07640000 | 0.251396256 | 1.974471e-15 | FALSE | TRUE |
| ENST00000676706 | ENSG00000104408 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | EIF3E | protein_coding | nonsense_mediated_decay | 275.7603 | 98.65668 | 455.7216 | 13.42772 | 16.61238 | 2.20755 | 9.328537 | 6.547626 | 12.45810 | 3.290357 | 6.387377 | 0.9269959 | 0.0508750 | 0.0638 | 0.02636667 | -0.03743333 | 0.916788023 | 1.974471e-15 | FALSE | TRUE |
| ENST00000677590 | ENSG00000104408 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | EIF3E | protein_coding | processed_transcript | 275.7603 | 98.65668 | 455.7216 | 13.42772 | 16.61238 | 2.20755 | 61.920409 | 14.003117 | 106.44157 | 2.422948 | 4.878890 | 2.9253474 | 0.1959083 | 0.1407 | 0.23436667 | 0.09366667 | 0.000204754 | 1.974471e-15 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000104408 | E001 | 0.6633060 | 2.346595e-02 | 8.535475e-01 | 9.093734e-01 | 8 | 108162787 | 108165423 | 2637 | - | 0.180 | 0.210 | 0.275 |
| ENSG00000104408 | E002 | 0.4428904 | 6.374405e-01 | 8.122292e-02 | 1.614598e-01 | 8 | 108192706 | 108192791 | 86 | - | 0.000 | 0.366 | 12.631 |
| ENSG00000104408 | E003 | 4.1719538 | 5.099196e-03 | 4.364053e-02 | 9.772308e-02 | 8 | 108200551 | 108201207 | 657 | - | 0.736 | 0.350 | -1.844 |
| ENSG00000104408 | E004 | 0.5922303 | 1.790036e-02 | 8.660187e-01 | 9.177213e-01 | 8 | 108201208 | 108201215 | 8 | - | 0.180 | 0.209 | 0.271 |
| ENSG00000104408 | E005 | 3.5448717 | 4.769482e-03 | 5.606807e-03 | 1.757027e-02 | 8 | 108201216 | 108201402 | 187 | - | 0.485 | 0.892 | 1.729 |
| ENSG00000104408 | E006 | 8.4281141 | 3.416467e-03 | 5.471715e-02 | 1.175017e-01 | 8 | 108201403 | 108201731 | 329 | - | 0.865 | 1.084 | 0.815 |
| ENSG00000104408 | E007 | 2.4734202 | 7.875093e-02 | 2.001678e-01 | 3.264625e-01 | 8 | 108201732 | 108201739 | 8 | - | 0.433 | 0.670 | 1.106 |
| ENSG00000104408 | E008 | 2.4734202 | 7.875093e-02 | 2.001678e-01 | 3.264625e-01 | 8 | 108201740 | 108201742 | 3 | - | 0.433 | 0.670 | 1.106 |
| ENSG00000104408 | E009 | 3.6577765 | 1.121386e-01 | 8.824958e-03 | 2.584501e-02 | 8 | 108201743 | 108201744 | 2 | - | 0.433 | 0.948 | 2.204 |
| ENSG00000104408 | E010 | 4.4328571 | 1.134738e-01 | 1.790288e-02 | 4.692698e-02 | 8 | 108201745 | 108201758 | 14 | - | 0.531 | 0.977 | 1.827 |
| ENSG00000104408 | E011 | 32.3507108 | 7.523715e-04 | 3.050551e-13 | 8.088423e-12 | 8 | 108201759 | 108201776 | 18 | - | 1.308 | 1.758 | 1.543 |
| ENSG00000104408 | E012 | 81.2719749 | 3.233572e-03 | 3.491248e-15 | 1.229380e-13 | 8 | 108201777 | 108201792 | 16 | - | 1.731 | 2.111 | 1.279 |
| ENSG00000104408 | E013 | 85.5899301 | 3.743579e-03 | 2.984729e-13 | 7.923877e-12 | 8 | 108201793 | 108201793 | 1 | - | 1.763 | 2.121 | 1.203 |
| ENSG00000104408 | E014 | 181.2331283 | 3.459419e-03 | 1.491224e-13 | 4.135482e-12 | 8 | 108201794 | 108201812 | 19 | - | 2.110 | 2.403 | 0.978 |
| ENSG00000104408 | E015 | 243.7781860 | 1.679563e-03 | 1.839888e-22 | 1.544356e-20 | 8 | 108201813 | 108201822 | 10 | - | 2.236 | 2.533 | 0.988 |
| ENSG00000104408 | E016 | 244.1382733 | 1.646610e-03 | 8.538170e-23 | 7.406276e-21 | 8 | 108201823 | 108201826 | 4 | - | 2.237 | 2.534 | 0.992 |
| ENSG00000104408 | E017 | 321.3071058 | 5.785579e-04 | 3.427117e-27 | 4.505601e-25 | 8 | 108201827 | 108201853 | 27 | - | 2.374 | 2.624 | 0.835 |
| ENSG00000104408 | E018 | 311.2092856 | 3.711464e-04 | 5.079732e-24 | 5.054307e-22 | 8 | 108201854 | 108201855 | 2 | - | 2.369 | 2.596 | 0.758 |
| ENSG00000104408 | E019 | 428.9210738 | 1.502046e-03 | 1.270081e-06 | 1.031612e-05 | 8 | 108201856 | 108201869 | 14 | - | 2.541 | 2.663 | 0.406 |
| ENSG00000104408 | E020 | 391.8461723 | 2.456183e-03 | 8.618085e-05 | 4.571385e-04 | 8 | 108201870 | 108201873 | 4 | - | 2.503 | 2.620 | 0.388 |
| ENSG00000104408 | E021 | 370.9814277 | 2.410838e-03 | 5.525133e-04 | 2.356045e-03 | 8 | 108201874 | 108201877 | 4 | - | 2.484 | 2.586 | 0.339 |
| ENSG00000104408 | E022 | 420.5928033 | 3.013121e-03 | 3.294608e-02 | 7.769774e-02 | 8 | 108201878 | 108201881 | 4 | - | 2.549 | 2.614 | 0.216 |
| ENSG00000104408 | E023 | 420.3284691 | 2.993844e-03 | 3.324362e-02 | 7.828053e-02 | 8 | 108201882 | 108201882 | 1 | - | 2.549 | 2.613 | 0.215 |
| ENSG00000104408 | E024 | 563.6402674 | 1.745279e-03 | 8.187527e-05 | 4.368687e-04 | 8 | 108201883 | 108201909 | 27 | - | 2.667 | 2.762 | 0.316 |
| ENSG00000104408 | E025 | 661.0116997 | 1.512741e-04 | 5.167810e-06 | 3.665803e-05 | 8 | 108201910 | 108201923 | 14 | - | 2.745 | 2.810 | 0.215 |
| ENSG00000104408 | E026 | 11.5058322 | 4.611963e-02 | 1.726671e-01 | 2.916726e-01 | 8 | 108201924 | 108202982 | 1059 | - | 0.989 | 1.164 | 0.635 |
| ENSG00000104408 | E027 | 641.2769760 | 1.167537e-04 | 8.062011e-07 | 6.829997e-06 | 8 | 108202983 | 108202989 | 7 | - | 2.731 | 2.802 | 0.236 |
| ENSG00000104408 | E028 | 1749.0652758 | 6.777052e-05 | 5.448837e-07 | 4.784768e-06 | 8 | 108202990 | 108203117 | 128 | - | 3.174 | 3.214 | 0.134 |
| ENSG00000104408 | E029 | 7.4019999 | 2.785956e-02 | 4.172447e-01 | 5.606070e-01 | 8 | 108203118 | 108203144 | 27 | - | 0.844 | 0.955 | 0.424 |
| ENSG00000104408 | E030 | 10.5126008 | 6.450017e-03 | 1.117173e-01 | 2.080807e-01 | 8 | 108203145 | 108203400 | 256 | - | 0.956 | 1.127 | 0.624 |
| ENSG00000104408 | E031 | 1653.7622684 | 2.222284e-04 | 7.394134e-04 | 3.040715e-03 | 8 | 108203401 | 108203469 | 69 | - | 3.152 | 3.181 | 0.097 |
| ENSG00000104408 | E032 | 1337.0258401 | 8.426177e-04 | 1.237593e-02 | 3.443663e-02 | 8 | 108203470 | 108203503 | 34 | - | 3.058 | 3.090 | 0.106 |
| ENSG00000104408 | E033 | 1967.2945365 | 2.051435e-04 | 2.589995e-03 | 9.035349e-03 | 8 | 108214607 | 108214716 | 110 | - | 3.229 | 3.251 | 0.073 |
| ENSG00000104408 | E034 | 1538.6521876 | 1.189609e-03 | 3.488964e-01 | 4.931130e-01 | 8 | 108216412 | 108216475 | 64 | - | 3.126 | 3.132 | 0.021 |
| ENSG00000104408 | E035 | 1175.6899059 | 7.463988e-04 | 1.024072e-01 | 1.941899e-01 | 8 | 108216476 | 108216513 | 38 | - | 3.021 | 2.979 | -0.140 |
| ENSG00000104408 | E036 | 6.5159582 | 2.493989e-03 | 1.087757e-02 | 3.087502e-02 | 8 | 108216514 | 108217092 | 579 | - | 0.894 | 0.456 | -1.880 |
| ENSG00000104408 | E037 | 2086.7263805 | 5.893706e-04 | 1.020378e-06 | 8.447281e-06 | 8 | 108217334 | 108217460 | 127 | - | 3.279 | 3.191 | -0.293 |
| ENSG00000104408 | E038 | 3.6087415 | 4.769263e-03 | 1.783969e-02 | 4.679371e-02 | 8 | 108217461 | 108217921 | 461 | - | 0.693 | 0.209 | -2.666 |
| ENSG00000104408 | E039 | 1.4791742 | 1.517080e-02 | 6.202591e-02 | 1.300330e-01 | 8 | 108219750 | 108219830 | 81 | - | 0.433 | 0.000 | -14.913 |
| ENSG00000104408 | E040 | 1.9125022 | 9.546182e-03 | 2.673636e-02 | 6.544425e-02 | 8 | 108221488 | 108221603 | 116 | - | 0.508 | 0.000 | -15.507 |
| ENSG00000104408 | E041 | 0.8878743 | 1.314157e-02 | 1.983691e-01 | 3.241760e-01 | 8 | 108225712 | 108225833 | 122 | - | 0.307 | 0.000 | -14.251 |
| ENSG00000104408 | E042 | 2.3542493 | 6.834535e-03 | 1.181936e-02 | 3.310227e-02 | 8 | 108226483 | 108227794 | 1312 | - | 0.572 | 0.000 | -15.938 |
| ENSG00000104408 | E043 | 1.3274313 | 3.115254e-01 | 2.008819e-01 | 3.272887e-01 | 8 | 108227795 | 108228176 | 382 | - | 0.404 | 0.000 | -13.418 |
| ENSG00000104408 | E044 | 2.1528869 | 3.298075e-02 | 9.752841e-01 | 9.886013e-01 | 8 | 108228177 | 108228266 | 90 | - | 0.460 | 0.456 | -0.020 |
| ENSG00000104408 | E045 | 1436.9116575 | 6.464294e-04 | 7.116711e-07 | 6.102288e-06 | 8 | 108228267 | 108228314 | 48 | - | 3.120 | 3.022 | -0.326 |
| ENSG00000104408 | E046 | 1292.3359682 | 1.367517e-03 | 7.763298e-02 | 1.556677e-01 | 8 | 108228315 | 108228391 | 77 | - | 3.064 | 3.010 | -0.179 |
| ENSG00000104408 | E047 | 1503.6260934 | 2.100316e-03 | 7.338954e-01 | 8.250364e-01 | 8 | 108229070 | 108229195 | 126 | - | 3.124 | 3.092 | -0.105 |
| ENSG00000104408 | E048 | 4.8885279 | 3.256588e-03 | 7.321388e-01 | 8.236713e-01 | 8 | 108229196 | 108230121 | 926 | - | 0.736 | 0.674 | -0.259 |
| ENSG00000104408 | E049 | 6.3318933 | 2.958457e-03 | 4.862226e-02 | 1.067190e-01 | 8 | 108230122 | 108230513 | 392 | - | 0.736 | 0.985 | 0.964 |
| ENSG00000104408 | E050 | 7.6154419 | 2.277622e-03 | 1.485438e-02 | 4.016324e-02 | 8 | 108230514 | 108230724 | 211 | - | 0.799 | 1.084 | 1.072 |
| ENSG00000104408 | E051 | 95.2073373 | 8.357778e-02 | 6.518573e-01 | 7.626425e-01 | 8 | 108230725 | 108231806 | 1082 | - | 1.876 | 2.043 | 0.562 |
| ENSG00000104408 | E052 | 156.0306976 | 1.742325e-02 | 1.367636e-02 | 3.748691e-02 | 8 | 108231807 | 108233393 | 1587 | - | 2.174 | 2.003 | -0.574 |
| ENSG00000104408 | E053 | 124.5007747 | 3.093056e-02 | 4.473439e-05 | 2.550311e-04 | 8 | 108233394 | 108233672 | 279 | - | 1.898 | 2.305 | 1.365 |
| ENSG00000104408 | E054 | 0.5827671 | 1.130563e-01 | 4.334656e-01 | 5.758800e-01 | 8 | 108234284 | 108234871 | 588 | - | 0.226 | 0.000 | -12.612 |
| ENSG00000104408 | E055 | 3.1334920 | 4.981084e-03 | 3.622664e-01 | 5.066536e-01 | 8 | 108234872 | 108234997 | 126 | - | 0.531 | 0.674 | 0.635 |
| ENSG00000104408 | E056 | 1243.6537846 | 1.294341e-03 | 1.624602e-01 | 2.783518e-01 | 8 | 108234998 | 108235053 | 56 | - | 3.046 | 2.996 | -0.167 |
| ENSG00000104408 | E057 | 1466.2976851 | 3.021966e-04 | 2.298394e-10 | 3.807152e-09 | 8 | 108235054 | 108235097 | 44 | - | 3.130 | 3.026 | -0.345 |
| ENSG00000104408 | E058 | 1242.9582051 | 9.597049e-05 | 2.222546e-11 | 4.375049e-10 | 8 | 108235098 | 108235102 | 5 | - | 3.057 | 2.958 | -0.329 |
| ENSG00000104408 | E059 | 1168.1969164 | 1.251183e-04 | 2.299683e-08 | 2.650855e-07 | 8 | 108236161 | 108236162 | 2 | - | 3.028 | 2.940 | -0.293 |
| ENSG00000104408 | E060 | 1397.5620077 | 2.720542e-04 | 3.380660e-07 | 3.095186e-06 | 8 | 108236163 | 108236203 | 41 | - | 3.105 | 3.020 | -0.284 |
| ENSG00000104408 | E061 | 4.2766014 | 6.015125e-02 | 5.816926e-01 | 7.062060e-01 | 8 | 108236204 | 108236907 | 704 | - | 0.646 | 0.728 | 0.343 |
| ENSG00000104408 | E062 | 2100.0004865 | 1.447656e-03 | 2.707033e-05 | 1.627648e-04 | 8 | 108239958 | 108240075 | 118 | - | 3.286 | 3.177 | -0.362 |
| ENSG00000104408 | E063 | 6.0101435 | 2.711182e-03 | 6.197729e-02 | 1.299432e-01 | 8 | 108240076 | 108240098 | 23 | - | 0.855 | 0.541 | -1.313 |
| ENSG00000104408 | E064 | 6.4313909 | 3.159538e-03 | 1.216675e-01 | 2.223143e-01 | 8 | 108240099 | 108241798 | 1700 | - | 0.865 | 0.613 | -1.030 |
| ENSG00000104408 | E065 | 1379.8935999 | 3.630113e-03 | 4.993489e-03 | 1.591095e-02 | 8 | 108241799 | 108241885 | 87 | - | 3.105 | 2.988 | -0.387 |
| ENSG00000104408 | E066 | 652.8377280 | 6.570623e-03 | 1.591091e-02 | 4.253425e-02 | 8 | 108241886 | 108241892 | 7 | - | 2.784 | 2.648 | -0.451 |
| ENSG00000104408 | E067 | 669.7206285 | 8.415004e-03 | 1.955020e-02 | 5.051867e-02 | 8 | 108241893 | 108241913 | 21 | - | 2.797 | 2.651 | -0.485 |
| ENSG00000104408 | E068 | 2.2657798 | 6.336798e-02 | 9.346967e-01 | 9.628729e-01 | 8 | 108241914 | 108242111 | 198 | - | 0.460 | 0.459 | -0.006 |
| ENSG00000104408 | E069 | 3.7966218 | 2.367064e-01 | 3.589623e-01 | 5.032959e-01 | 8 | 108242112 | 108242256 | 145 | - | 0.553 | 0.816 | 1.108 |
| ENSG00000104408 | E070 | 3.9504159 | 9.065001e-02 | 4.761454e-01 | 6.148214e-01 | 8 | 108242257 | 108242346 | 90 | - | 0.611 | 0.729 | 0.501 |
| ENSG00000104408 | E071 | 9.5573041 | 2.285371e-03 | 5.242420e-01 | 6.578380e-01 | 8 | 108242347 | 108243292 | 946 | - | 0.948 | 1.013 | 0.241 |
| ENSG00000104408 | E072 | 9.7471899 | 1.705461e-03 | 9.036832e-01 | 9.427212e-01 | 8 | 108243293 | 108243463 | 171 | - | 0.980 | 0.985 | 0.020 |
| ENSG00000104408 | E073 | 26.7722504 | 7.090489e-04 | 2.711987e-03 | 9.409277e-03 | 8 | 108243464 | 108248469 | 5006 | - | 1.439 | 1.165 | -0.960 |
| ENSG00000104408 | E074 | 2.3605894 | 6.225804e-03 | 9.112834e-01 | 9.476545e-01 | 8 | 108248470 | 108248612 | 143 | - | 0.485 | 0.456 | -0.142 |
| ENSG00000104408 | E075 | 872.5653705 | 9.020632e-03 | 1.667339e-01 | 2.839424e-01 | 8 | 108248613 | 108248802 | 190 | - | 2.902 | 2.802 | -0.336 |
| 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 | 0.1451727 | 4.356793e-02 | 1.000000e+00 | 8 | 108309336 | 108309463 | 128 | - | 0.069 | 0.000 | -11.051 | |
| ENSG00000104408 | E081 | 0.2987644 | 2.772434e-02 | 1.000000e+00 | 8 | 108337365 | 108340395 | 3031 | - | 0.128 | 0.000 | -12.284 | |
| 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 | 0.1482932 | 4.115975e-02 | 1.161208e-01 | 8 | 108434373 | 108434487 | 115 | - | 0.000 | 0.209 | 12.456 | |
| ENSG00000104408 | E086 | 0.0000000 | 8 | 108434488 | 108434493 | 6 | - | ||||||
| ENSG00000104408 | E087 | 0.1515154 | 4.427407e-02 | 1.000000e+00 | 8 | 108435154 | 108435333 | 180 | - | 0.069 | 0.000 | -11.043 | |
| ENSG00000104408 | E088 | 0.0000000 | 8 | 108443365 | 108443369 | 5 | - | ||||||
| ENSG00000104408 | E089 | 0.1482932 | 4.115975e-02 | 1.161208e-01 | 8 | 108443370 | 108443496 | 127 | - | 0.000 | 0.209 | 12.456 |