Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000133706
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000274562 | ENSG00000133706 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | LARS1 | protein_coding | protein_coding | 71.07439 | 22.59221 | 105.6962 | 3.275426 | 4.074287 | 2.225524 | 9.092573 | 4.9667104 | 7.992094 | 0.74495739 | 0.5925975 | 0.6851851 | 0.17073750 | 0.219500000 | 0.07540000 | -0.14410000 | 7.046435e-15 | 7.046435e-15 | FALSE | TRUE |
| ENST00000394434 | ENSG00000133706 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | LARS1 | protein_coding | protein_coding | 71.07439 | 22.59221 | 105.6962 | 3.275426 | 4.074287 | 2.225524 | 18.029931 | 7.6908481 | 23.583010 | 2.23810843 | 0.5319959 | 1.6152703 | 0.27980417 | 0.322866667 | 0.22360000 | -0.09926667 | 6.301487e-01 | 7.046435e-15 | FALSE | TRUE |
| ENST00000511505 | ENSG00000133706 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | LARS1 | protein_coding | processed_transcript | 71.07439 | 22.59221 | 105.6962 | 3.275426 | 4.074287 | 2.225524 | 3.253069 | 0.1155999 | 6.944890 | 0.06671347 | 0.1902174 | 5.7911207 | 0.03044167 | 0.005433333 | 0.06590000 | 0.06046667 | 3.402661e-05 | 7.046435e-15 | FALSE | TRUE |
| ENST00000674310 | ENSG00000133706 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | LARS1 | protein_coding | nonsense_mediated_decay | 71.07439 | 22.59221 | 105.6962 | 3.275426 | 4.074287 | 2.225524 | 8.143777 | 0.0712846 | 14.649328 | 0.04070177 | 2.7264264 | 7.4946212 | 0.07104167 | 0.003866667 | 0.13713333 | 0.13326667 | 2.427505e-06 | 7.046435e-15 | TRUE | TRUE |
| MSTRG.27111.19 | ENSG00000133706 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | LARS1 | protein_coding | 71.07439 | 22.59221 | 105.6962 | 3.275426 | 4.074287 | 2.225524 | 2.544154 | 2.2413700 | 1.969747 | 1.66576667 | 1.4431098 | -0.1854872 | 0.06948333 | 0.088400000 | 0.01973333 | -0.06866667 | 6.985388e-01 | 7.046435e-15 | FALSE | TRUE | |
| MSTRG.27111.25 | ENSG00000133706 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | LARS1 | protein_coding | 71.07439 | 22.59221 | 105.6962 | 3.275426 | 4.074287 | 2.225524 | 19.998852 | 4.2316029 | 32.700301 | 0.83593433 | 3.0942175 | 2.9470635 | 0.24288333 | 0.196733333 | 0.30800000 | 0.11126667 | 4.867884e-01 | 7.046435e-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_6hB | HEK293_OSMI2_6hA | log2fold_HEK293_OSMI2_6hA_HEK293_TMG_6hB |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000133706 | E001 | 5.2684317 | 0.0051123909 | 1.531368e-02 | 7.924839e-02 | 5 | 146110566 | 146113033 | 2468 | - | 0.779 | 0.360 | -1.958 |
| ENSG00000133706 | E002 | 2.6556287 | 0.0088625378 | 7.395874e-01 | 8.601608e-01 | 5 | 146113034 | 146113042 | 9 | - | 0.468 | 0.554 | 0.412 |
| ENSG00000133706 | E003 | 285.6731822 | 0.0063949498 | 1.330177e-09 | 7.590546e-08 | 5 | 146113043 | 146113853 | 811 | - | 2.277 | 2.596 | 1.064 |
| ENSG00000133706 | E004 | 75.5463014 | 0.0163550520 | 3.158086e-02 | 1.320064e-01 | 5 | 146113854 | 146113895 | 42 | - | 1.734 | 1.951 | 0.729 |
| ENSG00000133706 | E005 | 67.1468142 | 0.0404595358 | 1.347753e-01 | 3.393370e-01 | 5 | 146113896 | 146113910 | 15 | - | 1.679 | 1.915 | 0.798 |
| ENSG00000133706 | E006 | 61.3988988 | 0.0676660518 | 1.015222e-01 | 2.845533e-01 | 5 | 146113911 | 146113933 | 23 | - | 1.616 | 1.928 | 1.053 |
| ENSG00000133706 | E007 | 116.1260509 | 0.0044082462 | 1.271138e-02 | 6.928842e-02 | 5 | 146113934 | 146113937 | 4 | - | 1.934 | 2.097 | 0.546 |
| ENSG00000133706 | E008 | 521.6230802 | 0.0061942536 | 6.420229e-04 | 6.936121e-03 | 5 | 146113938 | 146114232 | 295 | - | 2.579 | 2.766 | 0.624 |
| ENSG00000133706 | E009 | 318.2821332 | 0.0445267996 | 2.909488e-02 | 1.246369e-01 | 5 | 146114233 | 146114311 | 79 | - | 2.346 | 2.600 | 0.849 |
| ENSG00000133706 | E010 | 1.7174261 | 0.1629696438 | 1.343948e-01 | 3.387206e-01 | 5 | 146119009 | 146119074 | 66 | - | 0.294 | 0.621 | 1.715 |
| ENSG00000133706 | E011 | 430.7785888 | 0.0831342442 | 1.006852e-01 | 2.830248e-01 | 5 | 146120371 | 146120503 | 133 | - | 2.483 | 2.716 | 0.776 |
| ENSG00000133706 | E012 | 398.2531048 | 0.0100853614 | 3.339518e-02 | 1.371728e-01 | 5 | 146122492 | 146122583 | 92 | - | 2.473 | 2.624 | 0.503 |
| ENSG00000133706 | E013 | 218.9449778 | 0.0002028396 | 1.484666e-02 | 7.748952e-02 | 5 | 146122584 | 146122587 | 4 | - | 2.226 | 2.332 | 0.357 |
| ENSG00000133706 | E014 | 0.1614157 | 0.0331338181 | 1.000000e+00 | 5 | 146123979 | 146123981 | 3 | - | 0.065 | 0.000 | -8.997 | |
| ENSG00000133706 | E015 | 460.5732267 | 0.0001819753 | 4.952713e-02 | 1.784795e-01 | 5 | 146123982 | 146124086 | 105 | - | 2.554 | 2.631 | 0.257 |
| ENSG00000133706 | E016 | 493.0571984 | 0.0005404495 | 7.365202e-02 | 2.320644e-01 | 5 | 146126435 | 146126545 | 111 | - | 2.584 | 2.660 | 0.255 |
| ENSG00000133706 | E017 | 422.8709862 | 0.0012407447 | 3.826824e-04 | 4.565708e-03 | 5 | 146128672 | 146128779 | 108 | - | 2.505 | 2.635 | 0.434 |
| ENSG00000133706 | E018 | 188.0858249 | 0.0002529332 | 5.275072e-02 | 1.861089e-01 | 5 | 146128780 | 146128782 | 3 | - | 2.163 | 2.260 | 0.325 |
| ENSG00000133706 | E019 | 356.4501707 | 0.0004158788 | 1.826352e-04 | 2.478675e-03 | 5 | 146128978 | 146129081 | 104 | - | 2.431 | 2.557 | 0.420 |
| ENSG00000133706 | E020 | 240.5151922 | 0.0010804788 | 9.009025e-04 | 9.101908e-03 | 5 | 146129082 | 146129118 | 37 | - | 2.259 | 2.398 | 0.464 |
| ENSG00000133706 | E021 | 396.1938341 | 0.0003320632 | 1.604656e-03 | 1.436069e-02 | 5 | 146130018 | 146130158 | 141 | - | 2.481 | 2.589 | 0.359 |
| ENSG00000133706 | E022 | 6.2860223 | 0.0816772324 | 1.942551e-02 | 9.393350e-02 | 5 | 146130159 | 146130867 | 709 | - | 0.656 | 1.081 | 1.649 |
| ENSG00000133706 | E023 | 2.3494651 | 0.2485555046 | 1.418512e-02 | 7.507590e-02 | 5 | 146130868 | 146130935 | 68 | - | 0.253 | 0.848 | 2.931 |
| ENSG00000133706 | E024 | 3.7355701 | 0.1571635793 | 3.367205e-02 | 1.379896e-01 | 5 | 146130936 | 146131018 | 83 | - | 0.442 | 0.925 | 2.069 |
| ENSG00000133706 | E025 | 301.1108488 | 0.0005385901 | 9.562531e-03 | 5.624026e-02 | 5 | 146131019 | 146131109 | 91 | - | 2.361 | 2.466 | 0.351 |
| ENSG00000133706 | E026 | 44.9324236 | 0.1563123846 | 1.654268e-01 | 3.844856e-01 | 5 | 146131110 | 146132897 | 1788 | - | 1.460 | 1.845 | 1.308 |
| ENSG00000133706 | E027 | 393.2748988 | 0.0001370008 | 2.364799e-01 | 4.725153e-01 | 5 | 146132898 | 146133081 | 184 | - | 2.489 | 2.552 | 0.211 |
| ENSG00000133706 | E028 | 259.0588232 | 0.0002115823 | 5.489836e-01 | 7.356182e-01 | 5 | 146135601 | 146135664 | 64 | - | 2.317 | 2.339 | 0.072 |
| ENSG00000133706 | E029 | 0.0000000 | 5 | 146139616 | 146139703 | 88 | - | ||||||
| ENSG00000133706 | E030 | 263.4085442 | 0.0001894859 | 2.127020e-01 | 4.449143e-01 | 5 | 146140204 | 146140261 | 58 | - | 2.329 | 2.334 | 0.015 |
| ENSG00000133706 | E031 | 160.4319747 | 0.1311418727 | 2.405216e-01 | 4.771685e-01 | 5 | 146140262 | 146142855 | 2594 | - | 2.036 | 2.332 | 0.989 |
| ENSG00000133706 | E032 | 7.4217994 | 0.0579527135 | 1.773069e-01 | 4.002011e-01 | 5 | 146142856 | 146142871 | 16 | - | 0.787 | 1.028 | 0.917 |
| ENSG00000133706 | E033 | 294.3080306 | 0.0002222344 | 7.798975e-03 | 4.837626e-02 | 5 | 146142872 | 146142990 | 119 | - | 2.383 | 2.351 | -0.105 |
| ENSG00000133706 | E034 | 287.1076884 | 0.0015869060 | 6.005179e-03 | 3.974852e-02 | 5 | 146142991 | 146143084 | 94 | - | 2.375 | 2.327 | -0.162 |
| ENSG00000133706 | E035 | 9.5134696 | 0.1244594486 | 6.637541e-02 | 2.169124e-01 | 5 | 146143244 | 146143411 | 168 | - | 0.821 | 1.230 | 1.510 |
| ENSG00000133706 | E036 | 288.8454794 | 0.0002175528 | 4.277823e-05 | 7.286587e-04 | 5 | 146143412 | 146143486 | 75 | - | 2.383 | 2.311 | -0.240 |
| ENSG00000133706 | E037 | 259.1430328 | 0.0003362972 | 5.905172e-06 | 1.331078e-04 | 5 | 146143487 | 146143550 | 64 | - | 2.340 | 2.246 | -0.312 |
| ENSG00000133706 | E038 | 305.0758543 | 0.0008581172 | 1.534626e-05 | 3.041723e-04 | 5 | 146144267 | 146144349 | 83 | - | 2.410 | 2.322 | -0.296 |
| ENSG00000133706 | E039 | 6.5149682 | 0.0509721641 | 4.404578e-01 | 6.590528e-01 | 5 | 146144350 | 146144471 | 122 | - | 0.805 | 0.692 | -0.454 |
| ENSG00000133706 | E040 | 343.2105874 | 0.0002019439 | 6.389227e-07 | 1.922803e-05 | 5 | 146144472 | 146144537 | 66 | - | 2.459 | 2.373 | -0.287 |
| ENSG00000133706 | E041 | 11.3021851 | 0.1485414223 | 7.616007e-01 | 8.735854e-01 | 5 | 146144538 | 146144623 | 86 | - | 0.971 | 1.098 | 0.466 |
| ENSG00000133706 | E042 | 266.9877240 | 0.0001972956 | 1.780058e-03 | 1.556375e-02 | 5 | 146144624 | 146144662 | 39 | - | 2.344 | 2.296 | -0.160 |
| ENSG00000133706 | E043 | 299.8062415 | 0.0002034637 | 8.114725e-04 | 8.377256e-03 | 5 | 146144663 | 146144709 | 47 | - | 2.393 | 2.344 | -0.165 |
| ENSG00000133706 | E044 | 32.2235744 | 0.2219479752 | 9.004584e-01 | 9.520861e-01 | 5 | 146144710 | 146146511 | 1802 | - | 1.405 | 1.517 | 0.388 |
| ENSG00000133706 | E045 | 44.8637411 | 0.1932389933 | 8.136394e-01 | 9.044444e-01 | 5 | 146146512 | 146148199 | 1688 | - | 1.554 | 1.627 | 0.248 |
| ENSG00000133706 | E046 | 24.8055413 | 0.0473919283 | 5.303965e-01 | 7.223392e-01 | 5 | 146148200 | 146149433 | 1234 | - | 1.296 | 1.405 | 0.378 |
| ENSG00000133706 | E047 | 7.7229897 | 0.0039645666 | 5.920275e-01 | 7.650368e-01 | 5 | 146149434 | 146149551 | 118 | - | 0.873 | 0.832 | -0.157 |
| ENSG00000133706 | E048 | 11.8646166 | 0.0048209713 | 6.067415e-01 | 7.747127e-01 | 5 | 146149552 | 146149621 | 70 | - | 1.008 | 1.100 | 0.336 |
| ENSG00000133706 | E049 | 261.5615395 | 0.0001995687 | 3.822342e-02 | 1.501658e-01 | 5 | 146149622 | 146149657 | 36 | - | 2.329 | 2.310 | -0.063 |
| ENSG00000133706 | E050 | 280.4535791 | 0.0001816336 | 3.793812e-03 | 2.798282e-02 | 5 | 146149658 | 146149699 | 42 | - | 2.365 | 2.326 | -0.131 |
| ENSG00000133706 | E051 | 0.2852693 | 0.2971352052 | 1.000000e+00 | 5 | 146151500 | 146151861 | 362 | - | 0.120 | 0.000 | -9.972 | |
| ENSG00000133706 | E052 | 402.9449860 | 0.0001499898 | 2.325010e-03 | 1.921738e-02 | 5 | 146151862 | 146152002 | 141 | - | 2.519 | 2.490 | -0.098 |
| ENSG00000133706 | E053 | 238.3328442 | 0.0002156251 | 4.185372e-04 | 4.910713e-03 | 5 | 146153174 | 146153227 | 54 | - | 2.299 | 2.233 | -0.220 |
| ENSG00000133706 | E054 | 247.0284084 | 0.0022202552 | 7.116559e-03 | 4.516613e-02 | 5 | 146153734 | 146153810 | 77 | - | 2.314 | 2.254 | -0.198 |
| ENSG00000133706 | E055 | 219.2185279 | 0.0006206466 | 5.089682e-07 | 1.571251e-05 | 5 | 146153893 | 146153980 | 88 | - | 2.274 | 2.147 | -0.426 |
| ENSG00000133706 | E056 | 0.2852693 | 0.2971352052 | 1.000000e+00 | 5 | 146157397 | 146157402 | 6 | - | 0.120 | 0.000 | -9.972 | |
| ENSG00000133706 | E057 | 401.7512258 | 0.0002051518 | 5.537819e-13 | 5.959753e-11 | 5 | 146157403 | 146157628 | 226 | - | 2.536 | 2.404 | -0.440 |
| ENSG00000133706 | E058 | 206.4176266 | 0.0013095302 | 3.264475e-03 | 2.497895e-02 | 5 | 146157728 | 146157795 | 68 | - | 2.237 | 2.171 | -0.218 |
| ENSG00000133706 | E059 | 0.6072928 | 0.0193874923 | 2.122678e-01 | 5 | 146158709 | 146158830 | 122 | - | 0.121 | 0.359 | 1.997 | |
| ENSG00000133706 | E060 | 221.8807906 | 0.0014594108 | 1.257711e-03 | 1.184561e-02 | 5 | 146159407 | 146159470 | 64 | - | 2.270 | 2.195 | -0.252 |
| ENSG00000133706 | E061 | 231.3551257 | 0.0005197064 | 1.544559e-08 | 6.942872e-07 | 5 | 146160374 | 146160486 | 113 | - | 2.300 | 2.156 | -0.479 |
| ENSG00000133706 | E062 | 2.3468469 | 0.0123445799 | 8.984323e-01 | 9.510226e-01 | 5 | 146161164 | 146161286 | 123 | - | 0.468 | 0.468 | 0.000 |
| ENSG00000133706 | E063 | 1.4612993 | 0.0968284934 | 9.397464e-01 | 9.720995e-01 | 5 | 146162528 | 146164309 | 1782 | - | 0.329 | 0.360 | 0.186 |
| ENSG00000133706 | E064 | 239.5280607 | 0.0004984649 | 3.827938e-09 | 1.969915e-07 | 5 | 146164310 | 146164471 | 162 | - | 2.314 | 2.166 | -0.494 |
| ENSG00000133706 | E065 | 121.5246489 | 0.0004010776 | 1.307926e-02 | 7.077139e-02 | 5 | 146168128 | 146168147 | 20 | - | 2.006 | 1.941 | -0.215 |
| ENSG00000133706 | E066 | 249.5046885 | 0.0006903881 | 3.939738e-06 | 9.379757e-05 | 5 | 146168148 | 146168265 | 118 | - | 2.324 | 2.218 | -0.354 |
| ENSG00000133706 | E067 | 234.2105784 | 0.0003172570 | 4.603543e-05 | 7.751982e-04 | 5 | 146171910 | 146171990 | 81 | - | 2.295 | 2.210 | -0.284 |
| ENSG00000133706 | E068 | 265.1053486 | 0.0003239643 | 1.458769e-05 | 2.909025e-04 | 5 | 146172687 | 146172774 | 88 | - | 2.350 | 2.265 | -0.285 |
| ENSG00000133706 | E069 | 326.0973013 | 0.0002191742 | 6.524737e-08 | 2.535584e-06 | 5 | 146177547 | 146177665 | 119 | - | 2.441 | 2.340 | -0.336 |
| ENSG00000133706 | E070 | 3.3462644 | 0.0069718009 | 4.091158e-01 | 6.353445e-01 | 5 | 146181012 | 146181187 | 176 | - | 0.592 | 0.467 | -0.587 |
| ENSG00000133706 | E071 | 3.8564456 | 0.0065424546 | 2.622681e-01 | 5.014371e-01 | 5 | 146182140 | 146182475 | 336 | - | 0.642 | 0.468 | -0.809 |
| ENSG00000133706 | E072 | 225.0068995 | 0.0008647183 | 3.068354e-07 | 1.005552e-05 | 5 | 146182488 | 146182561 | 74 | - | 2.286 | 2.150 | -0.451 |
| ENSG00000133706 | E073 | 163.3926389 | 0.0022492347 | 1.799421e-05 | 3.493576e-04 | 5 | 146182562 | 146182621 | 60 | - | 2.149 | 2.001 | -0.498 |
| ENSG00000133706 | E074 | 34.0768157 | 0.0093559036 | 7.546979e-01 | 8.694993e-01 | 5 | 146182622 | 146182722 | 101 | - | 1.455 | 1.465 | 0.035 |