Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000196305
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000375643 | ENSG00000196305 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | IARS1 | protein_coding | protein_coding | 135.7931 | 70.93227 | 181.4334 | 24.36847 | 6.299924 | 1.354802 | 13.452978 | 4.929603 | 16.559801 | 2.865772 | 3.189260 | 1.7460892 | 0.08366250 | 0.06663333 | 0.09266667 | 0.02603333 | 8.110870e-01 | 4.397816e-08 | FALSE | TRUE |
| ENST00000443024 | ENSG00000196305 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | IARS1 | protein_coding | protein_coding | 135.7931 | 70.93227 | 181.4334 | 24.36847 | 6.299924 | 1.354802 | 57.067095 | 21.373670 | 86.445187 | 8.111016 | 2.681527 | 2.0154431 | 0.37237083 | 0.28376667 | 0.47660000 | 0.19283333 | 2.070430e-03 | 4.397816e-08 | FALSE | TRUE |
| ENST00000627121 | ENSG00000196305 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | IARS1 | protein_coding | nonsense_mediated_decay | 135.7931 | 70.93227 | 181.4334 | 24.36847 | 6.299924 | 1.354802 | 6.965030 | 6.003785 | 6.463407 | 2.849743 | 2.331246 | 0.1062520 | 0.06014583 | 0.07240000 | 0.03660000 | -0.03580000 | 5.833521e-01 | 4.397816e-08 | FALSE | TRUE |
| ENST00000684445 | ENSG00000196305 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | IARS1 | protein_coding | nonsense_mediated_decay | 135.7931 | 70.93227 | 181.4334 | 24.36847 | 6.299924 | 1.354802 | 9.828224 | 2.820558 | 15.290120 | 2.820558 | 3.557906 | 2.4343848 | 0.06026667 | 0.03050000 | 0.08306667 | 0.05256667 | 2.922037e-01 | 4.397816e-08 | TRUE | TRUE |
| MSTRG.32984.38 | ENSG00000196305 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | IARS1 | protein_coding | 135.7931 | 70.93227 | 181.4334 | 24.36847 | 6.299924 | 1.354802 | 23.219238 | 25.757837 | 16.192822 | 9.665760 | 2.648879 | -0.6693264 | 0.23050000 | 0.34586667 | 0.08843333 | -0.25743333 | 4.397816e-08 | 4.397816e-08 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000196305 | E001 | 0.3751086 | 6.011127e-02 | 4.403652e-02 | 9 | 92210207 | 92210210 | 4 | - | 0.000 | 0.314 | 12.128 | |
| ENSG00000196305 | E002 | 4.1977618 | 8.932271e-03 | 1.386702e-02 | 7.382380e-02 | 9 | 92210211 | 92210237 | 27 | - | 0.529 | 0.895 | 1.526 |
| ENSG00000196305 | E003 | 6.6013277 | 5.010540e-03 | 5.330481e-02 | 1.874432e-01 | 9 | 92210238 | 92210239 | 2 | - | 0.745 | 0.998 | 0.974 |
| ENSG00000196305 | E004 | 7.1187110 | 7.748851e-03 | 1.129634e-01 | 3.041037e-01 | 9 | 92210240 | 92210242 | 3 | - | 0.789 | 0.998 | 0.796 |
| ENSG00000196305 | E005 | 18.0828347 | 3.449597e-02 | 2.528050e-03 | 2.051703e-02 | 9 | 92210243 | 92210344 | 102 | - | 1.095 | 1.455 | 1.267 |
| ENSG00000196305 | E006 | 30.6581248 | 8.755116e-03 | 5.060027e-03 | 3.494831e-02 | 9 | 92210345 | 92210348 | 4 | - | 1.369 | 1.603 | 0.803 |
| ENSG00000196305 | E007 | 186.4493445 | 7.150389e-03 | 2.483237e-06 | 6.308312e-05 | 9 | 92210349 | 92210417 | 69 | - | 2.134 | 2.394 | 0.868 |
| ENSG00000196305 | E008 | 215.0110222 | 3.819603e-03 | 3.626406e-11 | 2.814658e-09 | 9 | 92210418 | 92210435 | 18 | - | 2.189 | 2.467 | 0.929 |
| ENSG00000196305 | E009 | 1945.9863396 | 8.281271e-04 | 2.356497e-23 | 1.015704e-20 | 9 | 92210436 | 92210889 | 454 | - | 3.187 | 3.358 | 0.568 |
| ENSG00000196305 | E010 | 0.7852767 | 1.711562e-02 | 5.575001e-01 | 9 | 92220492 | 92220591 | 100 | - | 0.202 | 0.312 | 0.824 | |
| ENSG00000196305 | E011 | 1268.5873016 | 8.472434e-04 | 1.612109e-19 | 4.422831e-17 | 9 | 92222520 | 92222672 | 153 | - | 3.003 | 3.170 | 0.556 |
| ENSG00000196305 | E012 | 977.4773846 | 3.401399e-04 | 6.951806e-23 | 2.824346e-20 | 9 | 92223346 | 92223429 | 84 | - | 2.895 | 3.051 | 0.518 |
| ENSG00000196305 | E013 | 789.5957311 | 4.722077e-04 | 6.888545e-13 | 7.284143e-11 | 9 | 92223430 | 92223489 | 60 | - | 2.811 | 2.944 | 0.442 |
| ENSG00000196305 | E014 | 43.9742626 | 1.790435e-01 | 5.691425e-02 | 1.958332e-01 | 9 | 92223490 | 92225908 | 2419 | - | 1.461 | 1.846 | 1.309 |
| ENSG00000196305 | E015 | 5.9087140 | 1.604723e-01 | 7.385401e-03 | 4.647761e-02 | 9 | 92228687 | 92229000 | 314 | - | 0.583 | 1.098 | 2.029 |
| ENSG00000196305 | E016 | 965.0314008 | 8.557893e-05 | 7.634400e-20 | 2.197452e-17 | 9 | 92229001 | 92229126 | 126 | - | 2.899 | 3.026 | 0.422 |
| ENSG00000196305 | E017 | 4.0099482 | 4.737899e-02 | 4.042891e-02 | 1.558522e-01 | 9 | 92229127 | 92230365 | 1239 | - | 0.553 | 0.889 | 1.389 |
| ENSG00000196305 | E018 | 0.5233527 | 2.111874e-02 | 8.513699e-01 | 9 | 92240289 | 92240298 | 10 | - | 0.145 | 0.184 | 0.413 | |
| ENSG00000196305 | E019 | 2.3833096 | 1.969695e-01 | 3.860785e-01 | 6.173574e-01 | 9 | 92240299 | 92240583 | 285 | - | 0.533 | 0.318 | -1.156 |
| ENSG00000196305 | E020 | 1.1833707 | 1.436385e-02 | 4.179671e-01 | 9 | 92240584 | 92240642 | 59 | - | 0.340 | 0.184 | -1.174 | |
| ENSG00000196305 | E021 | 20.6026383 | 1.032085e-01 | 5.267066e-01 | 7.196281e-01 | 9 | 92240643 | 92240691 | 49 | - | 1.272 | 1.332 | 0.209 |
| ENSG00000196305 | E022 | 0.3088520 | 2.562940e-02 | 4.783257e-01 | 9 | 92240692 | 92240762 | 71 | - | 0.078 | 0.183 | 1.406 | |
| ENSG00000196305 | E023 | 2.2699213 | 9.676551e-03 | 5.901149e-01 | 7.638218e-01 | 9 | 92240763 | 92240855 | 93 | - | 0.502 | 0.411 | -0.462 |
| ENSG00000196305 | E024 | 753.1939091 | 7.915235e-04 | 5.015136e-08 | 1.999731e-06 | 9 | 92240856 | 92240961 | 106 | - | 2.794 | 2.910 | 0.386 |
| ENSG00000196305 | E025 | 1146.9832411 | 7.751426e-05 | 2.798113e-07 | 9.273692e-06 | 9 | 92242154 | 92242330 | 177 | - | 2.992 | 3.064 | 0.238 |
| ENSG00000196305 | E026 | 2.3010660 | 1.703494e-01 | 2.526419e-01 | 4.907680e-01 | 9 | 92242331 | 92242613 | 283 | - | 0.413 | 0.621 | 1.001 |
| ENSG00000196305 | E027 | 1.9890211 | 6.760137e-01 | 7.146880e-01 | 8.447335e-01 | 9 | 92242614 | 92242687 | 74 | - | 0.421 | 0.492 | 0.363 |
| ENSG00000196305 | E028 | 2.4050233 | 1.459539e-01 | 2.888043e-01 | 5.294307e-01 | 9 | 92242688 | 92243215 | 528 | - | 0.411 | 0.632 | 1.063 |
| ENSG00000196305 | E029 | 915.5205819 | 1.073517e-04 | 1.385590e-03 | 1.279596e-02 | 9 | 92243216 | 92243311 | 96 | - | 2.901 | 2.955 | 0.178 |
| ENSG00000196305 | E030 | 2.6933311 | 3.209981e-01 | 8.661977e-01 | 9.338634e-01 | 9 | 92243312 | 92243449 | 138 | - | 0.568 | 0.480 | -0.417 |
| ENSG00000196305 | E031 | 0.1308682 | 3.264919e-02 | 1.741513e-01 | 9 | 92243475 | 92243799 | 325 | - | 0.000 | 0.183 | 13.808 | |
| ENSG00000196305 | E032 | 942.0010703 | 9.965065e-05 | 9.431212e-05 | 1.423677e-03 | 9 | 92244959 | 92245071 | 113 | - | 2.911 | 2.973 | 0.208 |
| ENSG00000196305 | E033 | 2.4950208 | 9.353262e-03 | 1.864558e-01 | 4.123838e-01 | 9 | 92245072 | 92245101 | 30 | - | 0.553 | 0.312 | -1.288 |
| ENSG00000196305 | E034 | 1154.2693393 | 1.320844e-04 | 1.535274e-03 | 1.384992e-02 | 9 | 92247377 | 92247551 | 175 | - | 3.001 | 3.051 | 0.167 |
| ENSG00000196305 | E035 | 2.9244497 | 1.206589e-02 | 4.157509e-01 | 6.403474e-01 | 9 | 92247552 | 92248597 | 1046 | - | 0.528 | 0.669 | 0.629 |
| ENSG00000196305 | E036 | 720.6335532 | 2.134734e-03 | 5.273955e-01 | 7.201522e-01 | 9 | 92249858 | 92249941 | 84 | - | 2.801 | 2.832 | 0.102 |
| ENSG00000196305 | E037 | 6.5685330 | 9.900664e-03 | 9.957846e-01 | 9.994807e-01 | 9 | 92249942 | 92249991 | 50 | - | 0.829 | 0.832 | 0.013 |
| ENSG00000196305 | E038 | 1.6895351 | 4.428565e-02 | 8.359996e-01 | 9.171552e-01 | 9 | 92249992 | 92250186 | 195 | - | 0.378 | 0.413 | 0.193 |
| ENSG00000196305 | E039 | 822.1194931 | 3.176410e-04 | 3.579760e-01 | 5.941364e-01 | 9 | 92250187 | 92250284 | 98 | - | 2.869 | 2.865 | -0.014 |
| ENSG00000196305 | E040 | 437.9990549 | 1.726554e-03 | 1.051375e-02 | 6.031812e-02 | 9 | 92250285 | 92250289 | 5 | - | 2.612 | 2.550 | -0.206 |
| ENSG00000196305 | E041 | 4.5591642 | 1.285950e-01 | 2.582311e-01 | 4.969694e-01 | 9 | 92250290 | 92250712 | 423 | - | 0.643 | 0.832 | 0.769 |
| ENSG00000196305 | E042 | 645.5358625 | 3.748446e-04 | 4.236684e-03 | 3.047380e-02 | 9 | 92250713 | 92250759 | 47 | - | 2.775 | 2.734 | -0.136 |
| ENSG00000196305 | E043 | 763.4260003 | 2.887843e-04 | 5.109117e-02 | 1.822908e-01 | 9 | 92250760 | 92250834 | 75 | - | 2.843 | 2.823 | -0.069 |
| ENSG00000196305 | E044 | 12.1105644 | 1.782508e-01 | 8.146061e-01 | 9.050023e-01 | 9 | 92250835 | 92251807 | 973 | - | 1.071 | 1.088 | 0.058 |
| ENSG00000196305 | E045 | 693.3542038 | 1.163774e-04 | 1.308036e-03 | 1.222199e-02 | 9 | 92251808 | 92251885 | 78 | - | 2.807 | 2.767 | -0.133 |
| ENSG00000196305 | E046 | 27.1607798 | 1.942837e-01 | 1.861796e-01 | 4.120398e-01 | 9 | 92251886 | 92252749 | 864 | - | 1.321 | 1.564 | 0.839 |
| ENSG00000196305 | E047 | 619.5117344 | 5.186994e-04 | 8.020196e-02 | 2.452091e-01 | 9 | 92253362 | 92253446 | 85 | - | 2.753 | 2.728 | -0.083 |
| ENSG00000196305 | E048 | 329.8161583 | 2.183703e-04 | 7.977398e-01 | 8.950723e-01 | 9 | 92253447 | 92253453 | 7 | - | 2.472 | 2.477 | 0.017 |
| ENSG00000196305 | E049 | 234.5229917 | 1.748176e-01 | 8.207880e-01 | 9.084920e-01 | 9 | 92253454 | 92255534 | 2081 | - | 2.322 | 2.333 | 0.037 |
| ENSG00000196305 | E050 | 21.3280125 | 2.588159e-01 | 9.447404e-01 | 9.746947e-01 | 9 | 92255535 | 92255604 | 70 | - | 1.302 | 1.301 | -0.005 |
| ENSG00000196305 | E051 | 109.5978314 | 2.508860e-01 | 8.219412e-01 | 9.090848e-01 | 9 | 92255605 | 92256679 | 1075 | - | 2.017 | 1.940 | -0.260 |
| ENSG00000196305 | E052 | 332.5231017 | 1.988030e-04 | 9.915069e-01 | 9.975310e-01 | 9 | 92256680 | 92256683 | 4 | - | 2.473 | 2.484 | 0.036 |
| ENSG00000196305 | E053 | 651.2045285 | 1.569999e-04 | 4.207359e-01 | 6.442392e-01 | 9 | 92256684 | 92256800 | 117 | - | 2.768 | 2.765 | -0.009 |
| ENSG00000196305 | E054 | 19.1403630 | 3.080299e-01 | 5.335490e-01 | 7.245928e-01 | 9 | 92256801 | 92258853 | 2053 | - | 1.203 | 1.374 | 0.601 |
| ENSG00000196305 | E055 | 703.6097885 | 1.537259e-04 | 3.736601e-01 | 6.070765e-01 | 9 | 92258854 | 92258998 | 145 | - | 2.802 | 2.799 | -0.011 |
| ENSG00000196305 | E056 | 633.0124888 | 1.156772e-04 | 2.589320e-04 | 3.312937e-03 | 9 | 92260151 | 92260234 | 84 | - | 2.769 | 2.719 | -0.166 |
| ENSG00000196305 | E057 | 0.6434498 | 1.938749e-02 | 2.564060e-01 | 9 | 92262136 | 92262232 | 97 | - | 0.253 | 0.000 | -13.525 | |
| ENSG00000196305 | E058 | 527.8273801 | 3.237735e-04 | 3.387570e-02 | 1.385175e-01 | 9 | 92262969 | 92263055 | 87 | - | 2.687 | 2.656 | -0.103 |
| ENSG00000196305 | E059 | 897.3467881 | 8.901229e-05 | 1.157926e-10 | 8.105626e-09 | 9 | 92264929 | 92265123 | 195 | - | 2.928 | 2.848 | -0.265 |
| ENSG00000196305 | E060 | 660.6210309 | 1.900724e-04 | 3.462214e-05 | 6.096046e-04 | 9 | 92265480 | 92265553 | 74 | - | 2.789 | 2.730 | -0.197 |
| ENSG00000196305 | E061 | 0.8086220 | 9.535189e-02 | 7.808205e-01 | 9 | 92267239 | 92267409 | 171 | - | 0.252 | 0.185 | -0.571 | |
| ENSG00000196305 | E062 | 791.2114534 | 1.270101e-04 | 4.197564e-06 | 9.899222e-05 | 9 | 92268174 | 92268300 | 127 | - | 2.868 | 2.809 | -0.195 |
| ENSG00000196305 | E063 | 2.8405096 | 8.068460e-03 | 6.247847e-01 | 7.872033e-01 | 9 | 92269878 | 92269884 | 7 | - | 0.528 | 0.618 | 0.409 |
| ENSG00000196305 | E064 | 714.4741303 | 1.236381e-04 | 2.563954e-06 | 6.476549e-05 | 9 | 92269885 | 92269978 | 94 | - | 2.826 | 2.763 | -0.210 |
| ENSG00000196305 | E065 | 370.6785180 | 2.143119e-04 | 9.702540e-03 | 5.683930e-02 | 9 | 92269979 | 92269983 | 5 | - | 2.535 | 2.490 | -0.151 |
| ENSG00000196305 | E066 | 701.4072265 | 9.843462e-04 | 5.755935e-05 | 9.407989e-04 | 9 | 92270985 | 92271076 | 92 | - | 2.820 | 2.745 | -0.250 |
| ENSG00000196305 | E067 | 745.7757111 | 2.788991e-03 | 1.225210e-03 | 1.161552e-02 | 9 | 92271533 | 92271655 | 123 | - | 2.848 | 2.767 | -0.269 |
| ENSG00000196305 | E068 | 0.7743180 | 1.750785e-02 | 7.359348e-01 | 9 | 92271759 | 92271902 | 144 | - | 0.253 | 0.183 | -0.592 | |
| ENSG00000196305 | E069 | 619.6789835 | 4.372428e-04 | 2.010110e-05 | 3.835969e-04 | 9 | 92274426 | 92274521 | 96 | - | 2.765 | 2.692 | -0.241 |
| ENSG00000196305 | E070 | 519.4917486 | 1.140646e-04 | 1.998008e-07 | 6.889497e-06 | 9 | 92277863 | 92277923 | 61 | - | 2.691 | 2.607 | -0.282 |
| ENSG00000196305 | E071 | 675.0814241 | 4.153711e-04 | 2.180075e-10 | 1.439452e-08 | 9 | 92278199 | 92278286 | 88 | - | 2.810 | 2.702 | -0.359 |
| ENSG00000196305 | E072 | 0.4514866 | 2.176816e-02 | 8.560593e-01 | 9 | 92280259 | 92280745 | 487 | - | 0.145 | 0.183 | 0.408 | |
| ENSG00000196305 | E073 | 696.6343426 | 1.398898e-03 | 3.597240e-07 | 1.157138e-05 | 9 | 92280746 | 92280893 | 148 | - | 2.824 | 2.714 | -0.368 |
| ENSG00000196305 | E074 | 707.0763935 | 7.774935e-04 | 4.831046e-11 | 3.652817e-09 | 9 | 92285722 | 92285839 | 118 | - | 2.834 | 2.710 | -0.413 |
| ENSG00000196305 | E075 | 7.5802688 | 6.422018e-03 | 3.319050e-01 | 5.707295e-01 | 9 | 92285840 | 92286535 | 696 | - | 0.920 | 0.797 | -0.478 |
| ENSG00000196305 | E076 | 553.8035939 | 4.737502e-04 | 3.395792e-11 | 2.650201e-09 | 9 | 92286536 | 92286618 | 83 | - | 2.729 | 2.602 | -0.420 |
| ENSG00000196305 | E077 | 10.2593893 | 6.408811e-01 | 2.780220e-01 | 5.181188e-01 | 9 | 92286619 | 92287790 | 1172 | - | 1.074 | 0.767 | -1.162 |
| ENSG00000196305 | E078 | 732.1006268 | 2.174725e-04 | 5.936802e-29 | 4.345713e-26 | 9 | 92287791 | 92287910 | 120 | - | 2.863 | 2.682 | -0.601 |
| ENSG00000196305 | E079 | 770.1835182 | 7.775217e-04 | 3.651684e-23 | 1.554235e-20 | 9 | 92288126 | 92288282 | 157 | - | 2.888 | 2.691 | -0.656 |
| ENSG00000196305 | E080 | 508.4886267 | 2.837900e-04 | 9.782180e-23 | 3.881400e-20 | 9 | 92289301 | 92289426 | 126 | - | 2.707 | 2.517 | -0.632 |
| ENSG00000196305 | E081 | 7.7662272 | 7.970957e-02 | 3.821531e-01 | 6.139809e-01 | 9 | 92290836 | 92290922 | 87 | - | 0.949 | 0.756 | -0.747 |
| ENSG00000196305 | E082 | 150.0816847 | 3.687278e-04 | 2.522047e-03 | 2.047624e-02 | 9 | 92293441 | 92293610 | 170 | - | 2.159 | 2.067 | -0.309 |
| ENSG00000196305 | E083 | 215.7889564 | 5.658087e-03 | 5.841180e-04 | 6.439670e-03 | 9 | 92293611 | 92293854 | 244 | - | 2.328 | 2.181 | -0.491 |