Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000153187
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000283179 | ENSG00000153187 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | HNRNPU | protein_coding | protein_coding | 382.3696 | 329.7775 | 425.3591 | 82.03748 | 17.96711 | 0.3671785 | 91.33059 | 85.90822 | 99.52583 | 20.471966 | 1.252796 | 0.2122519 | 0.24024167 | 0.2630000 | 0.23486667 | -0.028133333 | 7.187525e-01 | 1.771028e-14 | FALSE | TRUE |
| ENST00000440865 | ENSG00000153187 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | HNRNPU | protein_coding | protein_coding | 382.3696 | 329.7775 | 425.3591 | 82.03748 | 17.96711 | 0.3671785 | 105.11123 | 86.73759 | 106.72710 | 28.970645 | 8.467398 | 0.2991661 | 0.27289167 | 0.2469667 | 0.25016667 | 0.003200000 | 9.998905e-01 | 1.771028e-14 | FALSE | TRUE |
| ENST00000638475 | ENSG00000153187 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | HNRNPU | protein_coding | protein_coding | 382.3696 | 329.7775 | 425.3591 | 82.03748 | 17.96711 | 0.3671785 | 18.70030 | 27.70478 | 0.00000 | 11.712370 | 0.000000 | -11.4364397 | 0.04766667 | 0.0725000 | 0.00000000 | -0.072500000 | 1.771028e-14 | 1.771028e-14 | FALSE | TRUE |
| ENST00000640056 | ENSG00000153187 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | HNRNPU | protein_coding | nonsense_mediated_decay | 382.3696 | 329.7775 | 425.3591 | 82.03748 | 17.96711 | 0.3671785 | 105.03820 | 89.91077 | 143.30796 | 21.739341 | 10.653766 | 0.6724931 | 0.27379583 | 0.2746333 | 0.33596667 | 0.061333333 | 2.165312e-01 | 1.771028e-14 | FALSE | TRUE |
| MSTRG.3412.5 | ENSG00000153187 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | HNRNPU | protein_coding | 382.3696 | 329.7775 | 425.3591 | 82.03748 | 17.96711 | 0.3671785 | 26.13416 | 17.23722 | 24.75473 | 3.445619 | 3.774928 | 0.5219232 | 0.06754167 | 0.0653000 | 0.05873333 | -0.006566667 | 1.000000e+00 | 1.771028e-14 | TRUE | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000153187 | E001 | 0.3807181 | 3.067536e-02 | 1.000000e+00 | 1 | 244775127 | 244775172 | 46 | - | 0.116 | 0.127 | 0.147 | |
| ENSG00000153187 | E002 | 0.8451886 | 1.726718e-02 | 1.580862e-01 | 1 | 244778749 | 244778845 | 97 | - | 0.116 | 0.372 | 2.145 | |
| ENSG00000153187 | E003 | 10.8504253 | 2.171224e-01 | 2.272490e-01 | 4.620957e-01 | 1 | 244840638 | 244840686 | 49 | - | 0.954 | 1.179 | 0.819 |
| ENSG00000153187 | E004 | 742.2309343 | 1.566021e-01 | 1.561356e-01 | 3.711044e-01 | 1 | 244840687 | 244843040 | 2354 | - | 2.729 | 2.985 | 0.853 |
| ENSG00000153187 | E005 | 34.8395023 | 6.093643e-01 | 1.980762e-01 | 4.272239e-01 | 1 | 244843041 | 244843123 | 83 | - | 1.349 | 1.703 | 1.211 |
| ENSG00000153187 | E006 | 22.8184885 | 5.079368e-01 | 1.833464e-01 | 4.082553e-01 | 1 | 244843124 | 244843127 | 4 | - | 1.173 | 1.525 | 1.227 |
| ENSG00000153187 | E007 | 34.5970825 | 6.038411e-01 | 1.581961e-01 | 3.740805e-01 | 1 | 244843128 | 244843141 | 14 | - | 1.303 | 1.719 | 1.426 |
| ENSG00000153187 | E008 | 43.8281274 | 7.136766e-01 | 2.142732e-01 | 4.466821e-01 | 1 | 244843142 | 244843181 | 40 | - | 1.427 | 1.809 | 1.303 |
| ENSG00000153187 | E009 | 130.7209055 | 1.400190e+00 | 4.519339e-01 | 6.670847e-01 | 1 | 244843182 | 244843767 | 586 | - | 1.968 | 2.239 | 0.910 |
| ENSG00000153187 | E010 | 221.8344947 | 3.597524e-01 | 4.711268e-01 | 6.809553e-01 | 1 | 244843768 | 244845199 | 1432 | - | 2.279 | 2.412 | 0.443 |
| ENSG00000153187 | E011 | 47.7561465 | 9.177013e-02 | 9.589236e-01 | 9.813506e-01 | 1 | 244845200 | 244845246 | 47 | - | 1.682 | 1.694 | 0.040 |
| ENSG00000153187 | E012 | 48.3552179 | 1.423984e-01 | 7.079767e-01 | 8.405334e-01 | 1 | 244845247 | 244845251 | 5 | - | 1.643 | 1.740 | 0.329 |
| ENSG00000153187 | E013 | 73.9589930 | 1.047289e-01 | 7.545798e-01 | 8.694542e-01 | 1 | 244845252 | 244845344 | 93 | - | 1.841 | 1.907 | 0.222 |
| ENSG00000153187 | E014 | 3.7537717 | 1.046988e-02 | 6.339913e-02 | 2.103479e-01 | 1 | 244845345 | 244845686 | 342 | - | 0.793 | 0.528 | -1.133 |
| ENSG00000153187 | E015 | 2.2606710 | 5.681234e-02 | 8.758053e-01 | 9.391477e-01 | 1 | 244846486 | 244846603 | 118 | - | 0.498 | 0.529 | 0.151 |
| ENSG00000153187 | E016 | 49.3478050 | 9.295161e-02 | 9.418511e-01 | 9.731821e-01 | 1 | 244846604 | 244846624 | 21 | - | 1.695 | 1.708 | 0.044 |
| ENSG00000153187 | E017 | 69.4961581 | 9.543403e-02 | 7.846708e-01 | 8.873383e-01 | 1 | 244846625 | 244846706 | 82 | - | 1.822 | 1.873 | 0.170 |
| ENSG00000153187 | E018 | 67.0792343 | 1.203315e-01 | 3.416757e-01 | 5.794741e-01 | 1 | 244846707 | 244847001 | 295 | - | 1.899 | 1.747 | -0.513 |
| ENSG00000153187 | E019 | 36.4438371 | 1.687416e-01 | 1.483438e-01 | 3.599399e-01 | 1 | 244847002 | 244847053 | 52 | - | 1.682 | 1.411 | -0.927 |
| ENSG00000153187 | E020 | 28.4793952 | 1.244574e-01 | 1.898106e-01 | 4.167372e-01 | 1 | 244847054 | 244847101 | 48 | - | 1.564 | 1.335 | -0.788 |
| ENSG00000153187 | E021 | 227.4492868 | 1.114349e-01 | 1.709946e-01 | 3.918764e-01 | 1 | 244847102 | 244848787 | 1686 | - | 2.449 | 2.232 | -0.725 |
| ENSG00000153187 | E022 | 61.8520901 | 8.556617e-02 | 7.624048e-01 | 8.740376e-01 | 1 | 244848788 | 244848856 | 69 | - | 1.816 | 1.777 | -0.134 |
| ENSG00000153187 | E023 | 172.5266462 | 9.504822e-02 | 8.922154e-02 | 2.623201e-01 | 1 | 244848857 | 244850296 | 1440 | - | 2.345 | 2.086 | -0.865 |
| ENSG00000153187 | E024 | 886.4103093 | 4.436670e-03 | 4.765652e-07 | 1.483897e-05 | 1 | 244850297 | 244853405 | 3109 | - | 3.020 | 2.853 | -0.553 |
| ENSG00000153187 | E025 | 167.0014116 | 8.393193e-03 | 7.298607e-01 | 8.541568e-01 | 1 | 244853406 | 244853466 | 61 | - | 2.198 | 2.249 | 0.172 |
| ENSG00000153187 | E026 | 542.0352352 | 2.195358e-02 | 5.028640e-01 | 7.027574e-01 | 1 | 244853467 | 244853689 | 223 | - | 2.678 | 2.788 | 0.367 |
| ENSG00000153187 | E027 | 284.8236022 | 3.236089e-02 | 3.270818e-01 | 5.661953e-01 | 1 | 244853690 | 244853695 | 6 | - | 2.372 | 2.531 | 0.528 |
| ENSG00000153187 | E028 | 561.3381193 | 2.169430e-02 | 1.018303e-01 | 2.850453e-01 | 1 | 244853696 | 244853751 | 56 | - | 2.654 | 2.834 | 0.600 |
| ENSG00000153187 | E029 | 2155.4277636 | 3.775017e-03 | 1.704427e-01 | 3.910294e-01 | 1 | 244853752 | 244853938 | 187 | - | 3.295 | 3.371 | 0.250 |
| ENSG00000153187 | E030 | 1471.7172006 | 1.145820e-03 | 3.553673e-01 | 5.920453e-01 | 1 | 244853939 | 244853981 | 43 | - | 3.146 | 3.190 | 0.145 |
| ENSG00000153187 | E031 | 2195.4308586 | 9.452245e-04 | 1.954378e-03 | 1.676135e-02 | 1 | 244853982 | 244854189 | 208 | - | 3.302 | 3.380 | 0.260 |
| ENSG00000153187 | E032 | 544.0001418 | 2.402612e-03 | 5.548340e-04 | 6.172928e-03 | 1 | 244854190 | 244854197 | 8 | - | 2.670 | 2.798 | 0.427 |
| ENSG00000153187 | E033 | 506.1783689 | 3.195252e-03 | 2.938108e-03 | 2.302433e-02 | 1 | 244854198 | 244854199 | 2 | - | 2.640 | 2.766 | 0.421 |
| ENSG00000153187 | E034 | 508.8851764 | 2.990568e-03 | 3.319807e-03 | 2.532020e-02 | 1 | 244854200 | 244854205 | 6 | - | 2.644 | 2.767 | 0.409 |
| ENSG00000153187 | E035 | 1536.6550027 | 6.026290e-03 | 1.274313e-02 | 6.941037e-02 | 1 | 244854206 | 244854317 | 112 | - | 3.116 | 3.252 | 0.453 |
| ENSG00000153187 | E036 | 1657.8036000 | 5.773289e-03 | 1.038945e-01 | 2.886671e-01 | 1 | 244854318 | 244854381 | 64 | - | 3.168 | 3.268 | 0.333 |
| ENSG00000153187 | E037 | 2902.0748727 | 2.003335e-03 | 2.856712e-02 | 1.230423e-01 | 1 | 244854382 | 244854503 | 122 | - | 3.422 | 3.502 | 0.264 |
| ENSG00000153187 | E038 | 34.4462871 | 1.384179e-01 | 7.120406e-03 | 4.518717e-02 | 1 | 244854504 | 244854972 | 469 | - | 1.726 | 1.207 | -1.788 |
| ENSG00000153187 | E039 | 2277.2731752 | 1.184876e-04 | 1.712049e-05 | 3.348443e-04 | 1 | 244854973 | 244855003 | 31 | - | 3.328 | 3.390 | 0.206 |
| ENSG00000153187 | E040 | 2394.1964706 | 5.601893e-05 | 5.238393e-03 | 3.587818e-02 | 1 | 244855004 | 244855036 | 33 | - | 3.358 | 3.403 | 0.149 |
| ENSG00000153187 | E041 | 1864.6706946 | 8.565632e-04 | 7.687691e-02 | 2.385432e-01 | 1 | 244855037 | 244855044 | 8 | - | 3.247 | 3.295 | 0.159 |
| ENSG00000153187 | E042 | 18.5656624 | 3.658466e-02 | 5.403582e-01 | 7.292506e-01 | 1 | 244855045 | 244855423 | 379 | - | 1.253 | 1.329 | 0.263 |
| ENSG00000153187 | E043 | 2899.2478417 | 1.803954e-04 | 6.986418e-08 | 2.691312e-06 | 1 | 244855424 | 244855525 | 102 | - | 3.427 | 3.499 | 0.239 |
| ENSG00000153187 | E044 | 2527.0214839 | 3.472509e-04 | 3.213100e-14 | 4.368761e-12 | 1 | 244855526 | 244855608 | 83 | - | 3.348 | 3.457 | 0.363 |
| ENSG00000153187 | E045 | 11.5419710 | 1.398192e-02 | 6.759888e-01 | 8.201940e-01 | 1 | 244855609 | 244855903 | 295 | - | 1.057 | 1.124 | 0.240 |
| ENSG00000153187 | E046 | 3825.5633836 | 2.394158e-04 | 2.538107e-05 | 4.673920e-04 | 1 | 244855904 | 244856096 | 193 | - | 3.552 | 3.614 | 0.206 |
| ENSG00000153187 | E047 | 2272.5221068 | 4.717945e-04 | 1.320044e-01 | 3.349729e-01 | 1 | 244856097 | 244856158 | 62 | - | 3.335 | 3.378 | 0.140 |
| ENSG00000153187 | E048 | 9.7417132 | 4.007306e-03 | 1.898387e-01 | 4.167612e-01 | 1 | 244856159 | 244856282 | 124 | - | 0.938 | 1.099 | 0.590 |
| ENSG00000153187 | E049 | 7.9692667 | 4.697486e-03 | 6.933192e-01 | 8.312474e-01 | 1 | 244856283 | 244856456 | 174 | - | 0.968 | 0.944 | -0.089 |
| ENSG00000153187 | E050 | 3586.2168905 | 2.008666e-04 | 6.499733e-01 | 8.035551e-01 | 1 | 244856457 | 244856625 | 169 | - | 3.545 | 3.565 | 0.065 |
| ENSG00000153187 | E051 | 3030.7792186 | 6.462715e-05 | 4.881282e-02 | 1.768096e-01 | 1 | 244856728 | 244856856 | 129 | - | 3.479 | 3.488 | 0.029 |
| ENSG00000153187 | E052 | 7.9841650 | 1.053133e-01 | 1.537702e-01 | 3.677159e-01 | 1 | 244856857 | 244857261 | 405 | - | 0.793 | 1.065 | 1.027 |
| ENSG00000153187 | E053 | 11.1449535 | 8.155342e-03 | 7.964548e-01 | 8.942702e-01 | 1 | 244857262 | 244857597 | 336 | - | 1.082 | 1.074 | -0.027 |
| ENSG00000153187 | E054 | 3022.9669548 | 1.084399e-04 | 1.121218e-05 | 2.314656e-04 | 1 | 244857598 | 244857717 | 120 | - | 3.487 | 3.475 | -0.041 |
| ENSG00000153187 | E055 | 4.1802837 | 7.090678e-03 | 7.924365e-01 | 8.918645e-01 | 1 | 244857718 | 244858010 | 293 | - | 0.724 | 0.705 | -0.079 |
| ENSG00000153187 | E056 | 1706.6387940 | 5.796403e-05 | 5.034817e-08 | 2.006636e-06 | 1 | 244858011 | 244858018 | 8 | - | 3.246 | 3.219 | -0.090 |
| ENSG00000153187 | E057 | 1885.5178756 | 1.155025e-04 | 3.155694e-07 | 1.031984e-05 | 1 | 244858019 | 244858047 | 29 | - | 3.289 | 3.263 | -0.088 |
| ENSG00000153187 | E058 | 2881.5543254 | 1.761649e-04 | 4.184167e-05 | 7.150008e-04 | 1 | 244858048 | 244858164 | 117 | - | 3.467 | 3.452 | -0.049 |
| ENSG00000153187 | E059 | 2739.3897990 | 1.972100e-04 | 8.646753e-03 | 5.224941e-02 | 1 | 244858165 | 244858274 | 110 | - | 3.439 | 3.436 | -0.009 |
| ENSG00000153187 | E060 | 0.7956878 | 6.299817e-01 | 8.437974e-01 | 1 | 244858275 | 244858728 | 454 | - | 0.293 | 0.214 | -0.591 | |
| ENSG00000153187 | E061 | 2772.0983009 | 1.547207e-04 | 4.032426e-21 | 1.358728e-18 | 1 | 244858729 | 244858835 | 107 | - | 3.472 | 3.410 | -0.207 |
| ENSG00000153187 | E062 | 1570.4068988 | 6.976342e-05 | 4.442487e-44 | 1.033475e-40 | 1 | 244858836 | 244858841 | 6 | - | 3.248 | 3.136 | -0.373 |
| ENSG00000153187 | E063 | 14.4052303 | 1.667263e-02 | 7.651468e-01 | 8.757390e-01 | 1 | 244858842 | 244859274 | 433 | - | 1.190 | 1.174 | -0.059 |
| ENSG00000153187 | E064 | 2840.9192843 | 3.325561e-04 | 8.928393e-24 | 3.979650e-21 | 1 | 244859275 | 244859374 | 100 | - | 3.495 | 3.406 | -0.295 |
| ENSG00000153187 | E065 | 17.8557791 | 9.769064e-03 | 3.093820e-02 | 1.301820e-01 | 1 | 244859375 | 244860334 | 960 | - | 1.353 | 1.172 | -0.636 |
| ENSG00000153187 | E066 | 1633.5538986 | 1.585723e-04 | 1.218755e-29 | 9.407844e-27 | 1 | 244860335 | 244860352 | 18 | - | 3.260 | 3.162 | -0.326 |
| ENSG00000153187 | E067 | 1449.6592231 | 3.950109e-04 | 6.115920e-23 | 2.496692e-20 | 1 | 244860353 | 244860357 | 5 | - | 3.213 | 3.101 | -0.373 |
| ENSG00000153187 | E068 | 2406.7611573 | 4.735485e-05 | 1.588792e-41 | 2.932755e-38 | 1 | 244860358 | 244860474 | 117 | - | 3.420 | 3.338 | -0.275 |
| ENSG00000153187 | E069 | 34.5709349 | 1.022659e-01 | 3.705428e-03 | 2.750413e-02 | 1 | 244860475 | 244860760 | 286 | - | 1.723 | 1.229 | -1.701 |
| ENSG00000153187 | E070 | 123.1627144 | 1.200482e-01 | 2.137774e-02 | 1.005849e-01 | 1 | 244860761 | 244862460 | 1700 | - | 2.240 | 1.848 | -1.315 |
| ENSG00000153187 | E071 | 1508.2533695 | 4.559208e-04 | 1.217689e-07 | 4.428084e-06 | 1 | 244862461 | 244862534 | 74 | - | 3.204 | 3.152 | -0.172 |
| ENSG00000153187 | E072 | 5.7754340 | 3.186200e-02 | 4.599432e-02 | 1.700312e-01 | 1 | 244862535 | 244862618 | 84 | - | 0.938 | 0.645 | -1.166 |
| ENSG00000153187 | E073 | 1283.8466123 | 4.210651e-03 | 7.817995e-01 | 8.857132e-01 | 1 | 244862619 | 244862730 | 112 | - | 3.105 | 3.114 | 0.029 |
| ENSG00000153187 | E074 | 106.0092906 | 2.846164e-02 | 2.588379e-03 | 2.089094e-02 | 1 | 244862731 | 244863106 | 376 | - | 2.140 | 1.868 | -0.913 |
| ENSG00000153187 | E075 | 155.5873942 | 1.037590e-02 | 3.885397e-03 | 2.850114e-02 | 1 | 244863617 | 244863673 | 57 | - | 2.090 | 2.290 | 0.670 |
| ENSG00000153187 | E076 | 3760.6007189 | 5.803570e-03 | 4.785115e-02 | 1.746627e-01 | 1 | 244863674 | 244864813 | 1140 | - | 3.529 | 3.620 | 0.302 |