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_2hA | HEK293_TMG_2hB | IARS1 | protein_coding | protein_coding | 135.7931 | 88.93402 | 196.9287 | 8.969213 | 6.474985 | 1.146777 | 13.452978 | 4.679282 | 29.007879 | 4.679282 | 4.959289 | 2.62950297 | 0.08366250 | 0.05143333 | 0.14630000 | 0.09486667 | 1.156037e-01 | 6.941771e-30 | FALSE | TRUE |
| ENST00000443024 | ENSG00000196305 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | IARS1 | protein_coding | protein_coding | 135.7931 | 88.93402 | 196.9287 | 8.969213 | 6.474985 | 1.146777 | 57.067095 | 21.272185 | 101.036620 | 1.372190 | 1.762864 | 2.24730284 | 0.37237083 | 0.24140000 | 0.51363333 | 0.27223333 | 1.469081e-24 | 6.941771e-30 | FALSE | TRUE |
| ENST00000627121 | ENSG00000196305 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | IARS1 | protein_coding | nonsense_mediated_decay | 135.7931 | 88.93402 | 196.9287 | 8.969213 | 6.474985 | 1.146777 | 6.965030 | 6.996632 | 7.269591 | 2.680251 | 1.452266 | 0.05513626 | 0.06014583 | 0.07396667 | 0.03710000 | -0.03686667 | 5.869680e-01 | 6.941771e-30 | FALSE | TRUE |
| ENST00000684445 | ENSG00000196305 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | IARS1 | protein_coding | nonsense_mediated_decay | 135.7931 | 88.93402 | 196.9287 | 8.969213 | 6.474985 | 1.146777 | 9.828224 | 4.507086 | 14.874085 | 1.190009 | 1.600027 | 1.72030631 | 0.06026667 | 0.05146667 | 0.07543333 | 0.02396667 | 5.050790e-01 | 6.941771e-30 | TRUE | TRUE |
| MSTRG.32984.38 | ENSG00000196305 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | IARS1 | protein_coding | 135.7931 | 88.93402 | 196.9287 | 8.969213 | 6.474985 | 1.146777 | 23.219238 | 41.198460 | 8.394988 | 5.848254 | 1.299660 | -2.29362295 | 0.23050000 | 0.46196667 | 0.04233333 | -0.41963333 | 6.941771e-30 | 6.941771e-30 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000196305 | E001 | 0.3634088 | 3.579563e-01 | 8.706187e-02 | 9 | 92210207 | 92210210 | 4 | - | 0.000 | 0.319 | 12.463 | |
| ENSG00000196305 | E002 | 5.6548802 | 2.997422e-03 | 1.117320e-02 | 3.158167e-02 | 9 | 92210211 | 92210237 | 27 | - | 0.657 | 1.006 | 1.368 |
| ENSG00000196305 | E003 | 7.2446805 | 2.415724e-03 | 8.803910e-03 | 2.579373e-02 | 9 | 92210238 | 92210239 | 2 | - | 0.758 | 1.090 | 1.258 |
| ENSG00000196305 | E004 | 7.3919295 | 2.235891e-03 | 1.201692e-02 | 3.357197e-02 | 9 | 92210240 | 92210242 | 3 | - | 0.772 | 1.090 | 1.199 |
| ENSG00000196305 | E005 | 26.8452515 | 6.508155e-03 | 8.958287e-14 | 2.564401e-12 | 9 | 92210243 | 92210344 | 102 | - | 1.140 | 1.736 | 2.063 |
| ENSG00000196305 | E006 | 45.0056816 | 2.259262e-03 | 3.726728e-07 | 3.381957e-06 | 9 | 92210345 | 92210348 | 4 | - | 1.512 | 1.826 | 1.068 |
| ENSG00000196305 | E007 | 273.2670959 | 7.807854e-03 | 2.668090e-16 | 1.090767e-14 | 9 | 92210349 | 92210417 | 69 | - | 2.227 | 2.652 | 1.419 |
| ENSG00000196305 | E008 | 325.7255204 | 6.412710e-03 | 9.909188e-22 | 7.643591e-20 | 9 | 92210418 | 92210435 | 18 | - | 2.290 | 2.738 | 1.494 |
| ENSG00000196305 | E009 | 2544.0121799 | 4.193001e-03 | 1.265550e-18 | 6.883569e-17 | 9 | 92210436 | 92210889 | 454 | - | 3.259 | 3.552 | 0.974 |
| ENSG00000196305 | E010 | 1.2062305 | 1.152939e-01 | 5.938607e-01 | 7.161689e-01 | 9 | 92220492 | 92220591 | 100 | - | 0.297 | 0.414 | 0.702 |
| ENSG00000196305 | E011 | 1572.6186181 | 2.465034e-03 | 1.650233e-15 | 6.063452e-14 | 9 | 92222520 | 92222672 | 153 | - | 3.082 | 3.305 | 0.741 |
| ENSG00000196305 | E012 | 1172.8089128 | 2.045576e-03 | 9.738149e-14 | 2.773813e-12 | 9 | 92223346 | 92223429 | 84 | - | 2.963 | 3.166 | 0.675 |
| ENSG00000196305 | E013 | 925.3175629 | 2.005088e-03 | 5.721238e-12 | 1.238852e-10 | 9 | 92223430 | 92223489 | 60 | - | 2.864 | 3.059 | 0.646 |
| ENSG00000196305 | E014 | 33.4583195 | 1.481407e-03 | 3.603614e-04 | 1.620330e-03 | 9 | 92223490 | 92225908 | 2419 | - | 1.408 | 1.660 | 0.860 |
| ENSG00000196305 | E015 | 3.0247372 | 5.457021e-03 | 4.079661e-01 | 5.515565e-01 | 9 | 92228687 | 92229000 | 314 | - | 0.527 | 0.678 | 0.673 |
| ENSG00000196305 | E016 | 1155.8216836 | 9.924582e-04 | 2.761299e-25 | 3.088074e-23 | 9 | 92229001 | 92229126 | 126 | - | 2.952 | 3.168 | 0.717 |
| ENSG00000196305 | E017 | 3.8521438 | 2.394571e-02 | 4.465698e-01 | 5.880563e-01 | 9 | 92229127 | 92230365 | 1239 | - | 0.618 | 0.764 | 0.612 |
| ENSG00000196305 | E018 | 0.4449813 | 2.126227e-02 | 8.363484e-01 | 8.976636e-01 | 9 | 92240289 | 92240298 | 10 | - | 0.144 | 0.187 | 0.449 |
| ENSG00000196305 | E019 | 1.0256721 | 2.748037e-01 | 5.710815e-01 | 6.974417e-01 | 9 | 92240299 | 92240583 | 285 | - | 0.338 | 0.185 | -1.150 |
| ENSG00000196305 | E020 | 0.5901540 | 2.003304e-02 | 9.349068e-01 | 9.630332e-01 | 9 | 92240584 | 92240642 | 59 | - | 0.202 | 0.187 | -0.136 |
| ENSG00000196305 | E021 | 18.1157301 | 3.781699e-02 | 2.967441e-01 | 4.380033e-01 | 9 | 92240643 | 92240691 | 49 | - | 1.192 | 1.338 | 0.515 |
| ENSG00000196305 | E022 | 0.3666179 | 3.832178e-02 | 4.827737e-01 | 6.208888e-01 | 9 | 92240692 | 92240762 | 71 | - | 0.078 | 0.187 | 1.455 |
| ENSG00000196305 | E023 | 1.7724220 | 1.293650e-02 | 7.123285e-02 | 1.453842e-01 | 9 | 92240763 | 92240855 | 93 | - | 0.298 | 0.626 | 1.713 |
| ENSG00000196305 | E024 | 895.6649048 | 8.801842e-05 | 4.585793e-31 | 8.293453e-29 | 9 | 92240856 | 92240961 | 106 | - | 2.860 | 3.035 | 0.583 |
| ENSG00000196305 | E025 | 1324.4925207 | 7.058167e-05 | 3.194660e-26 | 3.879608e-24 | 9 | 92242154 | 92242330 | 177 | - | 3.043 | 3.182 | 0.463 |
| ENSG00000196305 | E026 | 2.2248033 | 1.414359e-02 | 2.774441e-02 | 6.750700e-02 | 9 | 92242331 | 92242613 | 283 | - | 0.339 | 0.724 | 1.862 |
| ENSG00000196305 | E027 | 2.2508276 | 6.602630e-03 | 8.650929e-02 | 1.698221e-01 | 9 | 92242614 | 92242687 | 74 | - | 0.376 | 0.678 | 1.450 |
| ENSG00000196305 | E028 | 1.6648277 | 1.862133e-02 | 2.400032e-01 | 3.741412e-01 | 9 | 92242688 | 92243215 | 528 | - | 0.339 | 0.566 | 1.182 |
| ENSG00000196305 | E029 | 1050.4404468 | 6.991330e-04 | 5.089728e-08 | 5.477978e-07 | 9 | 92243216 | 92243311 | 96 | - | 2.950 | 3.066 | 0.388 |
| ENSG00000196305 | E030 | 2.1819169 | 6.578196e-03 | 5.354455e-01 | 6.672710e-01 | 9 | 92243312 | 92243449 | 138 | - | 0.443 | 0.567 | 0.602 |
| ENSG00000196305 | E031 | 0.3686942 | 4.277965e-02 | 4.844102e-01 | 6.224264e-01 | 9 | 92243475 | 92243799 | 325 | - | 0.078 | 0.187 | 1.456 |
| ENSG00000196305 | E032 | 1115.6485878 | 1.037438e-04 | 3.714192e-08 | 4.106463e-07 | 9 | 92244959 | 92245071 | 113 | - | 2.985 | 3.077 | 0.305 |
| ENSG00000196305 | E033 | 2.9526148 | 5.968992e-02 | 8.242426e-02 | 1.633269e-01 | 9 | 92245072 | 92245101 | 30 | - | 0.443 | 0.767 | 1.452 |
| ENSG00000196305 | E034 | 1310.0838236 | 7.752198e-05 | 2.070699e-03 | 7.443226e-03 | 9 | 92247377 | 92247551 | 175 | - | 3.066 | 3.125 | 0.197 |
| ENSG00000196305 | E035 | 2.1337555 | 6.179792e-02 | 2.104644e-01 | 3.390810e-01 | 9 | 92247552 | 92248597 | 1046 | - | 0.376 | 0.627 | 1.234 |
| ENSG00000196305 | E036 | 802.8732747 | 1.103881e-04 | 9.203172e-01 | 9.536676e-01 | 9 | 92249858 | 92249941 | 84 | - | 2.864 | 2.891 | 0.088 |
| ENSG00000196305 | E037 | 4.6294897 | 6.303442e-03 | 6.575247e-01 | 7.668632e-01 | 9 | 92249942 | 92249991 | 50 | - | 0.727 | 0.679 | -0.200 |
| ENSG00000196305 | E038 | 1.1145283 | 3.074665e-02 | 1.208329e-01 | 2.211369e-01 | 9 | 92249992 | 92250186 | 195 | - | 0.202 | 0.498 | 1.861 |
| ENSG00000196305 | E039 | 975.6807288 | 2.250173e-04 | 1.744787e-02 | 4.592989e-02 | 9 | 92250187 | 92250284 | 98 | - | 2.960 | 2.951 | -0.031 |
| ENSG00000196305 | E040 | 492.0369487 | 2.172206e-03 | 1.107123e-02 | 3.133740e-02 | 9 | 92250285 | 92250289 | 5 | - | 2.674 | 2.624 | -0.167 |
| ENSG00000196305 | E041 | 2.8838204 | 8.438137e-03 | 4.954181e-01 | 6.322235e-01 | 9 | 92250290 | 92250712 | 423 | - | 0.597 | 0.498 | -0.457 |
| ENSG00000196305 | E042 | 754.2923147 | 1.851315e-04 | 2.301398e-04 | 1.092331e-03 | 9 | 92250713 | 92250759 | 47 | - | 2.855 | 2.822 | -0.109 |
| ENSG00000196305 | E043 | 896.2631132 | 8.311504e-05 | 1.468951e-05 | 9.392432e-05 | 9 | 92250760 | 92250834 | 75 | - | 2.930 | 2.897 | -0.112 |
| ENSG00000196305 | E044 | 9.5815149 | 2.035705e-03 | 7.894665e-01 | 8.652559e-01 | 9 | 92250835 | 92251807 | 973 | - | 0.976 | 1.029 | 0.194 |
| ENSG00000196305 | E045 | 831.4807161 | 8.516550e-05 | 5.207922e-04 | 2.237550e-03 | 9 | 92251808 | 92251885 | 78 | - | 2.894 | 2.871 | -0.079 |
| ENSG00000196305 | E046 | 18.4859998 | 3.868826e-02 | 7.603937e-01 | 8.445268e-01 | 9 | 92251886 | 92252749 | 864 | - | 1.264 | 1.263 | -0.003 |
| ENSG00000196305 | E047 | 761.6506297 | 2.066081e-04 | 1.263067e-02 | 3.503994e-02 | 9 | 92253362 | 92253446 | 85 | - | 2.853 | 2.838 | -0.049 |
| ENSG00000196305 | E048 | 407.3375426 | 2.047878e-04 | 5.344291e-02 | 1.152776e-01 | 9 | 92253447 | 92253453 | 7 | - | 2.581 | 2.566 | -0.049 |
| ENSG00000196305 | E049 | 160.8707586 | 4.358258e-04 | 3.178872e-06 | 2.364459e-05 | 9 | 92253454 | 92255534 | 2081 | - | 2.210 | 2.079 | -0.439 |
| ENSG00000196305 | E050 | 14.2398618 | 6.648386e-03 | 2.433444e-01 | 3.780960e-01 | 9 | 92255535 | 92255604 | 70 | - | 1.175 | 1.071 | -0.374 |
| ENSG00000196305 | E051 | 65.7728715 | 4.632678e-03 | 3.717069e-03 | 1.234616e-02 | 9 | 92255605 | 92256679 | 1075 | - | 1.831 | 1.675 | -0.525 |
| ENSG00000196305 | E052 | 418.6455781 | 1.441521e-04 | 3.503414e-03 | 1.173485e-02 | 9 | 92256680 | 92256683 | 4 | - | 2.599 | 2.566 | -0.110 |
| ENSG00000196305 | E053 | 799.4563808 | 3.410536e-04 | 4.897745e-03 | 1.564535e-02 | 9 | 92256684 | 92256800 | 117 | - | 2.877 | 2.854 | -0.075 |
| ENSG00000196305 | E054 | 12.9209519 | 3.244428e-03 | 9.600407e-01 | 9.788956e-01 | 9 | 92256801 | 92258853 | 2053 | - | 1.108 | 1.126 | 0.066 |
| ENSG00000196305 | E055 | 860.0376377 | 4.399776e-04 | 1.273851e-04 | 6.473024e-04 | 9 | 92258854 | 92258998 | 145 | - | 2.914 | 2.873 | -0.135 |
| ENSG00000196305 | E056 | 759.9914609 | 3.829942e-04 | 6.592046e-08 | 6.936477e-07 | 9 | 92260151 | 92260234 | 84 | - | 2.868 | 2.800 | -0.227 |
| ENSG00000196305 | E057 | 1.1501176 | 1.374696e-02 | 9.671626e-01 | 9.834197e-01 | 9 | 92262136 | 92262232 | 97 | - | 0.298 | 0.318 | 0.131 |
| ENSG00000196305 | E058 | 647.2667656 | 5.057962e-04 | 4.804039e-07 | 4.263613e-06 | 9 | 92262969 | 92263055 | 87 | - | 2.800 | 2.729 | -0.235 |
| ENSG00000196305 | E059 | 1068.3381962 | 3.173630e-04 | 1.865932e-15 | 6.811082e-14 | 9 | 92264929 | 92265123 | 195 | - | 3.023 | 2.929 | -0.313 |
| ENSG00000196305 | E060 | 763.4131771 | 6.456604e-04 | 6.228169e-15 | 2.116047e-13 | 9 | 92265480 | 92265553 | 74 | - | 2.885 | 2.758 | -0.423 |
| ENSG00000196305 | E061 | 1.2284810 | 2.891015e-02 | 8.536831e-01 | 9.094631e-01 | 9 | 92267239 | 92267409 | 171 | - | 0.339 | 0.317 | -0.137 |
| ENSG00000196305 | E062 | 943.4469192 | 6.201859e-04 | 2.445885e-16 | 1.004260e-14 | 9 | 92268174 | 92268300 | 127 | - | 2.976 | 2.852 | -0.413 |
| ENSG00000196305 | E063 | 1.7015498 | 8.088063e-03 | 4.563859e-01 | 5.968215e-01 | 9 | 92269878 | 92269884 | 7 | - | 0.443 | 0.317 | -0.719 |
| ENSG00000196305 | E064 | 819.2489477 | 8.777731e-05 | 1.389916e-23 | 1.311985e-21 | 9 | 92269885 | 92269978 | 94 | - | 2.915 | 2.794 | -0.403 |
| ENSG00000196305 | E065 | 425.8019151 | 2.342142e-04 | 3.718456e-09 | 4.957427e-08 | 9 | 92269979 | 92269983 | 5 | - | 2.625 | 2.530 | -0.320 |
| ENSG00000196305 | E066 | 790.0423287 | 9.633218e-05 | 1.417778e-23 | 1.336953e-21 | 9 | 92270985 | 92271076 | 92 | - | 2.900 | 2.776 | -0.414 |
| ENSG00000196305 | E067 | 852.7901135 | 1.139316e-04 | 5.321357e-30 | 8.976983e-28 | 9 | 92271533 | 92271655 | 123 | - | 2.937 | 2.795 | -0.474 |
| ENSG00000196305 | E068 | 0.7300161 | 5.314503e-02 | 1.597721e-01 | 2.748120e-01 | 9 | 92271759 | 92271902 | 144 | - | 0.297 | 0.000 | -12.164 |
| ENSG00000196305 | E069 | 684.4948811 | 1.229447e-03 | 1.687091e-12 | 3.982237e-11 | 9 | 92274426 | 92274521 | 96 | - | 2.841 | 2.699 | -0.473 |
| ENSG00000196305 | E070 | 575.7774462 | 2.573012e-03 | 7.789440e-09 | 9.795459e-08 | 9 | 92277863 | 92277923 | 61 | - | 2.769 | 2.615 | -0.512 |
| ENSG00000196305 | E071 | 737.7512578 | 3.769719e-03 | 7.062334e-08 | 7.382541e-07 | 9 | 92278199 | 92278286 | 88 | - | 2.878 | 2.716 | -0.537 |
| ENSG00000196305 | E072 | 0.0000000 | 9 | 92280259 | 92280745 | 487 | - | ||||||
| ENSG00000196305 | E073 | 789.9866569 | 3.051586e-03 | 4.928653e-10 | 7.723704e-09 | 9 | 92280746 | 92280893 | 148 | - | 2.910 | 2.736 | -0.577 |
| ENSG00000196305 | E074 | 808.2398782 | 5.408226e-03 | 1.229187e-07 | 1.227159e-06 | 9 | 92285722 | 92285839 | 118 | - | 2.923 | 2.735 | -0.627 |
| ENSG00000196305 | E075 | 7.0254039 | 2.852909e-03 | 8.921807e-01 | 9.351219e-01 | 9 | 92285840 | 92286535 | 696 | - | 0.863 | 0.903 | 0.151 |
| ENSG00000196305 | E076 | 638.8474734 | 5.177423e-03 | 6.555124e-07 | 5.664592e-06 | 9 | 92286536 | 92286618 | 83 | - | 2.818 | 2.644 | -0.579 |
| ENSG00000196305 | E077 | 6.9869837 | 2.905764e-03 | 6.712294e-01 | 7.775055e-01 | 9 | 92286619 | 92287790 | 1172 | - | 0.875 | 0.840 | -0.133 |
| ENSG00000196305 | E078 | 822.4086544 | 5.196717e-03 | 6.145445e-09 | 7.889917e-08 | 9 | 92287791 | 92287910 | 120 | - | 2.934 | 2.729 | -0.682 |
| ENSG00000196305 | E079 | 885.3242262 | 4.123810e-03 | 5.135077e-15 | 1.763372e-13 | 9 | 92288126 | 92288282 | 157 | - | 2.976 | 2.721 | -0.851 |
| ENSG00000196305 | E080 | 593.8217538 | 5.650130e-03 | 6.497929e-11 | 1.182075e-09 | 9 | 92289301 | 92289426 | 126 | - | 2.803 | 2.552 | -0.835 |
| ENSG00000196305 | E081 | 8.0292069 | 4.141182e-03 | 3.841149e-01 | 5.282972e-01 | 9 | 92290836 | 92290922 | 87 | - | 0.958 | 0.872 | -0.324 |
| ENSG00000196305 | E082 | 192.9016170 | 2.845807e-02 | 1.309791e-02 | 3.613509e-02 | 9 | 92293441 | 92293610 | 170 | - | 2.303 | 2.110 | -0.646 |
| ENSG00000196305 | E083 | 266.1206121 | 3.147478e-03 | 8.456700e-12 | 1.782484e-10 | 9 | 92293611 | 92293854 | 244 | - | 2.453 | 2.209 | -0.813 |