Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000122218
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000368069 | ENSG00000122218 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | COPA | protein_coding | protein_coding | 72.33282 | 73.35179 | 72.50416 | 11.83941 | 0.7533574 | -0.01676595 | 11.187920 | 9.91643386 | 11.137553 | 3.24033647 | 2.3642936 | 0.1673796 | 0.15375000 | 0.133433333 | 0.15353333 | 0.02010000 | 8.710576e-01 | 6.074002e-46 | FALSE | TRUE |
| ENST00000545284 | ENSG00000122218 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | COPA | protein_coding | retained_intron | 72.33282 | 73.35179 | 72.50416 | 11.83941 | 0.7533574 | -0.01676595 | 7.091427 | 10.32290006 | 5.183410 | 1.77396535 | 0.7834028 | -0.9924911 | 0.09652500 | 0.141500000 | 0.07133333 | -0.07016667 | 5.356895e-03 | 6.074002e-46 | FALSE | FALSE |
| ENST00000647899 | ENSG00000122218 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | COPA | protein_coding | protein_coding | 72.33282 | 73.35179 | 72.50416 | 11.83941 | 0.7533574 | -0.01676595 | 4.182075 | 0.00000000 | 6.931835 | 0.00000000 | 0.6532317 | 9.4391733 | 0.05725417 | 0.000000000 | 0.09550000 | 0.09550000 | 6.074002e-46 | 6.074002e-46 | FALSE | TRUE |
| ENST00000648280 | ENSG00000122218 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | COPA | protein_coding | protein_coding | 72.33282 | 73.35179 | 72.50416 | 11.83941 | 0.7533574 | -0.01676595 | 5.461514 | 14.28548202 | 0.000000 | 4.40364978 | 0.0000000 | -10.4813436 | 0.07382917 | 0.191200000 | 0.00000000 | -0.19120000 | 1.577536e-28 | 6.074002e-46 | FALSE | TRUE |
| ENST00000648501 | ENSG00000122218 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | COPA | protein_coding | nonsense_mediated_decay | 72.33282 | 73.35179 | 72.50416 | 11.83941 | 0.7533574 | -0.01676595 | 9.649368 | 3.73345096 | 13.610620 | 1.81645543 | 1.3253693 | 1.8633516 | 0.13545417 | 0.047800000 | 0.18800000 | 0.14020000 | 5.879745e-03 | 6.074002e-46 | FALSE | TRUE |
| ENST00000648805 | ENSG00000122218 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | COPA | protein_coding | nonsense_mediated_decay | 72.33282 | 73.35179 | 72.50416 | 11.83941 | 0.7533574 | -0.01676595 | 8.176714 | 8.45039757 | 6.528800 | 2.02607696 | 0.5087969 | -0.3716997 | 0.11208333 | 0.111800000 | 0.09016667 | -0.02163333 | 4.984993e-01 | 6.074002e-46 | FALSE | TRUE |
| ENST00000649676 | ENSG00000122218 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | COPA | protein_coding | protein_coding | 72.33282 | 73.35179 | 72.50416 | 11.83941 | 0.7533574 | -0.01676595 | 9.579691 | 17.30675299 | 5.627716 | 2.40005126 | 1.3825292 | -1.6189858 | 0.13194167 | 0.238666667 | 0.07726667 | -0.16140000 | 5.118339e-04 | 6.074002e-46 | FALSE | TRUE |
| ENST00000649787 | ENSG00000122218 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | COPA | protein_coding | protein_coding | 72.33282 | 73.35179 | 72.50416 | 11.83941 | 0.7533574 | -0.01676595 | 7.351247 | 2.61578173 | 11.566651 | 1.14010719 | 1.3498068 | 2.1403991 | 0.10310833 | 0.039533333 | 0.15990000 | 0.12036667 | 9.341419e-02 | 6.074002e-46 | FALSE | TRUE |
| ENST00000696210 | ENSG00000122218 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | COPA | protein_coding | retained_intron | 72.33282 | 73.35179 | 72.50416 | 11.83941 | 0.7533574 | -0.01676595 | 2.778696 | 0.09771894 | 5.741315 | 0.05700395 | 0.4660257 | 5.7385480 | 0.03817500 | 0.001133333 | 0.07913333 | 0.07800000 | 1.390810e-36 | 6.074002e-46 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000122218 | E001 | 5.0041291 | 0.2034328903 | 2.679306e-01 | 4.063162e-01 | 1 | 160288594 | 160288658 | 65 | - | 0.605 | 0.876 | 1.106 |
| ENSG00000122218 | E002 | 5.4824198 | 0.1392964338 | 1.307889e-01 | 2.352509e-01 | 1 | 160288659 | 160288685 | 27 | - | 0.605 | 0.925 | 1.295 |
| ENSG00000122218 | E003 | 47.2697164 | 0.0284802872 | 3.651449e-01 | 5.094833e-01 | 1 | 160288686 | 160289200 | 515 | - | 1.629 | 1.726 | 0.328 |
| ENSG00000122218 | E004 | 25.3560185 | 0.0073616295 | 4.886481e-01 | 6.261866e-01 | 1 | 160289201 | 160289272 | 72 | - | 1.394 | 1.447 | 0.182 |
| ENSG00000122218 | E005 | 29.1823655 | 0.0034372796 | 1.190505e-03 | 4.608921e-03 | 1 | 160289273 | 160289290 | 18 | - | 1.345 | 1.574 | 0.788 |
| ENSG00000122218 | E006 | 26.1710664 | 0.0007715074 | 1.861179e-05 | 1.163218e-04 | 1 | 160289291 | 160289292 | 2 | - | 1.249 | 1.549 | 1.038 |
| ENSG00000122218 | E007 | 25.9130008 | 0.0007856220 | 1.222994e-05 | 7.961669e-05 | 1 | 160289293 | 160289294 | 2 | - | 1.241 | 1.549 | 1.067 |
| ENSG00000122218 | E008 | 30.0218844 | 0.0024579178 | 9.790128e-06 | 6.523919e-05 | 1 | 160289295 | 160289300 | 6 | - | 1.303 | 1.609 | 1.054 |
| ENSG00000122218 | E009 | 231.5913934 | 0.0061312194 | 5.329601e-15 | 1.826147e-13 | 1 | 160289301 | 160289353 | 53 | - | 2.135 | 2.489 | 1.182 |
| ENSG00000122218 | E010 | 711.5108060 | 0.0042647009 | 4.573555e-22 | 3.669827e-20 | 1 | 160289354 | 160289614 | 261 | - | 2.640 | 2.966 | 1.085 |
| ENSG00000122218 | E011 | 250.1618861 | 0.0043730546 | 1.299413e-14 | 4.208032e-13 | 1 | 160289615 | 160289626 | 12 | - | 2.205 | 2.511 | 1.021 |
| ENSG00000122218 | E012 | 550.3560369 | 0.0029195175 | 3.256111e-25 | 3.624327e-23 | 1 | 160289627 | 160289780 | 154 | - | 2.539 | 2.853 | 1.048 |
| ENSG00000122218 | E013 | 226.2812791 | 0.0006250552 | 5.408840e-32 | 1.041350e-29 | 1 | 160289781 | 160289795 | 15 | - | 2.155 | 2.476 | 1.073 |
| ENSG00000122218 | E014 | 1002.9549129 | 0.0012457725 | 5.687382e-27 | 7.319683e-25 | 1 | 160289796 | 160290216 | 421 | - | 2.871 | 3.083 | 0.704 |
| ENSG00000122218 | E015 | 3.5277174 | 0.2960228615 | 8.598559e-01 | 9.136177e-01 | 1 | 160290217 | 160290491 | 275 | - | 0.637 | 0.686 | 0.209 |
| ENSG00000122218 | E016 | 684.0868051 | 0.0005798940 | 1.733966e-11 | 3.469891e-10 | 1 | 160290492 | 160290686 | 195 | - | 2.770 | 2.886 | 0.387 |
| ENSG00000122218 | E017 | 1.2177701 | 0.0105791977 | 9.288767e-01 | 9.592627e-01 | 1 | 160291245 | 160291334 | 90 | - | 0.369 | 0.354 | -0.087 |
| ENSG00000122218 | E018 | 599.1737463 | 0.0001111260 | 1.544057e-14 | 4.955395e-13 | 1 | 160291335 | 160291496 | 162 | - | 2.714 | 2.829 | 0.383 |
| ENSG00000122218 | E019 | 472.5230680 | 0.0001529527 | 4.435277e-07 | 3.964191e-06 | 1 | 160291819 | 160291929 | 111 | - | 2.630 | 2.715 | 0.284 |
| ENSG00000122218 | E020 | 558.6544564 | 0.0001178413 | 3.772970e-08 | 4.166829e-07 | 1 | 160292012 | 160292198 | 187 | - | 2.702 | 2.787 | 0.282 |
| ENSG00000122218 | E021 | 413.9921498 | 0.0009719768 | 1.351724e-03 | 5.148891e-03 | 1 | 160292484 | 160292560 | 77 | - | 2.580 | 2.650 | 0.233 |
| ENSG00000122218 | E022 | 393.4896608 | 0.0002166734 | 8.788227e-04 | 3.540012e-03 | 1 | 160292561 | 160292620 | 60 | - | 2.565 | 2.626 | 0.206 |
| ENSG00000122218 | E023 | 425.9751908 | 0.0001233820 | 9.681738e-05 | 5.071440e-04 | 1 | 160293166 | 160293234 | 69 | - | 2.596 | 2.664 | 0.227 |
| ENSG00000122218 | E024 | 451.5601781 | 0.0002052087 | 1.308821e-04 | 6.626413e-04 | 1 | 160293386 | 160293463 | 78 | - | 2.622 | 2.690 | 0.225 |
| ENSG00000122218 | E025 | 7.1288430 | 0.0049081739 | 1.041110e-01 | 1.967610e-01 | 1 | 160293706 | 160294483 | 778 | - | 1.002 | 0.805 | -0.751 |
| ENSG00000122218 | E026 | 527.3380516 | 0.0014495235 | 1.980010e-02 | 5.106219e-02 | 1 | 160294484 | 160294593 | 110 | - | 2.694 | 2.749 | 0.182 |
| ENSG00000122218 | E027 | 354.8846818 | 0.0021656589 | 9.758648e-01 | 9.889571e-01 | 1 | 160294768 | 160294802 | 35 | - | 2.554 | 2.555 | 0.004 |
| ENSG00000122218 | E028 | 249.1814135 | 0.0002088445 | 3.217243e-01 | 4.649703e-01 | 1 | 160294803 | 160294806 | 4 | - | 2.417 | 2.394 | -0.076 |
| ENSG00000122218 | E029 | 369.1331265 | 0.0003159061 | 3.937018e-01 | 5.375929e-01 | 1 | 160294807 | 160294857 | 51 | - | 2.583 | 2.566 | -0.058 |
| ENSG00000122218 | E030 | 522.6705277 | 0.0001191443 | 3.379563e-01 | 4.818388e-01 | 1 | 160295736 | 160295859 | 124 | - | 2.715 | 2.730 | 0.049 |
| ENSG00000122218 | E031 | 0.6986918 | 0.0159085717 | 3.387678e-01 | 4.826506e-01 | 1 | 160295860 | 160296060 | 201 | - | 0.126 | 0.290 | 1.498 |
| ENSG00000122218 | E032 | 449.6863751 | 0.0001371080 | 1.368248e-01 | 2.436624e-01 | 1 | 160296061 | 160296149 | 89 | - | 2.645 | 2.670 | 0.084 |
| ENSG00000122218 | E033 | 454.2552793 | 0.0001134185 | 6.712289e-01 | 7.775055e-01 | 1 | 160297343 | 160297438 | 96 | - | 2.667 | 2.659 | -0.026 |
| ENSG00000122218 | E034 | 603.3009656 | 0.0001045035 | 1.991360e-03 | 7.199975e-03 | 1 | 160297556 | 160297745 | 190 | - | 2.811 | 2.764 | -0.155 |
| ENSG00000122218 | E035 | 3.2376747 | 0.0047937578 | 8.993649e-01 | 9.397914e-01 | 1 | 160297746 | 160298149 | 404 | - | 0.639 | 0.619 | -0.085 |
| ENSG00000122218 | E036 | 426.8514022 | 0.0001673154 | 1.320514e-03 | 5.045428e-03 | 1 | 160298845 | 160298931 | 87 | - | 2.668 | 2.610 | -0.192 |
| ENSG00000122218 | E037 | 356.6266733 | 0.0001953980 | 1.056201e-05 | 6.981895e-05 | 1 | 160298932 | 160298991 | 60 | - | 2.604 | 2.518 | -0.287 |
| ENSG00000122218 | E038 | 6.2700038 | 0.0025778049 | 1.745694e-02 | 4.594816e-02 | 1 | 160298992 | 160299101 | 110 | - | 1.002 | 0.708 | -1.139 |
| ENSG00000122218 | E039 | 331.0527731 | 0.0001425904 | 1.210957e-08 | 1.470968e-07 | 1 | 160299102 | 160299140 | 39 | - | 2.585 | 2.471 | -0.378 |
| ENSG00000122218 | E040 | 479.2006030 | 0.0007320040 | 5.693120e-05 | 3.162052e-04 | 1 | 160299141 | 160299264 | 124 | - | 2.730 | 2.643 | -0.290 |
| ENSG00000122218 | E041 | 1.8239335 | 0.0344278727 | 1.840600e-02 | 4.802369e-02 | 1 | 160299265 | 160299279 | 15 | - | 0.639 | 0.212 | -2.410 |
| ENSG00000122218 | E042 | 1.7067717 | 0.0201227334 | 6.913065e-01 | 7.928105e-01 | 1 | 160305231 | 160305432 | 202 | - | 0.479 | 0.411 | -0.353 |
| ENSG00000122218 | E043 | 509.9731252 | 0.0007723264 | 1.043036e-08 | 1.280804e-07 | 1 | 160305433 | 160305571 | 139 | - | 2.774 | 2.651 | -0.408 |
| ENSG00000122218 | E044 | 12.5537859 | 0.0022216707 | 5.824832e-02 | 1.236217e-01 | 1 | 160305572 | 160305598 | 27 | - | 1.224 | 1.046 | -0.640 |
| ENSG00000122218 | E045 | 418.9139816 | 0.0042951135 | 2.117114e-04 | 1.014060e-03 | 1 | 160305688 | 160305773 | 86 | - | 2.699 | 2.549 | -0.499 |
| ENSG00000122218 | E046 | 4.3354677 | 0.0087660958 | 1.514868e-01 | 2.636951e-01 | 1 | 160305774 | 160305924 | 151 | - | 0.826 | 0.619 | -0.848 |
| ENSG00000122218 | E047 | 446.5953359 | 0.0050540242 | 7.575841e-05 | 4.079185e-04 | 1 | 160306354 | 160306454 | 101 | - | 2.734 | 2.567 | -0.557 |
| ENSG00000122218 | E048 | 277.5099237 | 0.0017667665 | 3.192055e-10 | 5.173013e-09 | 1 | 160306455 | 160306493 | 39 | - | 2.542 | 2.349 | -0.643 |
| ENSG00000122218 | E049 | 345.5367769 | 0.0013675948 | 3.652763e-09 | 4.877740e-08 | 1 | 160307163 | 160307245 | 83 | - | 2.622 | 2.462 | -0.533 |
| ENSG00000122218 | E050 | 7.5109975 | 0.0257173447 | 1.570117e-05 | 9.974983e-05 | 1 | 160308180 | 160308929 | 750 | - | 1.168 | 0.548 | -2.438 |
| ENSG00000122218 | E051 | 2.8501453 | 0.2383963791 | 1.717626e-02 | 4.533030e-02 | 1 | 160308930 | 160309100 | 171 | - | 0.823 | 0.214 | -3.155 |
| ENSG00000122218 | E052 | 340.4962876 | 0.0032787071 | 1.075053e-04 | 5.566456e-04 | 1 | 160309101 | 160309176 | 76 | - | 2.605 | 2.468 | -0.455 |
| ENSG00000122218 | E053 | 3.0477548 | 0.0392311844 | 5.248791e-02 | 1.135914e-01 | 1 | 160309177 | 160309781 | 605 | - | 0.755 | 0.413 | -1.559 |
| ENSG00000122218 | E054 | 0.0000000 | 1 | 160309782 | 160309808 | 27 | - | ||||||
| ENSG00000122218 | E055 | 3.5952968 | 0.0722648726 | 2.943802e-01 | 4.354845e-01 | 1 | 160309809 | 160310191 | 383 | - | 0.756 | 0.550 | -0.883 |
| ENSG00000122218 | E056 | 309.8549252 | 0.0017697447 | 3.052842e-04 | 1.400876e-03 | 1 | 160310192 | 160310258 | 67 | - | 2.551 | 2.442 | -0.362 |
| ENSG00000122218 | E057 | 10.2517865 | 0.1553413717 | 1.995934e-01 | 3.257188e-01 | 1 | 160310259 | 160311867 | 1609 | - | 1.168 | 0.905 | -0.964 |
| ENSG00000122218 | E058 | 441.5756878 | 0.0025073413 | 9.488451e-07 | 7.908309e-06 | 1 | 160311868 | 160312018 | 151 | - | 2.725 | 2.571 | -0.512 |
| ENSG00000122218 | E059 | 303.8036652 | 0.0020488904 | 9.845053e-11 | 1.738549e-09 | 1 | 160313085 | 160313167 | 83 | - | 2.585 | 2.385 | -0.665 |
| ENSG00000122218 | E060 | 358.2158530 | 0.0020459259 | 1.964008e-09 | 2.754074e-08 | 1 | 160313990 | 160314125 | 136 | - | 2.647 | 2.466 | -0.603 |
| ENSG00000122218 | E061 | 340.2342045 | 0.0031819411 | 1.651299e-07 | 1.608482e-06 | 1 | 160323431 | 160323530 | 100 | - | 2.626 | 2.442 | -0.612 |
| ENSG00000122218 | E062 | 217.4472027 | 0.0043948412 | 1.225261e-04 | 6.254465e-04 | 1 | 160325543 | 160325568 | 26 | - | 2.422 | 2.261 | -0.539 |
| ENSG00000122218 | E063 | 330.5268945 | 0.0036634207 | 6.749420e-08 | 7.087115e-07 | 1 | 160325569 | 160325652 | 84 | - | 2.620 | 2.422 | -0.660 |
| ENSG00000122218 | E064 | 0.9233738 | 0.0140303830 | 3.765977e-01 | 5.209225e-01 | 1 | 160325653 | 160325919 | 267 | - | 0.369 | 0.213 | -1.086 |
| ENSG00000122218 | E065 | 344.4751323 | 0.0036006809 | 1.231405e-09 | 1.792853e-08 | 1 | 160332448 | 160332557 | 110 | - | 2.648 | 2.425 | -0.741 |
| ENSG00000122218 | E066 | 12.5080475 | 0.0015413478 | 7.015765e-07 | 6.022274e-06 | 1 | 160332558 | 160333461 | 904 | - | 1.331 | 0.845 | -1.767 |
| ENSG00000122218 | E067 | 9.6561064 | 0.0019068537 | 9.329392e-01 | 9.617357e-01 | 1 | 160333462 | 160333602 | 141 | - | 1.030 | 1.020 | -0.036 |
| ENSG00000122218 | E068 | 316.3862440 | 0.0051098687 | 5.064589e-06 | 3.599592e-05 | 1 | 160333603 | 160333679 | 77 | - | 2.599 | 2.403 | -0.650 |
| ENSG00000122218 | E069 | 2.5633111 | 0.0202911351 | 7.710849e-02 | 1.548521e-01 | 1 | 160333680 | 160335241 | 1562 | - | 0.701 | 0.410 | -1.355 |
| ENSG00000122218 | E070 | 291.8787030 | 0.0077386486 | 1.136400e-03 | 4.425505e-03 | 1 | 160335242 | 160335322 | 81 | - | 2.551 | 2.382 | -0.565 |
| ENSG00000122218 | E071 | 3.9126220 | 0.0043847939 | 3.489415e-01 | 4.931511e-01 | 1 | 160336749 | 160339436 | 2688 | - | 0.755 | 0.619 | -0.569 |
| ENSG00000122218 | E072 | 0.6256415 | 0.0175707290 | 2.905441e-01 | 4.313692e-01 | 1 | 160339437 | 160339908 | 472 | - | 0.302 | 0.119 | -1.668 |
| ENSG00000122218 | E073 | 260.6588892 | 0.0072818702 | 1.163941e-03 | 4.518484e-03 | 1 | 160339909 | 160339982 | 74 | - | 2.500 | 2.336 | -0.548 |
| ENSG00000122218 | E074 | 1.4027854 | 0.0095795172 | 7.632728e-02 | 1.536285e-01 | 1 | 160339983 | 160340180 | 198 | - | 0.524 | 0.213 | -1.892 |
| ENSG00000122218 | E075 | 287.9262181 | 0.0087913785 | 7.807118e-05 | 4.188644e-04 | 1 | 160340181 | 160340294 | 114 | - | 2.563 | 2.355 | -0.695 |
| ENSG00000122218 | E076 | 199.4629143 | 0.0064567663 | 3.113662e-07 | 2.870573e-06 | 1 | 160343131 | 160343566 | 436 | - | 2.422 | 2.176 | -0.820 |