Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000163539
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000476251 | ENSG00000163539 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | CLASP2 | protein_coding | nonsense_mediated_decay | 17.54645 | 4.892005 | 32.97678 | 0.3195421 | 1.463314 | 2.750444 | 0.1275885 | 0.3054669 | 0.000000 | 0.3054669 | 0.0000000 | -4.979417 | 0.02274167 | 0.06946667 | 0.00000000 | -0.069466667 | 6.655847e-01 | 1.820083e-12 | TRUE | TRUE |
| ENST00000480013 | ENSG00000163539 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | CLASP2 | protein_coding | protein_coding | 17.54645 | 4.892005 | 32.97678 | 0.3195421 | 1.463314 | 2.750444 | 0.2968513 | 0.1213792 | 0.000000 | 0.1213792 | 0.0000000 | -3.715665 | 0.06639167 | 0.02210000 | 0.00000000 | -0.022100000 | 6.190198e-01 | 1.820083e-12 | FALSE | TRUE |
| ENST00000487553 | ENSG00000163539 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | CLASP2 | protein_coding | protein_coding | 17.54645 | 4.892005 | 32.97678 | 0.3195421 | 1.463314 | 2.750444 | 1.0518115 | 0.2919532 | 2.226765 | 0.1468258 | 1.1160513 | 2.889017 | 0.05027500 | 0.06020000 | 0.06613333 | 0.005933333 | 1.000000e+00 | 1.820083e-12 | FALSE | TRUE |
| ENST00000494261 | ENSG00000163539 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | CLASP2 | protein_coding | retained_intron | 17.54645 | 4.892005 | 32.97678 | 0.3195421 | 1.463314 | 2.750444 | 1.1896312 | 0.4083450 | 2.433875 | 0.1507026 | 0.4352810 | 2.546405 | 0.07145417 | 0.08383333 | 0.07296667 | -0.010866667 | 1.000000e+00 | 1.820083e-12 | FALSE | FALSE |
| MSTRG.22689.1 | ENSG00000163539 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | CLASP2 | protein_coding | 17.54645 | 4.892005 | 32.97678 | 0.3195421 | 1.463314 | 2.750444 | 1.7921782 | 0.7165816 | 2.998558 | 0.1887170 | 0.3039831 | 2.049876 | 0.14462500 | 0.14276667 | 0.09090000 | -0.051866667 | 5.629057e-01 | 1.820083e-12 | FALSE | TRUE | |
| MSTRG.22689.10 | ENSG00000163539 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | CLASP2 | protein_coding | 17.54645 | 4.892005 | 32.97678 | 0.3195421 | 1.463314 | 2.750444 | 0.4499719 | 0.9738454 | 0.000000 | 0.4131682 | 0.0000000 | -6.620360 | 0.07425000 | 0.20256667 | 0.00000000 | -0.202566667 | 7.021168e-06 | 1.820083e-12 | FALSE | TRUE | |
| MSTRG.22689.12 | ENSG00000163539 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | CLASP2 | protein_coding | 17.54645 | 4.892005 | 32.97678 | 0.3195421 | 1.463314 | 2.750444 | 2.5898340 | 0.0000000 | 4.761966 | 0.0000000 | 0.2408245 | 8.898440 | 0.08604167 | 0.00000000 | 0.14500000 | 0.145000000 | 1.820083e-12 | 1.820083e-12 | FALSE | TRUE | |
| MSTRG.22689.9 | ENSG00000163539 | HEK293_OSMI2_6hA | HEK293_TMG_6hB | CLASP2 | protein_coding | 17.54645 | 4.892005 | 32.97678 | 0.3195421 | 1.463314 | 2.750444 | 7.6654268 | 1.2517899 | 17.369789 | 0.7089791 | 0.6134580 | 3.783867 | 0.34744583 | 0.24986667 | 0.52793333 | 0.278066667 | 6.830445e-01 | 1.820083e-12 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000163539 | E001 | 0.0000000 | 3 | 33496245 | 33496248 | 4 | - | ||||||
| ENSG00000163539 | E002 | 17.6731995 | 0.5409279024 | 1.138431e-01 | 3.055279e-01 | 3 | 33496249 | 33496992 | 744 | - | 0.997 | 1.500 | 1.780 |
| ENSG00000163539 | E003 | 21.0868550 | 0.6187754154 | 1.150608e-01 | 3.075886e-01 | 3 | 33496993 | 33497133 | 141 | - | 1.046 | 1.614 | 1.988 |
| ENSG00000163539 | E004 | 119.7138107 | 1.4359878997 | 3.091366e-01 | 5.496534e-01 | 3 | 33497134 | 33497754 | 621 | - | 1.801 | 2.288 | 1.636 |
| ENSG00000163539 | E005 | 148.2477606 | 1.5127969470 | 3.391085e-01 | 5.771828e-01 | 3 | 33497755 | 33498134 | 380 | - | 1.899 | 2.365 | 1.560 |
| ENSG00000163539 | E006 | 112.8455476 | 1.4039572853 | 2.640544e-01 | 5.033333e-01 | 3 | 33498135 | 33498466 | 332 | - | 1.756 | 2.307 | 1.849 |
| ENSG00000163539 | E007 | 54.4138109 | 0.9131353966 | 1.981910e-01 | 4.273356e-01 | 3 | 33498467 | 33498512 | 46 | - | 1.457 | 1.970 | 1.737 |
| ENSG00000163539 | E008 | 76.5000576 | 1.2877188990 | 3.234719e-01 | 5.627987e-01 | 3 | 33498513 | 33498583 | 71 | - | 1.626 | 2.055 | 1.448 |
| ENSG00000163539 | E009 | 104.5867151 | 1.4105318261 | 3.724787e-01 | 6.060809e-01 | 3 | 33498584 | 33498717 | 134 | - | 1.769 | 2.161 | 1.318 |
| ENSG00000163539 | E010 | 97.9040446 | 0.0701884439 | 1.132502e-01 | 3.045629e-01 | 3 | 33501652 | 33501768 | 117 | - | 1.770 | 2.035 | 0.892 |
| ENSG00000163539 | E011 | 15.7031936 | 0.1470511930 | 1.616916e-03 | 1.444144e-02 | 3 | 33501769 | 33505451 | 3683 | - | 0.852 | 1.616 | 2.721 |
| ENSG00000163539 | E012 | 141.8956106 | 0.0003488501 | 4.226781e-03 | 3.041413e-02 | 3 | 33510558 | 33510764 | 207 | - | 1.942 | 2.150 | 0.696 |
| ENSG00000163539 | E013 | 0.5657866 | 0.0232494153 | 9.391001e-02 | 3 | 33514580 | 33514679 | 100 | - | 0.092 | 0.440 | 2.896 | |
| ENSG00000163539 | E014 | 128.9164095 | 0.0087531631 | 9.787266e-02 | 2.780608e-01 | 3 | 33516023 | 33516151 | 129 | - | 1.900 | 2.099 | 0.669 |
| ENSG00000163539 | E015 | 195.0977847 | 0.0093326905 | 5.148132e-01 | 7.115242e-01 | 3 | 33516981 | 33517174 | 194 | - | 2.089 | 2.227 | 0.462 |
| ENSG00000163539 | E016 | 176.9130430 | 0.0069304657 | 9.561465e-01 | 9.799968e-01 | 3 | 33535233 | 33535372 | 140 | - | 2.052 | 2.153 | 0.339 |
| ENSG00000163539 | E017 | 122.9795750 | 0.0027180875 | 4.142181e-01 | 6.391923e-01 | 3 | 33535373 | 33535461 | 89 | - | 1.890 | 2.028 | 0.465 |
| ENSG00000163539 | E018 | 140.2170640 | 0.0040269001 | 6.583532e-01 | 8.088984e-01 | 3 | 33538789 | 33538922 | 134 | - | 1.957 | 2.031 | 0.250 |
| ENSG00000163539 | E019 | 76.3219525 | 0.0050983880 | 6.121861e-01 | 7.783080e-01 | 3 | 33538923 | 33538942 | 20 | - | 1.686 | 1.816 | 0.439 |
| ENSG00000163539 | E020 | 132.2419613 | 0.0019302283 | 7.137034e-01 | 8.441926e-01 | 3 | 33543433 | 33543539 | 107 | - | 1.930 | 2.010 | 0.268 |
| ENSG00000163539 | E021 | 133.1538119 | 0.0004479538 | 6.833983e-01 | 8.248529e-01 | 3 | 33544698 | 33544841 | 144 | - | 1.929 | 2.042 | 0.383 |
| ENSG00000163539 | E022 | 9.6682733 | 0.0645459532 | 6.347750e-01 | 7.934186e-01 | 3 | 33544842 | 33545111 | 270 | - | 0.834 | 0.999 | 0.623 |
| ENSG00000163539 | E023 | 109.4770328 | 0.0119265846 | 7.438512e-01 | 8.628965e-01 | 3 | 33551252 | 33551395 | 144 | - | 1.841 | 1.971 | 0.438 |
| ENSG00000163539 | E024 | 1.6824528 | 0.0199434969 | 2.547585e-03 | 2.064340e-02 | 3 | 33558336 | 33559124 | 789 | - | 0.201 | 0.797 | 3.159 |
| ENSG00000163539 | E025 | 2.2739151 | 0.0094280448 | 1.123193e-02 | 6.331963e-02 | 3 | 33559125 | 33559175 | 51 | - | 0.289 | 0.798 | 2.483 |
| ENSG00000163539 | E026 | 81.8245023 | 0.0205496199 | 8.366474e-01 | 9.176288e-01 | 3 | 33559307 | 33559385 | 79 | - | 1.722 | 1.815 | 0.316 |
| ENSG00000163539 | E027 | 87.3565427 | 0.0052341135 | 4.707187e-02 | 1.727026e-01 | 3 | 33560808 | 33560971 | 164 | - | 1.767 | 1.737 | -0.103 |
| ENSG00000163539 | E028 | 0.0000000 | 3 | 33563964 | 33563966 | 3 | - | ||||||
| ENSG00000163539 | E029 | 3.8879656 | 0.2604788986 | 9.296475e-01 | 9.668295e-01 | 3 | 33566732 | 33566734 | 3 | - | 0.527 | 0.663 | 0.603 |
| ENSG00000163539 | E030 | 11.3144403 | 0.0028747799 | 2.677882e-01 | 5.074308e-01 | 3 | 33570727 | 33570730 | 4 | - | 0.932 | 0.856 | -0.291 |
| ENSG00000163539 | E031 | 41.8156000 | 0.0009611995 | 1.189137e-01 | 3.140643e-01 | 3 | 33570731 | 33570790 | 60 | - | 1.457 | 1.424 | -0.112 |
| ENSG00000163539 | E032 | 68.3866692 | 0.0008188997 | 6.317730e-02 | 2.098492e-01 | 3 | 33573110 | 33573169 | 60 | - | 1.661 | 1.637 | -0.084 |
| ENSG00000163539 | E033 | 137.0623196 | 0.0007937247 | 3.019268e-02 | 1.279103e-01 | 3 | 33573170 | 33573354 | 185 | - | 1.957 | 1.954 | -0.008 |
| ENSG00000163539 | E034 | 0.0000000 | 3 | 33574473 | 33574496 | 24 | - | ||||||
| ENSG00000163539 | E035 | 122.2095663 | 0.0041052322 | 6.962165e-02 | 2.240163e-01 | 3 | 33576169 | 33576275 | 107 | - | 1.908 | 1.908 | 0.001 |
| ENSG00000163539 | E036 | 0.0000000 | 3 | 33576276 | 33576421 | 146 | - | ||||||
| ENSG00000163539 | E037 | 0.1614157 | 0.0332694788 | 1.000000e+00 | 3 | 33577202 | 33577264 | 63 | - | 0.048 | 0.000 | -9.542 | |
| ENSG00000163539 | E038 | 133.7163683 | 0.0169523270 | 1.015309e-01 | 2.845730e-01 | 3 | 33581821 | 33581928 | 108 | - | 1.948 | 1.930 | -0.060 |
| ENSG00000163539 | E039 | 141.3847169 | 0.0333668029 | 2.656341e-01 | 5.050347e-01 | 3 | 33584750 | 33584920 | 171 | - | 1.968 | 1.982 | 0.047 |
| ENSG00000163539 | E040 | 0.0000000 | 3 | 33588705 | 33588731 | 27 | - | ||||||
| ENSG00000163539 | E041 | 0.0000000 | 3 | 33592213 | 33592239 | 27 | - | ||||||
| ENSG00000163539 | E042 | 103.4523278 | 0.0073889730 | 4.428473e-02 | 1.658156e-01 | 3 | 33592395 | 33592496 | 102 | - | 1.840 | 1.812 | -0.097 |
| ENSG00000163539 | E043 | 2.2361808 | 0.0131484061 | 4.896206e-01 | 6.937337e-01 | 3 | 33594951 | 33594968 | 18 | - | 0.362 | 0.561 | 1.021 |
| ENSG00000163539 | E044 | 1.5935388 | 0.0124995772 | 6.893558e-01 | 8.286550e-01 | 3 | 33596711 | 33596734 | 24 | - | 0.315 | 0.274 | -0.273 |
| ENSG00000163539 | E045 | 0.0000000 | 3 | 33602413 | 33602442 | 30 | - | ||||||
| ENSG00000163539 | E046 | 0.0000000 | 3 | 33602443 | 33602443 | 1 | - | ||||||
| ENSG00000163539 | E047 | 0.4820342 | 0.0214760565 | 1.000000e+00 | 3 | 33602444 | 33602589 | 146 | - | 0.132 | 0.000 | -11.126 | |
| ENSG00000163539 | E048 | 0.8567829 | 0.2251109328 | 5.647882e-01 | 3 | 33602590 | 33602951 | 362 | - | 0.205 | 0.000 | -11.894 | |
| ENSG00000163539 | E049 | 121.2977744 | 0.0067336920 | 2.667236e-03 | 2.138511e-02 | 3 | 33602952 | 33603125 | 174 | - | 1.914 | 1.821 | -0.313 |
| ENSG00000163539 | E050 | 83.6132618 | 0.0103341312 | 9.903292e-03 | 5.772462e-02 | 3 | 33604154 | 33604209 | 56 | - | 1.755 | 1.653 | -0.345 |
| ENSG00000163539 | E051 | 116.1674939 | 0.0063123590 | 1.274978e-02 | 6.943546e-02 | 3 | 33606591 | 33606758 | 168 | - | 1.891 | 1.833 | -0.197 |
| ENSG00000163539 | E052 | 86.9643044 | 0.0006050230 | 1.373732e-03 | 1.271758e-02 | 3 | 33607384 | 33607461 | 78 | - | 1.772 | 1.679 | -0.315 |
| ENSG00000163539 | E053 | 77.0867268 | 0.0010973706 | 2.141143e-04 | 2.831233e-03 | 3 | 33608567 | 33608626 | 60 | - | 1.726 | 1.580 | -0.496 |
| ENSG00000163539 | E054 | 65.3471529 | 0.0007282674 | 9.224292e-03 | 5.481862e-02 | 3 | 33612001 | 33612008 | 8 | - | 1.649 | 1.570 | -0.271 |
| ENSG00000163539 | E055 | 99.7732325 | 0.0021898511 | 2.957270e-03 | 2.314407e-02 | 3 | 33612009 | 33612071 | 63 | - | 1.828 | 1.752 | -0.255 |
| ENSG00000163539 | E056 | 111.9100113 | 0.0039247520 | 2.973391e-03 | 2.323574e-02 | 3 | 33619603 | 33619689 | 87 | - | 1.876 | 1.798 | -0.265 |
| ENSG00000163539 | E057 | 81.5228303 | 0.0004703417 | 1.202068e-03 | 1.144725e-02 | 3 | 33619690 | 33619738 | 49 | - | 1.746 | 1.645 | -0.343 |
| ENSG00000163539 | E058 | 61.7014007 | 0.0008048586 | 4.238914e-02 | 1.609601e-01 | 3 | 33622135 | 33622152 | 18 | - | 1.622 | 1.580 | -0.143 |
| ENSG00000163539 | E059 | 62.8343293 | 0.0006692638 | 8.370064e-02 | 2.521893e-01 | 3 | 33622153 | 33622186 | 34 | - | 1.628 | 1.609 | -0.064 |
| ENSG00000163539 | E060 | 75.6609910 | 0.0051386865 | 4.431973e-02 | 1.658881e-01 | 3 | 33622187 | 33622280 | 94 | - | 1.710 | 1.668 | -0.139 |
| ENSG00000163539 | E061 | 75.8540585 | 0.0018299688 | 3.945927e-05 | 6.802391e-04 | 3 | 33626988 | 33627080 | 93 | - | 1.725 | 1.537 | -0.639 |
| ENSG00000163539 | E062 | 57.4298862 | 0.0050773721 | 2.226197e-04 | 2.921860e-03 | 3 | 33632292 | 33632371 | 80 | - | 1.608 | 1.393 | -0.738 |
| ENSG00000163539 | E063 | 7.2360500 | 0.0461512960 | 3.263591e-01 | 5.655539e-01 | 3 | 33632372 | 33632374 | 3 | - | 0.768 | 0.655 | -0.465 |
| ENSG00000163539 | E064 | 0.7860845 | 0.0169193651 | 5.158876e-01 | 3 | 33644382 | 33644756 | 375 | - | 0.201 | 0.000 | -11.863 | |
| ENSG00000163539 | E065 | 81.7108932 | 0.0032001354 | 6.747584e-04 | 7.222330e-03 | 3 | 33644757 | 33644903 | 147 | - | 1.749 | 1.618 | -0.446 |
| ENSG00000163539 | E066 | 0.0000000 | 3 | 33645003 | 33645281 | 279 | - | ||||||
| ENSG00000163539 | E067 | 1.5721690 | 0.0115356492 | 1.651846e-01 | 3.842074e-01 | 3 | 33645282 | 33645343 | 62 | - | 0.339 | 0.000 | -12.862 |
| ENSG00000163539 | E068 | 1.5533880 | 0.0119025826 | 1.657212e-01 | 3.847553e-01 | 3 | 33645344 | 33645503 | 160 | - | 0.338 | 0.000 | -12.862 |
| ENSG00000163539 | E069 | 0.7507353 | 0.0211848311 | 5.211361e-01 | 3 | 33658974 | 33659009 | 36 | - | 0.201 | 0.000 | -11.860 | |
| ENSG00000163539 | E070 | 0.6246688 | 0.0191326519 | 7.011417e-01 | 3 | 33659010 | 33659441 | 432 | - | 0.168 | 0.000 | -11.541 | |
| ENSG00000163539 | E071 | 0.1426347 | 0.0316147836 | 1.000000e+00 | 3 | 33659507 | 33659672 | 166 | - | 0.048 | 0.000 | -9.540 | |
| ENSG00000163539 | E072 | 73.4217113 | 0.0005023049 | 2.261097e-04 | 2.958519e-03 | 3 | 33663445 | 33663515 | 71 | - | 1.706 | 1.559 | -0.499 |
| ENSG00000163539 | E073 | 4.7821075 | 0.0072063112 | 2.543687e-02 | 1.135585e-01 | 3 | 33682979 | 33683604 | 626 | - | 0.527 | 0.951 | 1.748 |
| ENSG00000163539 | E074 | 99.1563970 | 0.0015619035 | 4.923728e-06 | 1.136862e-04 | 3 | 33684359 | 33684456 | 98 | - | 1.835 | 1.654 | -0.613 |
| ENSG00000163539 | E075 | 92.5235377 | 0.0045033432 | 7.336454e-06 | 1.603473e-04 | 3 | 33687060 | 33687135 | 76 | - | 1.808 | 1.591 | -0.736 |
| ENSG00000163539 | E076 | 90.0331151 | 0.0063652896 | 3.129866e-06 | 7.707703e-05 | 3 | 33688277 | 33688368 | 92 | - | 1.800 | 1.548 | -0.858 |
| ENSG00000163539 | E077 | 0.0000000 | 3 | 33689730 | 33689828 | 99 | - | ||||||
| ENSG00000163539 | E078 | 89.5088894 | 0.0044380605 | 4.823284e-06 | 1.115794e-04 | 3 | 33689829 | 33689932 | 104 | - | 1.796 | 1.569 | -0.769 |
| ENSG00000163539 | E079 | 64.7535930 | 0.0068474354 | 2.645575e-04 | 3.370691e-03 | 3 | 33696855 | 33696933 | 79 | - | 1.656 | 1.451 | -0.702 |
| ENSG00000163539 | E080 | 59.7809361 | 0.0047643680 | 8.978108e-01 | 9.507233e-01 | 3 | 33717808 | 33718356 | 549 | - | 1.589 | 1.678 | 0.302 |