Isoforom Switch Analysis
WANG Ziyi
Date: 19 5月 2022
ENSG00000167978
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000301740 | ENSG00000167978 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | SRRM2 | protein_coding | protein_coding | 315.8004 | 374.0554 | 259.4917 | 34.1818 | 11.23205 | -0.5275465 | 122.053378 | 103.97683 | 129.5717934 | 16.255955 | 3.2233441 | 0.31746217 | 0.40800833 | 0.28676667 | 0.5002333333 | 0.21346667 | 5.012598e-02 | 4.744333e-32 | FALSE | TRUE |
| ENST00000570539 | ENSG00000167978 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | SRRM2 | protein_coding | protein_coding | 315.8004 | 374.0554 | 259.4917 | 34.1818 | 11.23205 | -0.5275465 | 16.254636 | 54.98536 | 0.0000000 | 18.704836 | 0.0000000 | -12.42509414 | 0.04155417 | 0.14290000 | 0.0000000000 | -0.14290000 | 1.250211e-20 | 4.744333e-32 | FALSE | |
| ENST00000573692 | ENSG00000167978 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | SRRM2 | protein_coding | nonsense_mediated_decay | 315.8004 | 374.0554 | 259.4917 | 34.1818 | 11.23205 | -0.5275465 | 8.293344 | 34.76904 | 0.0000000 | 12.383602 | 0.0000000 | -11.76400229 | 0.02116667 | 0.08866667 | 0.0000000000 | -0.08866667 | 1.736860e-15 | 4.744333e-32 | FALSE | |
| ENST00000574331 | ENSG00000167978 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | SRRM2 | protein_coding | retained_intron | 315.8004 | 374.0554 | 259.4917 | 34.1818 | 11.23205 | -0.5275465 | 19.518310 | 14.21823 | 15.1678112 | 2.414825 | 0.2989888 | 0.09320713 | 0.06057917 | 0.03780000 | 0.0585666667 | 0.02076667 | 2.223163e-02 | 4.744333e-32 | FALSE | |
| ENST00000576674 | ENSG00000167978 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | SRRM2 | protein_coding | processed_transcript | 315.8004 | 374.0554 | 259.4917 | 34.1818 | 11.23205 | -0.5275465 | 53.830087 | 65.58574 | 38.7486577 | 8.253688 | 3.5072938 | -0.75908349 | 0.16692917 | 0.17673333 | 0.1489000000 | -0.02783333 | 6.622209e-01 | 4.744333e-32 | FALSE | TRUE |
| MSTRG.11891.26 | ENSG00000167978 | HEK293_OSMI2_2hA | HEK293_TMG_2hB | SRRM2 | protein_coding | 315.8004 | 374.0554 | 259.4917 | 34.1818 | 11.23205 | -0.5275465 | 18.051746 | 53.76746 | 0.2318305 | 10.052680 | 0.1444057 | -7.79686141 | 0.04758333 | 0.14113333 | 0.0009666667 | -0.14016667 | 1.620330e-07 | 4.744333e-32 | 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_2hB | HEK293_OSMI2_2hA | log2fold_HEK293_OSMI2_2hA_HEK293_TMG_2hB |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000167978 | E001 | 5.859677e+00 | 0.0617876213 | 1.117279e-01 | 2.080963e-01 | 16 | 2752626 | 2752637 | 12 | + | 0.956 | 0.687 | -1.058 |
| ENSG00000167978 | E002 | 1.058491e+01 | 0.1105873807 | 4.806095e-03 | 1.539099e-02 | 16 | 2752638 | 2752649 | 12 | + | 1.285 | 0.766 | -1.917 |
| ENSG00000167978 | E003 | 1.729801e+01 | 0.0815406163 | 2.316633e-04 | 1.098516e-03 | 16 | 2752650 | 2752658 | 9 | + | 1.506 | 0.916 | -2.101 |
| ENSG00000167978 | E004 | 1.972430e+01 | 0.1247721866 | 8.253656e-04 | 3.349895e-03 | 16 | 2752659 | 2752661 | 3 | + | 1.566 | 0.963 | -2.129 |
| ENSG00000167978 | E005 | 2.258658e+01 | 0.1329761986 | 3.435840e-04 | 1.554374e-03 | 16 | 2752662 | 2752666 | 5 | + | 1.638 | 0.978 | -2.320 |
| ENSG00000167978 | E006 | 2.816340e+01 | 0.0906607106 | 2.117182e-06 | 1.637878e-05 | 16 | 2752667 | 2752674 | 8 | + | 1.755 | 0.986 | -2.689 |
| ENSG00000167978 | E007 | 1.107709e+02 | 0.0847472061 | 1.190710e-09 | 1.739351e-08 | 16 | 2752675 | 2752713 | 39 | + | 2.366 | 1.453 | -3.076 |
| ENSG00000167978 | E008 | 1.083435e+02 | 0.0669585320 | 4.239131e-12 | 9.379708e-11 | 16 | 2752714 | 2752715 | 2 | + | 2.362 | 1.413 | -3.204 |
| ENSG00000167978 | E009 | 2.490289e+02 | 0.0689151190 | 3.261216e-09 | 4.395160e-08 | 16 | 2752716 | 2752846 | 131 | + | 2.692 | 1.913 | -2.602 |
| ENSG00000167978 | E010 | 2.733893e+01 | 0.0379658356 | 9.872523e-10 | 1.465653e-08 | 16 | 2752847 | 2752854 | 8 | + | 1.741 | 0.989 | -2.629 |
| ENSG00000167978 | E011 | 6.340025e+00 | 0.0026472808 | 3.349162e-05 | 1.968261e-04 | 16 | 2753443 | 2753645 | 203 | + | 1.104 | 0.557 | -2.165 |
| ENSG00000167978 | E012 | 4.375704e+02 | 0.0221179908 | 8.886590e-10 | 1.330124e-08 | 16 | 2756334 | 2756606 | 273 | + | 2.854 | 2.381 | -1.574 |
| ENSG00000167978 | E013 | 2.672962e+02 | 0.0228386483 | 7.195047e-10 | 1.097183e-08 | 16 | 2757472 | 2757475 | 4 | + | 2.648 | 2.155 | -1.644 |
| ENSG00000167978 | E014 | 5.357532e+02 | 0.0235206829 | 6.023701e-09 | 7.750948e-08 | 16 | 2757476 | 2757579 | 104 | + | 2.937 | 2.479 | -1.526 |
| ENSG00000167978 | E015 | 3.360236e+00 | 0.0045263108 | 1.944448e-02 | 5.029764e-02 | 16 | 2757580 | 2757780 | 201 | + | 0.812 | 0.438 | -1.657 |
| ENSG00000167978 | E016 | 4.605110e+02 | 0.0216247417 | 1.157428e-08 | 1.410921e-07 | 16 | 2757781 | 2757831 | 51 | + | 2.863 | 2.428 | -1.448 |
| ENSG00000167978 | E017 | 6.343307e+02 | 0.0135125218 | 2.730980e-14 | 8.418094e-13 | 16 | 2757832 | 2757945 | 114 | + | 3.013 | 2.547 | -1.549 |
| ENSG00000167978 | E018 | 6.028157e+02 | 0.0109160805 | 7.456548e-16 | 2.865356e-14 | 16 | 2758470 | 2758547 | 78 | + | 2.986 | 2.534 | -1.502 |
| ENSG00000167978 | E019 | 4.566480e+00 | 0.0761317139 | 9.325823e-03 | 2.709849e-02 | 16 | 2758854 | 2758907 | 54 | + | 0.956 | 0.484 | -1.974 |
| ENSG00000167978 | E020 | 3.192927e+00 | 0.0438317442 | 1.969646e-02 | 5.084529e-02 | 16 | 2758908 | 2758923 | 16 | + | 0.811 | 0.391 | -1.908 |
| ENSG00000167978 | E021 | 3.945092e+00 | 0.0040494075 | 2.491843e-03 | 8.740135e-03 | 16 | 2758924 | 2758947 | 24 | + | 0.900 | 0.438 | -1.998 |
| ENSG00000167978 | E022 | 4.288797e+00 | 0.0038361378 | 1.486116e-05 | 9.494494e-05 | 16 | 2758948 | 2758984 | 37 | + | 0.990 | 0.334 | -2.920 |
| ENSG00000167978 | E023 | 5.286589e+02 | 0.0131934153 | 1.311779e-11 | 2.680538e-10 | 16 | 2758985 | 2759047 | 63 | + | 2.916 | 2.501 | -1.381 |
| ENSG00000167978 | E024 | 9.084591e+00 | 0.0186483087 | 3.431588e-07 | 3.137568e-06 | 16 | 2759048 | 2759139 | 92 | + | 1.277 | 0.591 | -2.629 |
| ENSG00000167978 | E025 | 4.574587e+02 | 0.0159278265 | 1.305529e-10 | 2.260772e-09 | 16 | 2759140 | 2759172 | 33 | + | 2.858 | 2.429 | -1.429 |
| ENSG00000167978 | E026 | 2.801329e+00 | 0.0074410464 | 8.138339e-02 | 1.617245e-01 | 16 | 2759173 | 2759351 | 179 | + | 0.731 | 0.437 | -1.336 |
| ENSG00000167978 | E027 | 4.920271e+02 | 0.0172110214 | 5.403061e-09 | 7.005637e-08 | 16 | 2759352 | 2759402 | 51 | + | 2.880 | 2.478 | -1.337 |
| ENSG00000167978 | E028 | 1.975449e+00 | 0.0755936267 | 1.200520e-02 | 3.354349e-02 | 16 | 2759403 | 2759548 | 146 | + | 0.702 | 0.198 | -2.803 |
| ENSG00000167978 | E029 | 5.272714e+02 | 0.0184022701 | 1.870437e-08 | 2.193023e-07 | 16 | 2759569 | 2759661 | 93 | + | 2.908 | 2.511 | -1.323 |
| ENSG00000167978 | E030 | 3.180863e+01 | 0.0034631700 | 2.267209e-27 | 3.039744e-25 | 16 | 2759662 | 2759746 | 85 | + | 1.820 | 0.987 | -2.904 |
| ENSG00000167978 | E031 | 5.621849e+01 | 0.0004950525 | 2.674514e-44 | 1.189387e-41 | 16 | 2759747 | 2759932 | 186 | + | 2.044 | 1.297 | -2.542 |
| ENSG00000167978 | E032 | 2.518823e+01 | 0.0008200456 | 1.029512e-23 | 9.895380e-22 | 16 | 2759933 | 2760008 | 76 | + | 1.714 | 0.931 | -2.754 |
| ENSG00000167978 | E033 | 1.545267e+01 | 0.0047097748 | 6.293555e-21 | 4.495834e-19 | 16 | 2760009 | 2760032 | 24 | + | 1.549 | 0.521 | -3.889 |
| ENSG00000167978 | E034 | 7.428343e+01 | 0.0004781727 | 2.886518e-71 | 4.557018e-68 | 16 | 2760033 | 2760300 | 268 | + | 2.186 | 1.316 | -2.951 |
| ENSG00000167978 | E035 | 6.734887e+02 | 0.0136743887 | 3.800188e-11 | 7.193588e-10 | 16 | 2760301 | 2760499 | 199 | + | 3.018 | 2.611 | -1.353 |
| ENSG00000167978 | E036 | 9.997266e+00 | 0.0065745532 | 5.322316e-06 | 3.764128e-05 | 16 | 2760500 | 2760846 | 347 | + | 1.277 | 0.750 | -1.953 |
| ENSG00000167978 | E037 | 5.773499e+02 | 0.0061957666 | 1.035834e-22 | 8.927919e-21 | 16 | 2761561 | 2761698 | 138 | + | 2.959 | 2.529 | -1.432 |
| ENSG00000167978 | E038 | 1.939447e+03 | 0.0145233427 | 1.774498e-11 | 3.543889e-10 | 16 | 2761699 | 2762276 | 578 | + | 3.477 | 3.069 | -1.356 |
| ENSG00000167978 | E039 | 6.149798e+02 | 0.0170095472 | 8.387023e-07 | 7.082221e-06 | 16 | 2762277 | 2762369 | 93 | + | 2.950 | 2.615 | -1.114 |
| ENSG00000167978 | E040 | 4.191990e+03 | 0.0132646085 | 5.226835e-10 | 8.156575e-09 | 16 | 2762370 | 2763501 | 1132 | + | 3.789 | 3.441 | -1.157 |
| ENSG00000167978 | E041 | 9.570719e+02 | 0.0103955529 | 1.410321e-07 | 1.392656e-06 | 16 | 2763502 | 2763582 | 81 | + | 3.120 | 2.836 | -0.944 |
| ENSG00000167978 | E042 | 1.886880e+03 | 0.0096525020 | 2.290146e-08 | 2.640505e-07 | 16 | 2763583 | 2763866 | 284 | + | 3.415 | 3.131 | -0.943 |
| ENSG00000167978 | E043 | 9.571119e+02 | 0.0072046587 | 2.556271e-07 | 2.399791e-06 | 16 | 2763867 | 2763938 | 72 | + | 3.099 | 2.860 | -0.796 |
| ENSG00000167978 | E044 | 4.125168e+03 | 0.0095120083 | 1.658316e-04 | 8.172389e-04 | 16 | 2763939 | 2764847 | 909 | + | 3.708 | 3.522 | -0.617 |
| ENSG00000167978 | E045 | 1.400223e+04 | 0.0025764139 | 3.731461e-01 | 5.175862e-01 | 16 | 2764848 | 2767506 | 2659 | + | 4.158 | 4.122 | -0.120 |
| ENSG00000167978 | E046 | 2.316745e+03 | 0.0009826969 | 2.638716e-21 | 1.956543e-19 | 16 | 2767507 | 2767721 | 215 | + | 3.266 | 3.403 | 0.458 |
| ENSG00000167978 | E047 | 2.130225e+03 | 0.0017048232 | 4.067653e-14 | 1.222406e-12 | 16 | 2767722 | 2767855 | 134 | + | 3.228 | 3.368 | 0.465 |
| ENSG00000167978 | E048 | 2.917678e+03 | 0.0030779237 | 2.375481e-13 | 6.405178e-12 | 16 | 2767856 | 2768080 | 225 | + | 3.339 | 3.517 | 0.592 |
| ENSG00000167978 | E049 | 2.075125e+03 | 0.0059003521 | 4.117833e-11 | 7.745345e-10 | 16 | 2768081 | 2768261 | 181 | + | 3.155 | 3.384 | 0.762 |
| ENSG00000167978 | E050 | 4.863532e+01 | 0.0027824648 | 6.129901e-02 | 1.288205e-01 | 16 | 2768505 | 2768527 | 23 | + | 1.753 | 1.621 | -0.448 |
| ENSG00000167978 | E051 | 4.907205e+01 | 0.0015243959 | 4.403832e-03 | 1.427508e-02 | 16 | 2768528 | 2768550 | 23 | + | 1.780 | 1.601 | -0.605 |
| ENSG00000167978 | E052 | 6.181899e+01 | 0.0028258542 | 3.862239e-03 | 1.275543e-02 | 16 | 2768551 | 2768599 | 49 | + | 1.878 | 1.703 | -0.592 |
| ENSG00000167978 | E053 | 9.088759e+01 | 0.0103518839 | 3.058980e-03 | 1.043945e-02 | 16 | 2768600 | 2768745 | 146 | + | 2.062 | 1.856 | -0.692 |
| ENSG00000167978 | E054 | 4.394190e+01 | 0.0011182101 | 3.795093e-09 | 5.053198e-08 | 16 | 2768746 | 2768767 | 22 | + | 1.815 | 1.464 | -1.194 |
| ENSG00000167978 | E055 | 8.927429e+01 | 0.0099343585 | 8.670143e-02 | 1.701243e-01 | 16 | 2768768 | 2768996 | 229 | + | 2.015 | 1.886 | -0.433 |
| ENSG00000167978 | E056 | 2.630099e+03 | 0.0047132615 | 3.056148e-22 | 2.499905e-20 | 16 | 2768997 | 2769284 | 288 | + | 3.199 | 3.508 | 1.028 |
| ENSG00000167978 | E057 | 7.276649e+01 | 0.0003744192 | 3.497673e-10 | 5.630246e-09 | 16 | 2769285 | 2769373 | 89 | + | 2.007 | 1.716 | -0.979 |
| ENSG00000167978 | E058 | 1.761005e+02 | 0.0099418262 | 4.379237e-06 | 3.157380e-05 | 16 | 2769374 | 2769627 | 254 | + | 2.383 | 2.103 | -0.935 |
| ENSG00000167978 | E059 | 2.152401e+02 | 0.0088631351 | 5.476960e-06 | 3.864121e-05 | 16 | 2769628 | 2769861 | 234 | + | 2.460 | 2.202 | -0.862 |
| ENSG00000167978 | E060 | 9.790224e+01 | 0.0014111847 | 9.277309e-07 | 7.753136e-06 | 16 | 2769862 | 2769894 | 33 | + | 2.101 | 1.877 | -0.749 |
| ENSG00000167978 | E061 | 2.445102e+02 | 0.0078493293 | 7.491720e-04 | 3.075705e-03 | 16 | 2769895 | 2770227 | 333 | + | 2.480 | 2.295 | -0.619 |
| ENSG00000167978 | E062 | 1.307206e+02 | 0.0036466970 | 5.120741e-04 | 2.204843e-03 | 16 | 2770228 | 2770351 | 124 | + | 2.205 | 2.031 | -0.584 |
| ENSG00000167978 | E063 | 9.107719e+02 | 0.0018094030 | 6.363102e-46 | 3.106883e-43 | 16 | 2770352 | 2770354 | 3 | + | 2.721 | 3.051 | 1.098 |
| ENSG00000167978 | E064 | 1.986491e+03 | 0.0037712898 | 2.482006e-32 | 4.918499e-30 | 16 | 2770355 | 2770465 | 111 | + | 3.045 | 3.396 | 1.166 |
| ENSG00000167978 | E065 | 8.857843e+02 | 0.0056554967 | 7.833932e-21 | 5.546020e-19 | 16 | 2770604 | 2770606 | 3 | + | 2.695 | 3.045 | 1.163 |
| ENSG00000167978 | E066 | 2.347924e+03 | 0.0057333978 | 8.096819e-25 | 8.730325e-23 | 16 | 2770607 | 2770717 | 111 | + | 3.104 | 3.473 | 1.226 |
| ENSG00000167978 | E067 | 1.871937e+03 | 0.0066900176 | 6.146867e-20 | 3.864802e-18 | 16 | 2770858 | 2770910 | 53 | + | 3.016 | 3.371 | 1.181 |
| ENSG00000167978 | E068 | 2.315092e+03 | 0.0081274228 | 2.167797e-17 | 1.012531e-15 | 16 | 2770911 | 2771049 | 139 | + | 3.105 | 3.464 | 1.194 |
| ENSG00000167978 | E069 | 5.524317e+02 | 0.0112056841 | 1.382602e-07 | 1.367636e-06 | 16 | 2771050 | 2771120 | 71 | + | 2.552 | 2.821 | 0.898 |
| ENSG00000167978 | E070 | 1.997057e+03 | 0.0097698654 | 3.876582e-16 | 1.545469e-14 | 16 | 2771121 | 2771277 | 157 | + | 3.024 | 3.405 | 1.265 |
| ENSG00000167978 | E071 | 1.162886e+03 | 0.0116199822 | 6.332410e-15 | 2.149536e-13 | 16 | 2771278 | 2771303 | 26 | + | 2.768 | 3.176 | 1.358 |
| ENSG00000167978 | E072 | 1.148793e+03 | 0.0101168850 | 2.404804e-17 | 1.114985e-15 | 16 | 2771304 | 2771368 | 65 | + | 2.757 | 3.172 | 1.382 |
| ENSG00000167978 | E073 | 3.701495e+02 | 0.0033023046 | 2.234360e-28 | 3.268671e-26 | 16 | 2771369 | 2771603 | 235 | + | 2.302 | 2.670 | 1.226 |
| ENSG00000167978 | E074 | 6.966155e-01 | 0.0172671820 | 3.962378e-01 | 5.400242e-01 | 16 | 2772322 | 2772538 | 217 | + | 0.135 | 0.272 | 1.250 |