ENSG00000140455

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
ENST00000380324 ENSG00000140455 HEK293_OSMI2_2hA HEK293_TMG_2hB USP3 protein_coding protein_coding 6.588331 3.941936 8.926925 0.6688626 0.4947787 1.177219 1.2525267 1.1867310 1.3078724 0.2255170 0.1302793 0.13911179 0.21527083 0.30323333 0.14726667 -0.1559666667 1.170943e-02 9.992455e-10 FALSE TRUE
ENST00000557884 ENSG00000140455 HEK293_OSMI2_2hA HEK293_TMG_2hB USP3 protein_coding nonsense_mediated_decay 6.588331 3.941936 8.926925 0.6688626 0.4947787 1.177219 0.3028859 0.0000000 0.5043173 0.0000000 0.1579731 5.68458664 0.04110000 0.00000000 0.05510000 0.0551000000 3.886802e-04 9.992455e-10 FALSE FALSE
ENST00000558285 ENSG00000140455 HEK293_OSMI2_2hA HEK293_TMG_2hB USP3 protein_coding protein_coding 6.588331 3.941936 8.926925 0.6688626 0.4947787 1.177219 2.1202649 1.2661352 3.0470966 0.1861202 0.4947237 1.26038093 0.29910417 0.34583333 0.34510000 -0.0007333333 1.000000e+00 9.992455e-10 FALSE TRUE
ENST00000559711 ENSG00000140455 HEK293_OSMI2_2hA HEK293_TMG_2hB USP3 protein_coding protein_coding 6.588331 3.941936 8.926925 0.6688626 0.4947787 1.177219 0.6989512 0.0000000 0.6233302 0.0000000 0.6233302 5.98488593 0.10007917 0.00000000 0.06780000 0.0678000000 9.558556e-01 9.992455e-10 FALSE TRUE
ENST00000559718 ENSG00000140455 HEK293_OSMI2_2hA HEK293_TMG_2hB USP3 protein_coding retained_intron 6.588331 3.941936 8.926925 0.6688626 0.4947787 1.177219 0.2857354 0.2119681 0.2232021 0.1690133 0.2232021 0.07122811 0.05520000 0.05976667 0.02426667 -0.0355000000 6.621704e-01 9.992455e-10   FALSE
ENST00000559771 ENSG00000140455 HEK293_OSMI2_2hA HEK293_TMG_2hB USP3 protein_coding protein_coding 6.588331 3.941936 8.926925 0.6688626 0.4947787 1.177219 0.3704912 0.0000000 1.3295923 0.0000000 0.3432846 7.06565013 0.04569167 0.00000000 0.14613333 0.1461333333 3.665000e-08 9.992455e-10 FALSE FALSE
ENST00000560070 ENSG00000140455 HEK293_OSMI2_2hA HEK293_TMG_2hB USP3 protein_coding protein_coding 6.588331 3.941936 8.926925 0.6688626 0.4947787 1.177219 0.7260180 0.0000000 1.3664827 0.0000000 0.1602141 7.10484262 0.07836250 0.00000000 0.15550000 0.1555000000 9.992455e-10 9.992455e-10 FALSE FALSE
ENST00000560202 ENSG00000140455 HEK293_OSMI2_2hA HEK293_TMG_2hB USP3 protein_coding nonsense_mediated_decay 6.588331 3.941936 8.926925 0.6688626 0.4947787 1.177219 0.3420105 0.9657125 0.0000000 0.6037596 0.0000000 -6.60838415 0.07354167 0.21253333 0.00000000 -0.2125333333 7.654670e-02 9.992455e-10 TRUE FALSE
  • 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
ENSG00000140455 E001 1.6083360 0.0511967845 9.809529e-01 9.921021e-01 15 63504511 63504592 82 + 0.414 0.414 -0.001
ENSG00000140455 E002 1.4600428 0.1559042433 7.851394e-01 8.622492e-01 15 63504593 63504593 1 + 0.414 0.344 -0.397
ENSG00000140455 E003 1.4600428 0.1559042433 7.851394e-01 8.622492e-01 15 63504594 63504594 1 + 0.414 0.344 -0.397
ENSG00000140455 E004 3.6441378 0.0053202190 1.386510e-01 2.462341e-01 15 63504595 63504611 17 + 0.742 0.530 -0.922
ENSG00000140455 E005 6.3066121 0.0030089432 3.485325e-02 8.136792e-02 15 63504612 63504634 23 + 0.954 0.697 -1.005
ENSG00000140455 E006 8.5993601 0.0020290452 1.575970e-02 4.219372e-02 15 63504635 63504655 21 + 1.076 0.817 -0.971
ENSG00000140455 E007 12.4117511 0.0014401387 5.574549e-03 1.748711e-02 15 63504656 63504673 18 + 1.223 0.971 -0.912
ENSG00000140455 E008 16.7587467 0.0011023472 7.261991e-03 2.190705e-02 15 63504674 63504733 60 + 1.332 1.125 -0.734
ENSG00000140455 E009 20.1158765 0.0009455667 7.207817e-04 2.973321e-03 15 63504734 63504830 97 + 1.420 1.174 -0.862
ENSG00000140455 E010 0.0000000       15 63515446 63515500 55 +      
ENSG00000140455 E011 0.1515154 0.0435090459 7.037021e-01   15 63527833 63528140 308 + 0.103 0.000 -11.477
ENSG00000140455 E012 4.7634290 0.1711674064 5.337436e-02 1.151599e-01 15 63529014 63529141 128 + 0.900 0.516 -1.607
ENSG00000140455 E013 3.1307528 0.0732386038 5.731491e-03 1.790442e-02 15 63529142 63529166 25 + 0.783 0.253 -2.685
ENSG00000140455 E014 0.1817044 0.0421947167 3.401560e-01   15 63530498 63530590 93 + 0.000 0.146 11.293
ENSG00000140455 E015 0.0000000       15 63532506 63532646 141 +      
ENSG00000140455 E016 22.1508465 0.0010169861 9.979537e-03 2.871409e-02 15 63532647 63532707 61 + 1.437 1.267 -0.592
ENSG00000140455 E017 1.3402425 0.0215852840 2.359244e-01 3.694487e-01 15 63533803 63533918 116 + 0.457 0.254 -1.232
ENSG00000140455 E018 28.2735278 0.0241595725 1.259536e-01 2.285105e-01 15 63537025 63537104 80 + 1.526 1.379 -0.507
ENSG00000140455 E019 18.5403576 0.0135865081 1.886672e-01 3.120574e-01 15 63537105 63537137 33 + 1.338 1.226 -0.392
ENSG00000140455 E020 17.1731484 0.0158993468 1.703594e-01 2.886357e-01 15 63537138 63537156 19 + 1.311 1.184 -0.447
ENSG00000140455 E021 0.7512344 0.3158945449 1.181572e-01 2.172959e-01 15 63542055 63542192 138 + 0.369 0.000 -12.886
ENSG00000140455 E022 0.0000000       15 63544625 63544728 104 +      
ENSG00000140455 E023 0.1451727 0.0433158175 7.045547e-01   15 63553333 63553714 382 + 0.102 0.000 -11.477
ENSG00000140455 E024 30.8569690 0.0117701859 1.076220e-01 2.020320e-01 15 63553715 63553798 84 + 1.552 1.434 -0.406
ENSG00000140455 E025 29.9394192 0.0007407644 3.369818e-02 7.915120e-02 15 63556667 63556748 82 + 1.538 1.422 -0.399
ENSG00000140455 E026 29.4776964 0.0020066802 1.945869e-01 3.194861e-01 15 63558106 63558188 83 + 1.511 1.442 -0.237
ENSG00000140455 E027 29.0488983 0.0007723627 3.826614e-01 5.268579e-01 15 63559857 63559970 114 + 1.496 1.460 -0.125
ENSG00000140455 E028 27.0548774 0.0110839475 3.104297e-01 4.528303e-01 15 63562895 63563008 114 + 1.477 1.403 -0.257
ENSG00000140455 E029 41.0739879 0.0005836866 4.350728e-03 1.412469e-02 15 63570433 63570579 147 + 1.682 1.546 -0.463
ENSG00000140455 E030 36.6515327 0.0005882589 3.760323e-02 8.658442e-02 15 63574046 63574152 107 + 1.620 1.521 -0.339
ENSG00000140455 E031 29.9013843 0.0069743802 1.849909e-01 3.074720e-01 15 63574323 63574403 81 + 1.528 1.446 -0.281
ENSG00000140455 E032 0.5964967 0.0204681808 5.089716e-01 6.443472e-01 15 63586608 63586758 151 + 0.255 0.145 -1.008
ENSG00000140455 E033 0.6277178 0.0200283388 5.121906e-01 6.471108e-01 15 63587970 63588304 335 + 0.255 0.145 -1.006
ENSG00000140455 E034 32.9760805 0.0100135394 4.270326e-01 5.698714e-01 15 63588305 63588423 119 + 1.554 1.516 -0.131
ENSG00000140455 E035 1.6115451 0.2339790083 7.020980e-01 8.009826e-01 15 63588520 63588701 182 + 0.455 0.345 -0.612
ENSG00000140455 E036 18.8229315 0.0118600238 4.229583e-01 5.660889e-01 15 63588702 63588728 27 + 1.327 1.273 -0.188
ENSG00000140455 E037 25.0563360 0.0008080791 9.252842e-01 9.569641e-01 15 63588729 63588815 87 + 1.415 1.429 0.046
ENSG00000140455 E038 22.7890924 0.0008576058 2.625566e-01 4.003522e-01 15 63588944 63589011 68 + 1.411 1.351 -0.207
ENSG00000140455 E039 109.1064385 0.0002809303 6.304207e-04 2.645153e-03 15 63590661 63591373 713 + 1.984 2.112 0.429
ENSG00000140455 E040 88.3856433 0.0038544455 9.100624e-07 7.621954e-06 15 63591374 63593781 2408 + 1.836 2.071 0.789
ENSG00000140455 E041 14.6607724 0.0056422650 3.060789e-06 2.285692e-05 15 63593782 63593915 134 + 0.941 1.400 1.644
ENSG00000140455 E042 41.0946535 0.0292364756 8.788990e-09 1.094778e-07 15 63593916 63594428 513 + 1.250 1.864 2.105
ENSG00000140455 E043 17.1222696 0.0111289617 2.403248e-08 2.757651e-07 15 63594429 63594640 212 + 0.927 1.494 2.019