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_DMSO_6hA HEK293_OSMI2_6hA USP3 protein_coding protein_coding 6.588331 4.132153 4.002697 0.8778416 0.5671294 -0.04580838 1.25252669 1.1541513 0.8476410 0.21512748 0.19644934 -0.44083269 0.21527083 0.28203333 0.20663333 -0.07540000 0.640065289 0.000131884 FALSE TRUE
ENST00000558218 ENSG00000140455 HEK293_DMSO_6hA HEK293_OSMI2_6hA USP3 protein_coding processed_transcript 6.588331 4.132153 4.002697 0.8778416 0.5671294 -0.04580838 0.15490039 0.6304453 0.1034429 0.06921265 0.10344293 -2.49710873 0.03281667 0.17006667 0.03253333 -0.13753333 0.274217510 0.000131884 FALSE TRUE
ENST00000558285 ENSG00000140455 HEK293_DMSO_6hA HEK293_OSMI2_6hA USP3 protein_coding protein_coding 6.588331 4.132153 4.002697 0.8778416 0.5671294 -0.04580838 2.12026491 0.1193799 0.7005773 0.11937990 0.70057729 2.45737802 0.29910417 0.03873333 0.18733333 0.14860000 0.984265534 0.000131884 FALSE TRUE
ENST00000559711 ENSG00000140455 HEK293_DMSO_6hA HEK293_OSMI2_6hA USP3 protein_coding protein_coding 6.588331 4.132153 4.002697 0.8778416 0.5671294 -0.04580838 0.69895116 0.8205770 0.8459195 0.51894324 0.45713001 0.04336121 0.10007917 0.16700000 0.20433333 0.03733333 0.980359186 0.000131884 FALSE TRUE
ENST00000559718 ENSG00000140455 HEK293_DMSO_6hA HEK293_OSMI2_6hA USP3 protein_coding retained_intron 6.588331 4.132153 4.002697 0.8778416 0.5671294 -0.04580838 0.28573542 0.6006417 0.5226963 0.35708835 0.09540722 -0.19701298 0.05520000 0.13133333 0.14033333 0.00900000 0.900969002 0.000131884   FALSE
ENST00000559771 ENSG00000140455 HEK293_DMSO_6hA HEK293_OSMI2_6hA USP3 protein_coding protein_coding 6.588331 4.132153 4.002697 0.8778416 0.5671294 -0.04580838 0.37049124 0.2454209 0.0000000 0.24542094 0.00000000 -4.67480491 0.04569167 0.07136667 0.00000000 -0.07136667 0.783788887 0.000131884 FALSE FALSE
ENST00000560070 ENSG00000140455 HEK293_DMSO_6hA HEK293_OSMI2_6hA USP3 protein_coding protein_coding 6.588331 4.132153 4.002697 0.8778416 0.5671294 -0.04580838 0.72601795 0.0000000 0.0000000 0.00000000 0.00000000 0.00000000 0.07836250 0.00000000 0.00000000 0.00000000   0.000131884 FALSE FALSE
ENST00000560202 ENSG00000140455 HEK293_DMSO_6hA HEK293_OSMI2_6hA USP3 protein_coding nonsense_mediated_decay 6.588331 4.132153 4.002697 0.8778416 0.5671294 -0.04580838 0.34201050 0.0000000 0.5340266 0.00000000 0.44669114 5.76560529 0.07354167 0.00000000 0.11203333 0.11203333 0.298108354 0.000131884 TRUE FALSE
ENST00000561381 ENSG00000140455 HEK293_DMSO_6hA HEK293_OSMI2_6hA USP3 protein_coding retained_intron 6.588331 4.132153 4.002697 0.8778416 0.5671294 -0.04580838 0.09023711 0.4060998 0.0000000 0.07776775 0.00000000 -5.37885779 0.01690417 0.09993333 0.00000000 -0.09993333 0.000131884 0.000131884 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_OSMI2_6hA HEK293_DMSO_6hA log2fold_HEK293_DMSO_6hA_HEK293_OSMI2_6hA
ENSG00000140455 E001 0.4654948 0.0228245714 0.5499878486   15 63504511 63504592 82 + 0.215 0.118 -1.039
ENSG00000140455 E002 0.4654948 0.0228245714 0.5499878486   15 63504593 63504593 1 + 0.215 0.118 -1.039
ENSG00000140455 E003 0.4654948 0.0228245714 0.5499878486   15 63504594 63504594 1 + 0.215 0.118 -1.039
ENSG00000140455 E004 2.1929768 0.0296683731 0.4432790187 0.79951914 15 63504595 63504611 17 + 0.587 0.458 -0.614
ENSG00000140455 E005 4.2033401 0.0825051621 0.5782071663 0.86603816 15 63504612 63504634 23 + 0.779 0.676 -0.420
ENSG00000140455 E006 6.6707914 0.0115573222 0.5177906641 0.83902866 15 63504635 63504655 21 + 0.924 0.841 -0.316
ENSG00000140455 E007 8.1265539 0.0038206325 0.2776123647 0.68102958 15 63504656 63504673 18 + 1.014 0.896 -0.441
ENSG00000140455 E008 10.1665562 0.0027300174 0.2586927686 0.66431402 15 63504674 63504733 60 + 1.100 0.989 -0.404
ENSG00000140455 E009 12.0395325 0.0024422864 0.2468750798 0.65233803 15 63504734 63504830 97 + 1.171 1.065 -0.378
ENSG00000140455 E010 0.1544607 0.0321743942 0.5118799966   15 63515446 63515500 55 + 0.000 0.118 8.526
ENSG00000140455 E011 0.3485388 0.0273777950 0.9774664225   15 63527833 63528140 308 + 0.121 0.118 -0.042
ENSG00000140455 E012 3.4042480 0.0395661233 0.1506390022 0.54022634 15 63529014 63529141 128 + 0.743 0.505 -1.045
ENSG00000140455 E013 2.0980312 0.0170237528 0.7427932802 0.93028822 15 63529142 63529166 25 + 0.512 0.459 -0.261
ENSG00000140455 E014 0.0000000       15 63530498 63530590 93 +      
ENSG00000140455 E015 0.0000000       15 63532506 63532646 141 +      
ENSG00000140455 E016 12.0491584 0.0064649439 0.2494283007 0.65499768 15 63532647 63532707 61 + 1.178 1.066 -0.405
ENSG00000140455 E017 0.8643453 0.5265068386 0.8243083859   15 63533803 63533918 116 + 0.308 0.211 -0.727
ENSG00000140455 E018 14.0882348 0.0023055662 0.2756929299 0.67936829 15 63537025 63537104 80 + 1.232 1.140 -0.324
ENSG00000140455 E019 9.4463104 0.0130198229 0.5250863179 0.84262733 15 63537105 63537137 33 + 0.983 1.054 0.260
ENSG00000140455 E020 8.1202467 0.0032244249 0.9064827737 0.97788771 15 63537138 63537156 19 + 0.971 0.960 -0.038
ENSG00000140455 E021 0.0000000       15 63542055 63542192 138 +      
ENSG00000140455 E022 0.0000000       15 63544625 63544728 104 +      
ENSG00000140455 E023 0.0000000       15 63553333 63553714 382 +      
ENSG00000140455 E024 15.5845023 0.0269223639 0.7741634589 0.94067763 15 63553715 63553798 84 + 1.252 1.212 -0.142
ENSG00000140455 E025 15.4831555 0.0302995599 0.8165909752 0.95353268 15 63556667 63556748 82 + 1.244 1.212 -0.113
ENSG00000140455 E026 18.2084463 0.0343337959 0.5930486790 0.87265677 15 63558106 63558188 83 + 1.326 1.264 -0.216
ENSG00000140455 E027 17.5354813 0.0019226303 0.5117744121 0.83576558 15 63559857 63559970 114 + 1.300 1.252 -0.166
ENSG00000140455 E028 16.1282152 0.0020029073 0.5796309023 0.86671060 15 63562895 63563008 114 + 1.263 1.221 -0.149
ENSG00000140455 E029 26.5380213 0.0011302139 0.0907060990 0.43985769 15 63570433 63570579 147 + 1.494 1.388 -0.365
ENSG00000140455 E030 26.4480834 0.0018401431 0.8440035136 0.96130578 15 63574046 63574152 107 + 1.438 1.430 -0.026
ENSG00000140455 E031 22.5677390 0.0013005221 0.4188105217 0.78560418 15 63574323 63574403 81 + 1.400 1.347 -0.182
ENSG00000140455 E032 2.8323254 0.0081389219 0.0013248060 0.06356358 15 63586608 63586758 151 + 0.216 0.755 2.865
ENSG00000140455 E033 2.3293259 0.0084942115 0.0007542865 0.04614764 15 63587970 63588304 335 + 0.121 0.704 3.659
ENSG00000140455 E034 26.1030265 0.0013044505 0.6856703047 0.91019870 15 63588305 63588423 119 + 1.438 1.415 -0.078
ENSG00000140455 E035 3.5361936 0.1782281749 0.7679843225 0.93891688 15 63588520 63588701 182 + 0.596 0.701 0.451
ENSG00000140455 E036 14.9450674 0.0033991059 0.6796189357 0.90801560 15 63588702 63588728 27 + 1.172 1.213 0.146
ENSG00000140455 E037 25.6726195 0.0057444169 0.9846480684 0.99622092 15 63588729 63588815 87 + 1.414 1.420 0.022
ENSG00000140455 E038 26.6235480 0.0139804371 0.7791966843 0.94208497 15 63588944 63589011 68 + 1.420 1.453 0.116
ENSG00000140455 E039 92.7474864 0.0047480381 0.5609708776 0.85846402 15 63590661 63591373 713 + 1.953 1.987 0.114
ENSG00000140455 E040 69.7023435 0.0005772814 0.0206232172 0.23867305 15 63591374 63593781 2408 + 1.793 1.890 0.326
ENSG00000140455 E041 14.8618388 0.0259116589 0.3217920260 0.71815599 15 63593782 63593915 134 + 1.129 1.237 0.387
ENSG00000140455 E042 35.7567400 0.0169377590 0.2917195657 0.69283061 15 63593916 63594428 513 + 1.518 1.592 0.253
ENSG00000140455 E043 12.3115703 0.0023822931 0.6106824865 0.88031373 15 63594429 63594640 212 + 1.089 1.140 0.186