ENSG00000039560

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
ENST00000265109 ENSG00000039560 HEK293_OSMI2_2hA HEK293_TMG_2hB RAI14 protein_coding protein_coding 11.97165 7.069117 20.18087 0.1509595 0.5982348 1.512062 7.4960475 2.776270 14.258875 0.3549180 0.3790593 2.356465 0.58482917 0.3921000 0.70700000 0.31490000 4.372753e-06 1.091407e-15 FALSE TRUE
ENST00000507883 ENSG00000039560 HEK293_OSMI2_2hA HEK293_TMG_2hB RAI14 protein_coding retained_intron 11.97165 7.069117 20.18087 0.1509595 0.5982348 1.512062 0.6384728 1.972627 0.000000 0.4741289 0.0000000 -7.631270 0.08800833 0.2819333 0.00000000 -0.28193333 1.091407e-15 1.091407e-15 FALSE FALSE
ENST00000510319 ENSG00000039560 HEK293_OSMI2_2hA HEK293_TMG_2hB RAI14 protein_coding nonsense_mediated_decay 11.97165 7.069117 20.18087 0.1509595 0.5982348 1.512062 0.3102875 0.000000 1.042728 0.0000000 0.1773647 6.717989 0.01907083 0.0000000 0.05203333 0.05203333 9.938609e-07 1.091407e-15 FALSE FALSE
ENST00000512629 ENSG00000039560 HEK293_OSMI2_2hA HEK293_TMG_2hB RAI14 protein_coding protein_coding 11.97165 7.069117 20.18087 0.1509595 0.5982348 1.512062 2.9231491 1.746665 4.161661 0.3466391 0.3213715 1.247783 0.24887083 0.2452000 0.20566667 -0.03953333 7.792892e-01 1.091407e-15 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
ENSG00000039560 E001 16.7352981 0.0010914042 7.846203e-02 1.570162e-01 5 34656328 34656398 71 + 1.192 1.093 -0.357
ENSG00000039560 E002 13.3867131 0.0012814633 2.383931e-01 3.722745e-01 5 34656399 34656400 2 + 1.093 1.043 -0.184
ENSG00000039560 E003 14.1930017 0.0012831611 2.400923e-01 3.742603e-01 5 34656401 34656410 10 + 1.115 1.068 -0.168
ENSG00000039560 E004 18.3689944 0.0009974454 4.357517e-02 9.760210e-02 5 34656411 34656431 21 + 1.234 1.115 -0.423
ENSG00000039560 E005 20.1749425 0.0009129452 1.145909e-01 2.122455e-01 5 34656432 34656438 7 + 1.261 1.196 -0.229
ENSG00000039560 E006 29.7157647 0.0007385900 4.651216e-02 1.029644e-01 5 34656439 34656469 31 + 1.423 1.350 -0.251
ENSG00000039560 E007 24.9980966 0.0008502058 1.619518e-02 4.315351e-02 5 34656470 34656475 6 + 1.359 1.232 -0.444
ENSG00000039560 E008 0.0000000       5 34656476 34656696 221 +      
ENSG00000039560 E009 0.0000000       5 34656845 34656959 115 +      
ENSG00000039560 E010 0.7469680 0.0182860920 2.363483e-01 3.699352e-01 5 34658996 34659072 77 + 0.253 0.000 -11.332
ENSG00000039560 E011 0.0000000       5 34667263 34667379 117 +      
ENSG00000039560 E012 0.0000000       5 34684507 34684517 11 +      
ENSG00000039560 E013 0.0000000       5 34684518 34684526 9 +      
ENSG00000039560 E014 0.0000000       5 34684527 34684535 9 +      
ENSG00000039560 E015 0.0000000       5 34684536 34684542 7 +      
ENSG00000039560 E016 0.0000000       5 34684543 34684551 9 +      
ENSG00000039560 E017 0.0000000       5 34684552 34684553 2 +      
ENSG00000039560 E018 0.0000000       5 34684554 34684652 99 +      
ENSG00000039560 E019 0.0000000       5 34684653 34684715 63 +      
ENSG00000039560 E020 0.0000000       5 34684716 34684775 60 +      
ENSG00000039560 E021 0.0000000       5 34685032 34685081 50 +      
ENSG00000039560 E022 0.0000000       5 34685700 34685703 4 +      
ENSG00000039560 E023 0.0000000       5 34685704 34685732 29 +      
ENSG00000039560 E024 0.0000000       5 34685733 34685814 82 +      
ENSG00000039560 E025 0.0000000       5 34686385 34686440 56 +      
ENSG00000039560 E026 0.0000000       5 34686862 34686871 10 +      
ENSG00000039560 E027 48.8111642 0.0009539472 3.887587e-02 8.895150e-02 5 34686872 34686955 84 + 1.628 1.585 -0.147
ENSG00000039560 E028 0.0000000       5 34687559 34687722 164 +      
ENSG00000039560 E029 0.0000000       5 34688068 34688188 121 +      
ENSG00000039560 E030 0.0000000       5 34688189 34688248 60 +      
ENSG00000039560 E031 0.0000000       5 34688249 34688309 61 +      
ENSG00000039560 E032 0.0000000       5 34716055 34716085 31 +      
ENSG00000039560 E033 0.1451727 0.0427270902 1.000000e+00   5 34716086 34716221 136 + 0.064 0.000 -8.886
ENSG00000039560 E034 0.1451727 0.0427270902 1.000000e+00   5 34716789 34716878 90 + 0.064 0.000 -8.886
ENSG00000039560 E035 0.0000000       5 34728545 34728573 29 +      
ENSG00000039560 E036 0.0000000       5 34728574 34728660 87 +      
ENSG00000039560 E037 0.5202097 0.0206934771 6.484156e-01 7.599300e-01 5 34733116 34733262 147 + 0.119 0.223 1.081
ENSG00000039560 E038 67.9226829 0.0026365769 2.275101e-02 5.723386e-02 5 34757468 34757582 115 + 1.769 1.726 -0.148
ENSG00000039560 E039 35.1749740 0.0067952310 1.975890e-01 3.231967e-01 5 34757583 34757598 16 + 1.484 1.464 -0.066
ENSG00000039560 E040 3.4427518 0.0045260873 5.968232e-01 7.187116e-01 5 34757599 34757614 16 + 0.548 0.700 0.664
ENSG00000039560 E041 4.9174615 0.0209680203 5.160882e-06 3.661575e-05 5 34757615 34757868 254 + 0.412 1.137 3.005
ENSG00000039560 E042 65.8940462 0.0091075370 6.282604e-02 1.314144e-01 5 34795939 34796027 89 + 1.754 1.711 -0.143
ENSG00000039560 E043 60.0678007 0.0075980640 1.498257e-02 4.044864e-02 5 34803712 34803776 65 + 1.721 1.638 -0.281
ENSG00000039560 E044 53.0719624 0.0006128431 5.322058e-06 3.764086e-05 5 34807800 34807857 58 + 1.688 1.484 -0.699
ENSG00000039560 E045 46.0661497 0.0005220891 1.113878e-04 5.741129e-04 5 34808584 34808654 71 + 1.627 1.454 -0.591
ENSG00000039560 E046 56.9778198 0.0003971117 2.311465e-05 1.412399e-04 5 34811012 34811118 107 + 1.714 1.546 -0.574
ENSG00000039560 E047 91.0852159 0.0047331832 1.560500e-03 5.831353e-03 5 34811767 34811945 179 + 1.900 1.808 -0.310
ENSG00000039560 E048 60.7252356 0.0029115834 5.475621e-03 1.722334e-02 5 34812180 34812208 29 + 1.727 1.642 -0.288
ENSG00000039560 E049 69.0804604 0.0021386940 2.166452e-05 1.332212e-04 5 34813574 34813660 87 + 1.797 1.635 -0.549
ENSG00000039560 E050 94.2649826 0.0052390444 2.474386e-04 1.164605e-03 5 34814583 34814669 87 + 1.922 1.799 -0.415
ENSG00000039560 E051 75.2592497 0.0003681303 1.550576e-05 9.863407e-05 5 34818797 34818851 55 + 1.829 1.692 -0.465
ENSG00000039560 E052 77.4447786 0.0015051565 3.067365e-05 1.820727e-04 5 34821732 34821850 119 + 1.842 1.704 -0.468
ENSG00000039560 E053 538.8362449 0.0017920833 5.817201e-03 1.813137e-02 5 34822956 34824491 1536 + 2.646 2.670 0.080
ENSG00000039560 E054 0.0000000       5 34826004 34826031 28 +      
ENSG00000039560 E055 0.0000000       5 34826032 34826329 298 +      
ENSG00000039560 E056 104.7307330 0.0003146417 2.611814e-02 6.418310e-02 5 34826330 34826479 150 + 1.899 2.070 0.574
ENSG00000039560 E057 77.0338990 0.0003380691 2.279324e-02 5.731422e-02 5 34829732 34829797 66 + 1.761 1.948 0.629
ENSG00000039560 E058 0.9329388 0.2611102130 8.356695e-01 8.972337e-01 5 34829798 34829840 43 + 0.254 0.223 -0.245
ENSG00000039560 E059 582.8003054 0.0081801705 5.862319e-16 2.284713e-14 5 34830688 34832612 1925 + 2.572 2.944 1.236