ENSMUSG00000036564

1 Isoform Switch

Summary Plot

Only the isoforms with fraction > 5% are shown below.

  • Note:

    • About the Coding Potential: Please check the spreadsheet in the “Results” tag to confirm the coding potential. The above figure only show the predicted coding potential. The “gene_biotype” in the result spreadsheet is from the database record. Therefore, if you find conflicts between “gene_biotype” and “codingPotential”, please trust the “gene_biotype”.

    • 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
ENSMUST00000073139 ENSMUSG00000036564 Control shVgll3 Ndrg4 protein_coding protein_coding 17.0891 21.59614 12.58206 0.4446279 0.5642838 -0.7789266 2.722734 2.895309 2.5501580 0.03788160 0.33859494 -0.1824589 0.1677500 0.1341667 0.2013333 0.06716667 0.294392440 0.001361207 FALSE TRUE
ENSMUST00000080666 ENSMUSG00000036564 Control shVgll3 Ndrg4 protein_coding protein_coding 17.0891 21.59614 12.58206 0.4446279 0.5642838 -0.7789266 7.928309 11.720132 4.1364861 0.18149574 0.31653777 -1.5002581 0.4371000 0.5428000 0.3314000 -0.21140000 0.001361207 0.001361207 FALSE TRUE
ENSMUST00000159632 ENSMUSG00000036564 Control shVgll3 Ndrg4 protein_coding retained_intron 17.0891 21.59614 12.58206 0.4446279 0.5642838 -0.7789266 1.920646 2.271603 1.5696895 0.24751919 0.06041997 -0.5304066 0.1154000 0.1052000 0.1256000 0.02040000 0.970665669 0.001361207   FALSE
ENSMUST00000212160 ENSMUSG00000036564 Control shVgll3 Ndrg4 protein_coding protein_coding 17.0891 21.59614 12.58206 0.4446279 0.5642838 -0.7789266 1.212099 1.771768 0.6524287 0.02991518 0.37015670 -1.4274728 0.0664500 0.0821000 0.0508000 -0.03130000 0.970665669 0.001361207 FALSE TRUE
MSTRG.22771.6 ENSMUSG00000036564 Control shVgll3 Ndrg4 protein_coding   17.0891 21.59614 12.58206 0.4446279 0.5642838 -0.7789266 2.688827 2.661730 2.7159233 0.21652056 0.20618494 0.0289709 0.1691167 0.1229667 0.2152667 0.09230000 0.007429215 0.001361207 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.

Help

Please Click HERE to learn more details about the results of IsoformSwitchAnalyzeR.

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 shVgll3 Control log2fold_Control_shVgll3
ENSMUSG00000036564 E001 0.0000000       8 96403608 96403720 113 +      
ENSMUSG00000036564 E002 0.0000000       8 96404281 96404499 219 +      
ENSMUSG00000036564 E003 0.0000000       8 96404713 96404872 160 +      
ENSMUSG00000036564 E004 0.0000000       8 96404873 96405011 139 +      
ENSMUSG00000036564 E005 0.0000000       8 96423822 96423916 95 +      
ENSMUSG00000036564 E006 0.0000000       8 96426741 96426785 45 +      
ENSMUSG00000036564 E007 0.4933433 0.0218953045 3.102444e-01   8 96429665 96429690 26 + 0.268 0.098 -1.746
ENSMUSG00000036564 E008 0.6592467 0.0723372266 6.226347e-01   8 96429691 96429694 4 + 0.268 0.179 -0.745
ENSMUSG00000036564 E009 2.6154034 0.2462746752 8.069014e-01 9.826240e-01 8 96429695 96429697 3 + 0.495 0.578 0.387
ENSMUSG00000036564 E010 34.0538076 0.0007068386 1.064154e-01 6.449255e-01 8 96429698 96429805 108 + 1.464 1.566 0.349
ENSMUSG00000036564 E011 0.3272567 0.0290602334 7.064780e-01   8 96432790 96432815 26 + 0.154 0.098 -0.746
ENSMUSG00000036564 E012 53.1070583 0.0003822150 1.838088e-01 7.608225e-01 8 96432816 96432921 106 + 1.676 1.743 0.227
ENSMUSG00000036564 E013 40.9265540 0.0047676822 9.847329e-01 1.000000e+00 8 96433159 96433201 43 + 1.609 1.609 0.000
ENSMUSG00000036564 E014 59.6629707 0.0003748633 3.037316e-01 8.445572e-01 8 96433202 96433279 78 + 1.738 1.787 0.165
ENSMUSG00000036564 E015 41.4456408 0.0111506953 2.924003e-01 8.378109e-01 8 96433365 96433427 63 + 1.561 1.643 0.280
ENSMUSG00000036564 E016 50.0867243 0.0004625365 2.004735e-01 7.765931e-01 8 96433557 96433617 61 + 1.652 1.719 0.225
ENSMUSG00000036564 E017 46.2574681 0.0107138492 2.017344e-01 7.768696e-01 8 96435236 96435322 87 + 1.599 1.694 0.323
ENSMUSG00000036564 E018 35.4958234 0.0007181840 1.787322e-01 7.571012e-01 8 96435405 96435461 57 + 1.495 1.578 0.284
ENSMUSG00000036564 E019 29.6295516 0.0006563586 8.959944e-01 9.956003e-01 8 96435711 96435737 27 + 1.477 1.469 -0.026
ENSMUSG00000036564 E020 49.3670666 0.0012750615 2.998047e-01 8.404484e-01 8 96435738 96435814 77 + 1.652 1.708 0.189
ENSMUSG00000036564 E021 34.3670622 0.0256636087 4.528791e-01 9.137770e-01 8 96436394 96436450 57 + 1.495 1.557 0.213
ENSMUSG00000036564 E022 2.4550097 0.0242039582 7.674547e-01 9.779907e-01 8 96436451 96436530 80 + 0.496 0.549 0.253
ENSMUSG00000036564 E023 12.0126441 0.0021872898 5.949692e-01 9.516577e-01 8 96436531 96436534 4 + 1.067 1.120 0.195
ENSMUSG00000036564 E024 22.8671266 0.0028396861 3.072565e-01 8.470590e-01 8 96436535 96436582 48 + 1.410 1.334 -0.264
ENSMUSG00000036564 E025 7.4053259 0.0028626667 2.418924e-01 8.044216e-01 8 96436583 96436902 320 + 0.816 0.960 0.553
ENSMUSG00000036564 E026 5.5970373 0.0039745164 2.546156e-01 8.074851e-01 8 96437094 96437273 180 + 0.893 0.746 -0.577
ENSMUSG00000036564 E027 3.2933847 0.0053829947 8.068321e-01 9.826240e-01 8 96437274 96437291 18 + 0.644 0.607 -0.161
ENSMUSG00000036564 E028 37.5521498 0.0047646504 3.421359e-01 8.712098e-01 8 96437292 96437339 48 + 1.609 1.548 -0.208
ENSMUSG00000036564 E029 35.5385028 0.0005516366 9.367475e-01 9.996345e-01 8 96437562 96437597 36 + 1.545 1.551 0.019
ENSMUSG00000036564 E030 45.8818232 0.0004347491 4.443197e-02 4.693918e-01 8 96437721 96437772 52 + 1.586 1.695 0.372
ENSMUSG00000036564 E031 99.2150674 0.0035547194 2.222717e-07 4.127198e-05 8 96437773 96438524 752 + 2.114 1.889 -0.756
ENSMUSG00000036564 E032 44.5746567 0.0004572153 9.227004e-07 1.332562e-04 8 96438525 96438952 428 + 1.786 1.532 -0.863
ENSMUSG00000036564 E033 11.8496322 0.0015501175 8.553652e-03 2.019468e-01 8 96438953 96438991 39 + 1.235 0.984 -0.907
ENSMUSG00000036564 E034 666.9816658 0.0012215841 3.201941e-01 8.558876e-01 8 96439806 96441747 1942 + 2.801 2.816 0.051

Help

Please Click HERE to learn more details about the results from DEXseq.