ENSMUSG00000020541

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
ENSMUST00000020849 ENSMUSG00000020541 Control shVgll3 Tom1l1 protein_coding protein_coding 1.699559 0.8142074 2.58491 0.04953753 0.1608773 1.654605 0.90961194 0.7949685 1.0242554 0.03497265 0.16269378 0.3615884 0.69251667 0.9785667 0.4064667 -0.5721000 5.732075e-05 5.732075e-05 FALSE TRUE
ENSMUST00000107868 ENSMUSG00000020541 Control shVgll3 Tom1l1 protein_coding protein_coding 1.699559 0.8142074 2.58491 0.04953753 0.1608773 1.654605 0.50828571 0.0000000 1.0165714 0.00000000 0.52296764 6.6816902 0.18651667 0.0000000 0.3730333 0.3730333 7.672076e-01 5.732075e-05 FALSE TRUE
ENSMUST00000107869 ENSMUSG00000020541 Control shVgll3 Tom1l1 protein_coding protein_coding 1.699559 0.8142074 2.58491 0.04953753 0.1608773 1.654605 0.14701790 0.0000000 0.2940358 0.00000000 0.29403580 4.9261693 0.06308333 0.0000000 0.1261667 0.1261667 1.000000e+00 5.732075e-05 FALSE TRUE
ENSMUST00000127034 ENSMUSG00000020541 Control shVgll3 Tom1l1 protein_coding retained_intron 1.699559 0.8142074 2.58491 0.04953753 0.1608773 1.654605 0.08105963 0.0000000 0.1621193 0.00000000 0.08938951 4.1053367 0.02950000 0.0000000 0.0590000 0.0590000 9.706657e-01 5.732075e-05   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.

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
ENSMUSG00000020541 E001 38.7969866 0.0235399210 2.170098e-14 1.208848e-11 11 90534291 90536515 2225 - 1.328 1.871 1.852
ENSMUSG00000020541 E002 1.4765284 0.0114315971 2.519081e-01 8.064151e-01 11 90536516 90536516 1 - 0.294 0.510 1.207
ENSMUSG00000020541 E003 28.6139818 0.0008356945 6.234282e-03 1.657469e-01 11 90536517 90537054 538 - 1.360 1.545 0.639
ENSMUSG00000020541 E004 3.4722723 0.0061535337 4.915262e-01 9.267463e-01 11 90537055 90537135 81 - 0.570 0.691 0.529
ENSMUSG00000020541 E005 3.1320285 0.0094578268 2.698595e-01 8.182921e-01 11 90537661 90537725 65 - 0.613 0.428 -0.886
ENSMUSG00000020541 E006 4.6360375 0.0297660738 1.416031e-04 1.016241e-02 11 90540174 90540249 76 - 0.808 0.000 -14.435
ENSMUSG00000020541 E007 0.6663347 0.0948058314 2.728395e-01 8.189943e-01 11 90540250 90540611 362 - 0.249 0.000 -12.141
ENSMUSG00000020541 E008 7.6101699 0.0296180093 2.953257e-05 2.878933e-03 11 90540612 90540714 103 - 0.988 0.193 -3.965
ENSMUSG00000020541 E009 0.1660866 0.0346011165 1.000000e+00   11 90540715 90540755 41 - 0.077 0.000 -10.454
ENSMUSG00000020541 E010 6.4062850 0.0403028410 1.207121e-05 1.307491e-03 11 90542737 90542788 52 - 0.932 0.000 -14.750
ENSMUSG00000020541 E011 8.0573138 0.0026343051 2.382122e-05 2.402247e-03 11 90547177 90547276 100 - 1.004 0.326 -3.026
ENSMUSG00000020541 E012 0.3281028 0.0262247277 6.541249e-01   11 90547898 90548539 642 - 0.142 0.000 -11.394
ENSMUSG00000020541 E013 6.1066807 0.0032656793 7.217985e-05 5.823172e-03 11 90548540 90548657 118 - 0.902 0.193 -3.641
ENSMUSG00000020541 E014 0.3274400 0.0275656743 6.536104e-01   11 90548658 90548973 316 - 0.142 0.000 -11.391
ENSMUSG00000020541 E015 4.1047487 0.0048567844 1.868344e-02 3.082636e-01 11 90548974 90549034 61 - 0.737 0.326 -1.995
ENSMUSG00000020541 E016 7.6017799 0.0033644033 2.673428e-01 8.166907e-01 11 90552582 90552715 134 - 0.912 0.780 -0.511
ENSMUSG00000020541 E017 0.6602759 0.0179914910 2.466821e-01   11 90552716 90554138 1423 - 0.249 0.000 -12.286
ENSMUSG00000020541 E018 2.3087172 0.0106023538 8.636228e-01 9.889212e-01 11 90561910 90561947 38 - 0.468 0.510 0.207
ENSMUSG00000020541 E019 2.3057158 0.0077532925 6.454503e-02 5.507372e-01 11 90561948 90562026 79 - 0.546 0.193 -2.172
ENSMUSG00000020541 E020 3.9729270 0.0121264982 4.138266e-03 1.261048e-01 11 90563659 90563763 105 - 0.737 0.193 -2.995
ENSMUSG00000020541 E021 3.9597760 0.0057324681 9.475937e-02 6.302892e-01 11 90564490 90564612 123 - 0.705 0.428 -1.279
ENSMUSG00000020541 E022 4.4647478 0.0060834981 1.552575e-03 6.827827e-02 11 90565496 90565645 150 - 0.781 0.193 -3.172
ENSMUSG00000020541 E023 3.2959337 0.0055808322 6.582289e-02 5.551523e-01 11 90574061 90574115 55 - 0.652 0.326 -1.641
ENSMUSG00000020541 E024 1.6367937 0.3092058701 9.056967e-01 9.956323e-01 11 90574116 90574139 24 - 0.371 0.428 0.316
ENSMUSG00000020541 E025 0.0000000       11 90574140 90574156 17 -      
ENSMUSG00000020541 E026 3.4577668 0.0053731841 1.767162e-01 7.567762e-01 11 90575888 90575972 85 - 0.652 0.428 -1.056
ENSMUSG00000020541 E027 1.9910802 0.0101324152 4.214780e-01 9.033740e-01 11 90578339 90578433 95 - 0.468 0.326 -0.793
ENSMUSG00000020541 E028 0.1660866 0.0346011165 1.000000e+00   11 90578553 90579192 640 - 0.077 0.000 -10.454

Help

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