ENSMUSG00000028364

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
ENSMUST00000030056 ENSMUSG00000028364 Control shVgll3 Tnc protein_coding protein_coding 129.4446 142.2792 116.61 2.822725 4.634962 -0.2870113 43.220850 47.890311 38.551389 2.4179091 1.2039488 -0.3128780 0.3339500 0.3363000 0.3316000 -0.004700000 1.00000000 0.01697182 FALSE  
ENSMUST00000107372 ENSMUSG00000028364 Control shVgll3 Tnc protein_coding protein_coding 129.4446 142.2792 116.61 2.822725 4.634962 -0.2870113 16.466039 14.634496 18.297582 0.7465073 0.9824490 0.3220827 0.1301167 0.1028333 0.1574000 0.054566667 0.01697182 0.01697182 FALSE  
ENSMUST00000107377 ENSMUSG00000028364 Control shVgll3 Tnc protein_coding protein_coding 129.4446 142.2792 116.61 2.822725 4.634962 -0.2870113 28.082622 34.190861 21.974384 1.0781397 3.0199673 -0.6375535 0.2138667 0.2405000 0.1872333 -0.053266667 0.66764579 0.01697182 FALSE  
MSTRG.16041.1 ENSMUSG00000028364 Control shVgll3 Tnc protein_coding   129.4446 142.2792 116.61 2.822725 4.634962 -0.2870113 9.372264 9.795975 8.948553 0.6666555 1.9223592 -0.1303954 0.0724500 0.0691000 0.0758000 0.006700000 1.00000000 0.01697182 FALSE  
MSTRG.16041.5 ENSMUSG00000028364 Control shVgll3 Tnc protein_coding   129.4446 142.2792 116.61 2.822725 4.634962 -0.2870113 31.680850 34.982241 28.379459 1.3770460 0.2805655 -0.3016797 0.2448333 0.2456667 0.2440000 -0.001666667 1.00000000 0.01697182 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
ENSMUSG00000028364 E001 0.8261889 1.721489e-02 0.810760385 0.98376893 4 63878022 63878038 17 - 0.235 0.280 0.330
ENSMUSG00000028364 E002 3942.7469518 2.574120e-03 0.680421244 0.96279690 4 63878039 63878780 742 - 3.587 3.600 0.044
ENSMUSG00000028364 E003 1106.7961616 2.769310e-03 0.763912252 0.97799068 4 63880224 63880387 164 - 3.036 3.048 0.039
ENSMUSG00000028364 E004 916.9847985 2.194849e-04 0.776944845 0.97887310 4 63882835 63882996 162 - 2.961 2.961 -0.002
ENSMUSG00000028364 E005 623.0654319 9.071583e-04 0.934816738 0.99963445 4 63883821 63883917 97 - 2.793 2.794 0.005
ENSMUSG00000028364 E006 1037.0705700 7.942722e-05 0.865146433 0.98892123 4 63884748 63884899 152 - 3.012 3.017 0.017
ENSMUSG00000028364 E007 1342.0032602 7.696339e-04 0.773640806 0.97808677 4 63885454 63885586 133 - 3.127 3.126 -0.004
ENSMUSG00000028364 E008 1215.8926409 6.664418e-04 0.437209151 0.91079676 4 63888551 63888681 131 - 3.075 3.091 0.054
ENSMUSG00000028364 E009 1178.1438179 7.945225e-05 0.768902428 0.97799068 4 63889395 63889538 144 - 3.070 3.070 -0.001
ENSMUSG00000028364 E010 718.9500745 3.120196e-04 0.034958686 0.42325292 4 63890915 63891034 120 - 2.871 2.842 -0.098
ENSMUSG00000028364 E011 662.0220014 6.679622e-04 0.904295821 0.99563225 4 63893439 63893582 144 - 2.819 2.820 0.003
ENSMUSG00000028364 E012 524.3292149 1.061308e-04 0.953499047 1.00000000 4 63894683 63894805 123 - 2.717 2.721 0.013
ENSMUSG00000028364 E013 432.7888011 1.503850e-04 0.443715341 0.91335964 4 63900888 63901160 273 - 2.627 2.643 0.056
ENSMUSG00000028364 E014 262.0664427 1.239817e-04 0.002290284 0.08587097 4 63902697 63902969 273 - 2.453 2.388 -0.217
ENSMUSG00000028364 E015 839.4077080 3.932937e-04 0.764133600 0.97799068 4 63911264 63911536 273 - 2.924 2.922 -0.005
ENSMUSG00000028364 E016 789.7509002 1.614812e-04 0.495781244 0.92681021 4 63913778 63914050 273 - 2.890 2.902 0.041
ENSMUSG00000028364 E017 705.8280818 3.994902e-04 0.986670578 1.00000000 4 63918150 63918422 273 - 2.846 2.849 0.010
ENSMUSG00000028364 E018 588.4445920 2.808830e-03 0.482327355 0.92372810 4 63918935 63919207 273 - 2.779 2.760 -0.063
ENSMUSG00000028364 E019 783.7691458 1.887945e-03 0.881569376 0.99216842 4 63924483 63924746 264 - 2.894 2.892 -0.006
ENSMUSG00000028364 E020 465.3945445 7.179551e-04 0.840403817 0.98677151 4 63925585 63925674 90 - 2.668 2.667 -0.005
ENSMUSG00000028364 E021 775.3806718 4.313713e-04 0.664062346 0.95817326 4 63925919 63926104 186 - 2.891 2.887 -0.014
ENSMUSG00000028364 E022 1036.8827838 2.537150e-04 0.282487978 0.82882979 4 63926851 63927120 270 - 3.021 3.009 -0.038
ENSMUSG00000028364 E023 0.9880320 1.470960e-02 0.824606404 0.98478718 4 63930906 63931304 399 - 0.318 0.280 -0.255
ENSMUSG00000028364 E024 780.6349739 1.356803e-03 0.766554960 0.97799068 4 63931305 63931461 157 - 2.894 2.889 -0.015
ENSMUSG00000028364 E025 438.5918474 6.199898e-04 0.792737429 0.98058592 4 63932166 63932281 116 - 2.643 2.640 -0.009
ENSMUSG00000028364 E026 585.7018349 2.606672e-03 0.493680217 0.92674629 4 63933132 63933395 264 - 2.777 2.759 -0.059
ENSMUSG00000028364 E027 2372.2635383 2.178824e-03 0.974318030 1.00000000 4 63935068 63936477 1410 - 3.372 3.375 0.008
ENSMUSG00000028364 E028 1283.3645652 2.567838e-03 0.287707666 0.83431550 4 63938381 63938962 582 - 3.091 3.120 0.096
ENSMUSG00000028364 E029 327.9443068 1.708766e-03 0.264565465 0.81433690 4 63964986 63965307 322 - 2.497 2.531 0.112

Help

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