ENSMUSG00000042396

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
ENSMUST00000170000 ENSMUSG00000042396 Control shVgll3 Rbm7 protein_coding protein_coding 30.06492 30.44404 29.6858 0.5590877 1.39107 -0.03637454 16.544196 18.296384 14.792009 0.2364422 0.7008196 -0.3065538 0.55011667 0.60146667 0.4987667 -0.10270000 0.1183000333 0.0001400185 FALSE TRUE
ENSMUST00000213276 ENSMUSG00000042396 Control shVgll3 Rbm7 protein_coding protein_coding 30.06492 30.44404 29.6858 0.5590877 1.39107 -0.03637454 1.738965 2.133577 1.344353 0.1832774 0.0829464 -0.6624167 0.05801667 0.07033333 0.0457000 -0.02463333 0.6174404521 0.0001400185 FALSE TRUE
ENSMUST00000214923 ENSMUSG00000042396 Control shVgll3 Rbm7 protein_coding nonsense_mediated_decay 30.06492 30.44404 29.6858 0.5590877 1.39107 -0.03637454 9.201249 7.098841 11.303657 0.5103259 0.7148788 0.6703791 0.30668333 0.23276667 0.3806000 0.14783333 0.0001400185 0.0001400185 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.

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
ENSMUSG00000042396 E001 0.1615462 3.440669e-02 4.917719e-01   9 48399996 48399999 4 - 0.000 0.123 9.036
ENSMUSG00000042396 E002 0.4933529 2.666030e-02 8.610130e-02   9 48400000 48400000 1 - 0.000 0.297 12.185
ENSMUSG00000042396 E003 0.6592563 1.423335e-01 5.612230e-02   9 48400001 48400001 1 - 0.000 0.364 11.983
ENSMUSG00000042396 E004 1.3095958 5.556551e-02 5.228678e-01 0.9337797524 9 48400002 48400008 7 - 0.299 0.421 0.727
ENSMUSG00000042396 E005 1.6368723 1.080264e-02 2.135666e-01 0.7863254999 9 48400009 48400014 6 - 0.299 0.518 1.211
ENSMUSG00000042396 E006 696.2023091 9.613816e-05 7.732915e-01 0.9780867667 9 48400015 48401288 1274 - 2.841 2.845 0.013
ENSMUSG00000042396 E007 46.6205327 3.071667e-03 4.172266e-03 0.1264434325 9 48401289 48402147 859 - 1.587 1.751 0.557
ENSMUSG00000042396 E008 144.4775208 2.262392e-04 1.998411e-02 0.3204280240 9 48402148 48402238 91 - 2.128 2.195 0.226
ENSMUSG00000042396 E009 6.2519020 6.869828e-03 9.782641e-01 1.0000000000 9 48402239 48402353 115 - 0.862 0.859 -0.011
ENSMUSG00000042396 E010 33.0894680 5.794769e-04 4.008487e-01 0.8907794966 9 48403897 48404706 810 - 1.506 1.557 0.176
ENSMUSG00000042396 E011 174.5435669 1.916979e-04 5.971479e-01 0.9520020264 9 48404707 48404794 88 - 2.237 2.251 0.049
ENSMUSG00000042396 E012 2.6301175 6.478070e-03 9.839362e-01 1.0000000000 9 48404795 48405318 524 - 0.561 0.559 -0.011
ENSMUSG00000042396 E013 237.8104113 1.316085e-04 1.867785e-02 0.3082635834 9 48405319 48405481 163 - 2.402 2.353 -0.165
ENSMUSG00000042396 E014 5.1149668 1.447205e-02 2.481443e-02 0.3529240974 9 48405482 48405582 101 - 0.918 0.597 -1.301
ENSMUSG00000042396 E015 46.3696555 4.841076e-04 3.981096e-06 0.0004801119 9 48405583 48405687 105 - 1.779 1.541 -0.808
ENSMUSG00000042396 E016 24.8540697 9.876307e-04 7.353027e-01 0.9729001432 9 48405688 48406454 767 - 1.400 1.424 0.084
ENSMUSG00000042396 E017 124.2221904 1.974249e-04 7.972300e-01 0.9811209784 9 48406455 48406715 261 - 2.101 2.094 -0.023

Help

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