ENSMUSG00000040410

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
ENSMUST00000039234 ENSMUSG00000040410 Control shVgll3 Fbxl4 protein_coding protein_coding 10.40451 10.56543 10.24358 0.2193083 0.4432127 -0.0445878 7.4827689 8.6584572 6.3070807 0.43481150 0.20557607 -0.4565172 0.7187333 0.8186667 0.6188 -0.1998667 0.0538938557 1.61629e-05 FALSE TRUE
ENSMUST00000184582 ENSMUSG00000040410 Control shVgll3 Fbxl4 protein_coding nonsense_mediated_decay 10.40451 10.56543 10.24358 0.2193083 0.4432127 -0.0445878 0.7372201 0.7086994 0.7657408 0.06059594 0.48416096 0.1101863 0.0708500 0.0672000 0.0745 0.0073000 0.9970954905 1.61629e-05 TRUE TRUE
ENSMUST00000185029 ENSMUSG00000040410 Control shVgll3 Fbxl4 protein_coding nonsense_mediated_decay 10.40451 10.56543 10.24358 0.2193083 0.4432127 -0.0445878 1.8456283 1.0644944 2.6267623 0.08797089 0.04153664 1.2951096 0.1790333 0.1009667 0.2571 0.1561333 0.0000161629 1.61629e-05 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
ENSMUSG00000040410 E001 0.1660866 0.0345109431 4.874095e-01   4 22357543 22357559 17 + 0.124 0.000 -9.994
ENSMUSG00000040410 E002 0.3274400 0.0262639025 1.996640e-01   4 22357560 22357570 11 + 0.220 0.000 -10.994
ENSMUSG00000040410 E003 9.7089943 0.0240891131 9.153233e-01 9.975128e-01 4 22357571 22357615 45 + 1.023 1.036 0.047
ENSMUSG00000040410 E004 20.5905326 0.0037432847 4.545051e-01 9.139571e-01 4 22357616 22357681 66 + 1.363 1.303 -0.210
ENSMUSG00000040410 E005 33.5969671 0.0005979311 7.655541e-01 9.779907e-01 4 22375661 22375770 110 + 1.531 1.547 0.055
ENSMUSG00000040410 E006 46.1051116 0.0004443983 3.867927e-01 8.856333e-01 4 22376496 22376632 137 + 1.651 1.693 0.143
ENSMUSG00000040410 E007 138.9527174 0.0002408081 6.329962e-01 9.564368e-01 4 22376633 22377077 445 + 2.140 2.152 0.039
ENSMUSG00000040410 E008 115.3999732 0.0006105130 5.537241e-02 5.165443e-01 4 22385907 22386252 346 + 2.035 2.095 0.200
ENSMUSG00000040410 E009 19.0993918 0.0037762459 3.277731e-02 4.080119e-01 4 22390677 22390713 37 + 1.208 1.381 0.604
ENSMUSG00000040410 E010 71.3859687 0.0003501141 1.937351e-01 7.695665e-01 4 22390714 22390921 208 + 1.834 1.884 0.171
ENSMUSG00000040410 E011 109.8418727 0.0016222766 3.011927e-01 8.425210e-01 4 22403532 22403745 214 + 2.027 2.062 0.120
ENSMUSG00000040410 E012 38.0208110 0.0005233832 3.847328e-02 4.421026e-01 4 22422717 22422788 72 + 1.531 1.644 0.388
ENSMUSG00000040410 E013 63.2305506 0.0003411818 9.006662e-17 5.853330e-14 4 22422789 22423927 1139 + 1.955 1.582 -1.264
ENSMUSG00000040410 E014 104.3239600 0.0007941243 7.266040e-01 9.710736e-01 4 22427150 22427462 313 + 2.017 2.028 0.035
ENSMUSG00000040410 E015 7.9122138 0.0116247442 6.086215e-01 9.533477e-01 4 22433146 22433258 113 + 0.981 0.916 -0.243
ENSMUSG00000040410 E016 57.4031174 0.0084006681 2.545779e-01 8.074851e-01 4 22433567 22434091 525 + 1.801 1.729 -0.241

Help

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