ENSMUSG00000020053

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
ENSMUST00000095360 ENSMUSG00000020053 Control shVgll3 Igf1 protein_coding protein_coding 40.1164 28.70811 51.52468 2.144573 3.280473 0.8435828 7.909455 8.629607 7.189303 0.2281941 0.2203892 -0.2631085 0.2221833 0.3034333 0.1409333 -0.1625000 5.629527e-06 5.629527e-06 FALSE FALSE
ENSMUST00000126490 ENSMUSG00000020053 Control shVgll3 Igf1 protein_coding protein_coding 40.1164 28.70811 51.52468 2.144573 3.280473 0.8435828 30.294953 18.579856 42.010050 2.1532940 3.3312031 1.1765623 0.7283333 0.6428667 0.8138000 0.1709333 4.074298e-04 5.629527e-06 FALSE 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
ENSMUSG00000020053 E001 4.4150300 0.0492541454 2.983522e-01 8.404484e-01 10 87694127 87694875 749 + 0.815 0.635 -0.737
ENSMUSG00000020053 E002 113.9993389 0.0033144122 2.677131e-02 3.667105e-01 10 87694930 87695119 190 + 2.107 2.008 -0.329
ENSMUSG00000020053 E003 98.4856780 0.0017001838 1.587144e-03 6.927764e-02 10 87695120 87695192 73 + 2.058 1.926 -0.441
ENSMUSG00000020053 E004 108.9173461 0.0003075567 4.927782e-04 2.811961e-02 10 87695193 87695274 82 + 2.098 1.975 -0.413
ENSMUSG00000020053 E005 0.8158866 0.0173840249 6.342296e-01 9.564604e-01 10 87695352 87695472 121 + 0.218 0.300 0.612
ENSMUSG00000020053 E006 0.6548895 0.0190828828 9.765235e-01   10 87695473 87695501 29 + 0.218 0.221 0.027
ENSMUSG00000020053 E007 7.2648286 0.0728361342 1.084609e-01 6.489904e-01 10 87695528 87695629 102 + 1.034 0.752 -1.077
ENSMUSG00000020053 E008 9.0908450 0.0154384735 2.955708e-02 3.867944e-01 10 87695892 87696467 576 + 1.116 0.844 -1.014
ENSMUSG00000020053 E009 13.0542458 0.0169290906 1.259113e-03 5.798860e-02 10 87696468 87697157 690 + 1.292 0.920 -1.348
ENSMUSG00000020053 E010 11.8578749 0.0016005950 1.072926e-05 1.184065e-03 10 87697158 87697190 33 + 1.277 0.823 -1.667
ENSMUSG00000020053 E011 16.7849976 0.0030879426 4.217142e-05 3.946570e-03 10 87697191 87697247 57 + 1.394 1.027 -1.305
ENSMUSG00000020053 E012 179.8062401 0.0002049795 8.574521e-11 2.865850e-08 10 87700593 87700749 157 + 2.335 2.160 -0.585
ENSMUSG00000020053 E013 281.0701942 0.0026069007 1.824292e-10 5.927935e-08 10 87749481 87749662 182 + 2.536 2.340 -0.654
ENSMUSG00000020053 E014 35.7303685 0.0005244593 2.796549e-04 1.797474e-02 10 87751160 87751211 52 + 1.660 1.440 -0.750
ENSMUSG00000020053 E015 7.7376501 0.0027868570 2.338749e-01 8.037828e-01 10 87751212 87751756 545 + 1.006 0.864 -0.533
ENSMUSG00000020053 E016 1277.5803876 0.0001373122 1.551992e-67 3.631040e-64 10 87766537 87772904 6368 + 3.048 3.160 0.373

Help

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