ENSMUSG00000055065

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
ENSMUST00000229877 ENSMUSG00000055065 Control shVgll3 Ddx17 protein_coding protein_coding 60.74775 63.92382 57.57168 0.7031941 0.5986515 -0.1509693 23.554943 29.37268 17.737204 0.40769339 0.9919168 -0.7273744 0.3838333 0.4597333 0.3079333 -0.15180000 1.743501e-05 1.743501e-05 FALSE TRUE
MSTRG.8283.3 ENSMUSG00000055065 Control shVgll3 Ddx17 protein_coding   60.74775 63.92382 57.57168 0.7031941 0.5986515 -0.1509693 28.881625 27.62839 30.134860 1.04773608 0.4866638 0.1252384 0.4777500 0.4319667 0.5235333 0.09156667 1.519929e-02 1.743501e-05 TRUE TRUE
MSTRG.8283.4 ENSMUSG00000055065 Control shVgll3 Ddx17 protein_coding   60.74775 63.92382 57.57168 0.7031941 0.5986515 -0.1509693 8.217758 6.90388 9.531636 0.07087599 0.3145287 0.4647412 0.1368167 0.1080000 0.1656333 0.05763333 4.322690e-04 1.743501e-05 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
ENSMUSG00000055065 E001 0.9772597 1.075224e-01 4.667006e-01 9.188233e-01 15 79411937 79411972 36 - 0.221 0.362 0.967
ENSMUSG00000055065 E002 4853.8729399 1.757534e-04 2.698468e-08 5.845681e-06 15 79411973 79414718 2746 - 3.670 3.701 0.104
ENSMUSG00000055065 E003 223.0246880 1.494914e-04 1.352549e-12 6.085429e-10 15 79414719 79415553 835 - 2.428 2.257 -0.571
ENSMUSG00000055065 E004 55.7767420 3.491233e-04 2.169293e-03 8.307142e-02 15 79415554 79415872 319 - 1.821 1.677 -0.489
ENSMUSG00000055065 E005 34.8557279 6.774244e-04 6.236468e-01 9.551420e-01 15 79415873 79415878 6 - 1.539 1.569 0.102
ENSMUSG00000055065 E006 593.6481475 1.113289e-04 1.629473e-02 2.870719e-01 15 79415879 79416115 237 - 2.755 2.792 0.122
ENSMUSG00000055065 E007 1099.1015655 2.475592e-04 5.006606e-05 4.436915e-03 15 79416116 79417411 1296 - 3.066 3.016 -0.165
ENSMUSG00000055065 E008 1486.5928505 5.301653e-04 6.911821e-08 1.443830e-05 15 79417412 79418861 1450 - 3.207 3.136 -0.234
ENSMUSG00000055065 E009 771.5770031 9.552242e-04 2.067119e-02 3.255907e-01 15 79418862 79420157 1296 - 2.909 2.866 -0.143
ENSMUSG00000055065 E010 134.4410956 1.662880e-03 2.125582e-01 7.847390e-01 15 79420158 79420217 60 - 2.108 2.154 0.153
ENSMUSG00000055065 E011 107.8866620 3.845226e-03 2.664670e-01 8.166443e-01 15 79421198 79421259 62 - 2.011 2.061 0.169
ENSMUSG00000055065 E012 226.3795800 3.255493e-03 3.615022e-01 8.753500e-01 15 79421636 79421746 111 - 2.340 2.373 0.111
ENSMUSG00000055065 E013 416.7492141 8.836973e-05 2.236743e-02 3.364534e-01 15 79422760 79422932 173 - 2.600 2.641 0.136
ENSMUSG00000055065 E014 278.5813973 1.211546e-03 4.347354e-01 9.088050e-01 15 79423019 79423179 161 - 2.435 2.457 0.071
ENSMUSG00000055065 E015 209.4350173 1.446506e-04 4.608711e-01 9.168276e-01 15 79423520 79423661 142 - 2.313 2.332 0.063
ENSMUSG00000055065 E016 129.4925141 1.685525e-04 3.802393e-01 8.802485e-01 15 79424614 79424679 66 - 2.101 2.129 0.094
ENSMUSG00000055065 E017 241.5752701 2.070942e-04 7.720841e-02 5.891430e-01 15 79425235 79425368 134 - 2.363 2.405 0.141
ENSMUSG00000055065 E018 149.1084119 1.756567e-04 7.535678e-02 5.846970e-01 15 79426688 79426787 100 - 2.149 2.201 0.176
ENSMUSG00000055065 E019 205.5855174 1.983470e-03 9.734639e-01 1.000000e+00 15 79427907 79428057 151 - 2.315 2.315 -0.002
ENSMUSG00000055065 E020 502.9387710 1.229247e-03 7.382821e-01 9.729001e-01 15 79430396 79430942 547 - 2.698 2.706 0.027

Help

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