ENSMUSG00000067365

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
ENSMUST00000087511 ENSMUSG00000067365 Control shVgll3 Tmem128 protein_coding protein_coding 16.1227 16.61041 15.63499 0.6338622 0.5597488 -0.08725573 8.884066 9.574104 8.194028 0.3262707 0.4742636 -0.2243111 0.5506167 0.5778667 0.52336667 -0.0545000 0.97066567 0.03012604 FALSE TRUE
ENSMUST00000119047 ENSMUSG00000067365 Control shVgll3 Tmem128 protein_coding protein_coding 16.1227 16.61041 15.63499 0.6338622 0.5597488 -0.08725573 4.822725 3.963372 5.682078 0.3740343 0.2927948 0.5185914 0.3007833 0.2377667 0.36380000 0.1260333 0.03012604 0.03012604 FALSE TRUE
ENSMUST00000128025 ENSMUSG00000067365 Control shVgll3 Tmem128 protein_coding retained_intron 16.1227 16.61041 15.63499 0.6338622 0.5597488 -0.08725573 1.810581 2.351319 1.269843 0.1125371 0.1095018 -0.8836263 0.1114833 0.1417333 0.08123333 -0.0605000 0.11591192 0.03012604 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
ENSMUSG00000067365 E001 1.8147010 0.0095810527 0.319056385 0.85507722 5 38417529 38417714 186 + 0.528 0.357 -0.894
ENSMUSG00000067365 E002 0.8264858 0.0165450543 0.609498657 0.95334770 5 38417715 38417727 13 + 0.305 0.215 -0.672
ENSMUSG00000067365 E003 0.1657302 0.0344985010 0.515831048   5 38417728 38417730 3 + 0.000 0.120 9.067
ENSMUSG00000067365 E004 39.8769076 0.0005345343 0.194869953 0.77082536 5 38417731 38417836 106 + 1.644 1.577 -0.230
ENSMUSG00000067365 E005 21.7308010 0.0011568556 0.848397360 0.98692843 5 38417837 38419340 1504 + 1.363 1.350 -0.043
ENSMUSG00000067365 E006 74.1358502 0.0043864929 0.426418648 0.90545038 5 38419341 38419482 142 + 1.855 1.894 0.133
ENSMUSG00000067365 E007 0.3316336 0.0258865873 0.217200949   5 38419483 38419653 171 + 0.000 0.215 10.097
ENSMUSG00000067365 E008 52.8625900 0.0004050524 0.596338750 0.95200203 5 38422156 38422240 85 + 1.742 1.719 -0.078
ENSMUSG00000067365 E009 53.3334546 0.0014441968 0.007889771 0.19446916 5 38422241 38422314 74 + 1.795 1.669 -0.427
ENSMUSG00000067365 E010 15.9547708 0.0012145046 0.002113377 0.08159171 5 38422315 38422734 420 + 1.074 1.338 0.936
ENSMUSG00000067365 E011 2.4749468 0.3024896238 0.870618194 0.98948659 5 38423862 38423894 33 + 0.570 0.510 -0.281
ENSMUSG00000067365 E012 52.8162665 0.0004255395 0.444745276 0.91335964 5 38424523 38424628 106 + 1.748 1.714 -0.114
ENSMUSG00000067365 E013 12.3129439 0.0094029532 0.723086828 0.97061080 5 38425042 38425251 210 + 1.142 1.108 -0.125
ENSMUSG00000067365 E014 136.3924479 0.0002308078 0.047881500 0.48286016 5 38426403 38426978 576 + 2.110 2.162 0.175

Help

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