ENSMUSG00000035142

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
ENSMUST00000040090 ENSMUSG00000035142 Control shVgll3 Nubpl protein_coding protein_coding 3.544602 3.016621 4.072583 0.4608891 1.31775 0.4317742 2.0570537 2.0658103 2.048297 0.1308313 0.1609868 -0.01222324 0.6647333 0.7240667 0.6054 -0.1186667 9.706657e-01 8.978433e-09 FALSE TRUE
ENSMUST00000159567 ENSMUSG00000035142 Control shVgll3 Nubpl protein_coding nonsense_mediated_decay 3.544602 3.016621 4.072583 0.4608891 1.31775 0.4317742 0.5125510 0.0000000 1.025102 0.0000000 0.4028868 6.69362924 0.1199500 0.0000000 0.2399 0.2399000 8.978433e-09 8.978433e-09 TRUE FALSE
ENSMUST00000162111 ENSMUSG00000035142 Control shVgll3 Nubpl protein_coding protein_coding_CDS_not_defined 3.544602 3.016621 4.072583 0.4608891 1.31775 0.4317742 0.9339932 0.9305713 0.937415 0.5301806 0.9374150 0.01045923 0.2047333 0.2688667 0.1406 -0.1282667 9.706657e-01 8.978433e-09 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
ENSMUSG00000035142 E001 0.4989225 0.0314873595 0.097541140   12 52144520 52144538 19 + 0.290 0.000 -10.755
ENSMUSG00000035142 E002 1.1534360 0.0137053309 0.299379288 0.84044841 12 52144539 52144543 5 + 0.413 0.226 -1.216
ENSMUSG00000035142 E003 13.8227236 0.0060580466 0.569389250 0.94354310 12 52144544 52144674 131 + 1.146 1.195 0.174
ENSMUSG00000035142 E004 13.3221333 0.0016317422 0.346881519 0.87431815 12 52145136 52145283 148 + 1.116 1.195 0.284
ENSMUSG00000035142 E005 11.3442185 0.0071671167 0.109300187 0.64991094 12 52147250 52147284 35 + 1.008 1.166 0.571
ENSMUSG00000035142 E006 0.0000000       12 52147285 52147866 582 +      
ENSMUSG00000035142 E007 0.4943822 0.0230037030 0.614709908   12 52152002 52152178 177 + 0.213 0.128 -0.895
ENSMUSG00000035142 E008 0.0000000       12 52179167 52179301 135 +      
ENSMUSG00000035142 E009 16.7988178 0.0013583802 0.308455344 0.84753465 12 52190752 52190842 91 + 1.288 1.205 -0.293
ENSMUSG00000035142 E010 0.0000000       12 52190843 52191563 721 +      
ENSMUSG00000035142 E011 0.0000000       12 52222870 52223058 189 +      
ENSMUSG00000035142 E012 11.8778403 0.0021888186 0.005072059 0.14436240 12 52227875 52227914 40 + 1.219 0.947 -0.985
ENSMUSG00000035142 E013 8.7174373 0.0022675487 0.692105376 0.96338942 12 52228000 52228090 91 + 1.009 0.963 -0.167
ENSMUSG00000035142 E014 0.0000000       12 52288060 52288222 163 +      
ENSMUSG00000035142 E015 17.0990222 0.0021888504 0.435925916 0.90996812 12 52317822 52317915 94 + 1.288 1.223 -0.229
ENSMUSG00000035142 E016 11.5037943 0.0244043829 0.379410232 0.88024846 12 52333121 52333206 86 + 1.146 1.038 -0.392
ENSMUSG00000035142 E017 12.0079832 0.0018027413 0.336532818 0.86669971 12 52349464 52349584 121 + 1.156 1.064 -0.332
ENSMUSG00000035142 E018 13.9773399 0.0020647651 0.785226772 0.97919769 12 52352581 52352663 83 + 1.166 1.186 0.072
ENSMUSG00000035142 E019 30.2763707 0.0006971919 0.002592763 0.09275272 12 52357485 52359527 2043 + 1.405 1.574 0.581

Help

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