ENSMUSG00000031851

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
ENSMUST00000034313 ENSMUSG00000031851 Control shVgll3 Ntpcr protein_coding protein_coding 15.32956 15.89411 14.765 0.4129294 1.152286 -0.1062415 8.5090675 7.928065 9.0900695 1.6210824 1.09304611 0.1970901 0.55683333 0.4951667 0.61850000 0.12333333 0.970665669 0.001461783 FALSE  
ENSMUST00000065135 ENSMUSG00000031851 Control shVgll3 Ntpcr protein_coding protein_coding 15.32956 15.89411 14.765 0.4129294 1.152286 -0.1062415 1.0161135 0.836458 1.1957689 0.0373379 0.04662006 0.5104430 0.06768333 0.0528000 0.08256667 0.02976667 0.662531310 0.001461783 FALSE  
ENSMUST00000123554 ENSMUSG00000031851 Control shVgll3 Ntpcr protein_coding retained_intron 15.32956 15.89411 14.765 0.4129294 1.152286 -0.1062415 1.4236446 1.869186 0.9781031 0.1885963 0.70276709 -0.9273746 0.08916667 0.1180667 0.06026667 -0.05780000 0.970665669 0.001461783 FALSE  
ENSMUST00000146055 ENSMUSG00000031851 Control shVgll3 Ntpcr protein_coding protein_coding_CDS_not_defined 15.32956 15.89411 14.765 0.4129294 1.152286 -0.1062415 1.0436920 1.167718 0.9196655 0.3107819 0.91966554 -0.3412110 0.06423333 0.0728000 0.05566667 -0.01713333 0.850118277 0.001461783    
MSTRG.23147.6 ENSMUSG00000031851 Control shVgll3 Ntpcr protein_coding   15.32956 15.89411 14.765 0.4129294 1.152286 -0.1062415 2.6640754 2.915607 2.4125436 1.7621670 0.52412162 -0.2722135 0.17930000 0.1872333 0.17136667 -0.01586667 0.999243110 0.001461783 FALSE  
MSTRG.23147.7 ENSMUSG00000031851 Control shVgll3 Ntpcr protein_coding   15.32956 15.89411 14.765 0.4129294 1.152286 -0.1062415 0.5885381 1.177076 0.0000000 0.4231017 0.00000000 -6.8912687 0.03695000 0.0739000 0.00000000 -0.07390000 0.001461783 0.001461783 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
ENSMUSG00000031851 E001 0.0000000       8 126456702 126456766 65 +      
ENSMUSG00000031851 E002 0.0000000       8 126456767 126456770 4 +      
ENSMUSG00000031851 E003 0.0000000       8 126456771 126456801 31 +      
ENSMUSG00000031851 E004 0.0000000       8 126459829 126459844 16 +      
ENSMUSG00000031851 E005 0.0000000       8 126459845 126459970 126 +      
ENSMUSG00000031851 E006 0.0000000       8 126460942 126460964 23 +      
ENSMUSG00000031851 E007 0.3230924 0.3103152512 0.262045910   8 126460965 126460971 7 + 0.000 0.221 11.344
ENSMUSG00000031851 E008 0.3230924 0.3103152512 0.262045910   8 126460972 126460976 5 + 0.000 0.221 11.348
ENSMUSG00000031851 E009 23.6838622 0.0011239280 0.744942274 0.97314738 8 126460977 126461088 112 + 1.381 1.404 0.077
ENSMUSG00000031851 E010 0.0000000       8 126462574 126462625 52 +      
ENSMUSG00000031851 E011 58.5084616 0.0023210352 0.454518227 0.91395711 8 126462807 126462964 158 + 1.757 1.792 0.118
ENSMUSG00000031851 E012 12.5085574 0.0132760733 0.353102330 0.87517695 8 126462965 126462969 5 + 1.175 1.079 -0.344
ENSMUSG00000031851 E013 3.2925387 0.0054090769 0.164399156 0.73825003 8 126462970 126463068 99 + 0.515 0.727 0.930
ENSMUSG00000031851 E014 53.1850196 0.0004027264 0.780220952 0.97903220 8 126464062 126464158 97 + 1.740 1.727 -0.044
ENSMUSG00000031851 E015 29.4624697 0.0006585431 0.028962251 0.38320676 8 126464794 126465918 1125 + 1.546 1.409 -0.468
ENSMUSG00000031851 E016 20.9049956 0.0179005226 0.076290406 0.58710222 8 126471975 126471978 4 + 1.415 1.247 -0.585
ENSMUSG00000031851 E017 115.8896461 0.0002131310 0.157069609 0.72598874 8 126471979 126472184 206 + 2.087 2.047 -0.136
ENSMUSG00000031851 E018 123.8228872 0.0003887005 0.002840812 0.09861073 8 126474437 126474974 538 + 2.053 2.136 0.275

Help

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