ENSMUSG00000029634

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
ENSMUST00000161859 ENSMUSG00000029634 Control shVgll3 Rnf6 protein_coding protein_coding 13.18118 11.72728 14.63508 0.1960658 0.6709582 0.3193182 7.467778 6.947908 7.987648 0.4067259 1.4127461 0.2009223 0.57080000 0.5939 0.5477000 -0.0462000 9.875634e-01 1.839935e-14 FALSE TRUE
ENSMUST00000162219 ENSMUSG00000029634 Control shVgll3 Rnf6 protein_coding protein_coding 13.18118 11.72728 14.63508 0.1960658 0.6709582 0.3193182 1.305356 0.000000 2.610712 0.0000000 0.4992568 8.0338148 0.08806667 0.0000 0.1761333 0.1761333 1.839935e-14 1.839935e-14 FALSE FALSE
ENSMUST00000169407 ENSMUSG00000029634 Control shVgll3 Rnf6 protein_coding protein_coding 13.18118 11.72728 14.63508 0.1960658 0.6709582 0.3193182 3.507824 3.767031 3.248617 0.8080186 1.6327462 -0.2129929 0.27075000 0.3198 0.2217000 -0.0981000 9.706657e-01 1.839935e-14 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
ENSMUSG00000029634 E001 0.0000000       5 146146002 146146005 4 -      
ENSMUSG00000029634 E002 195.6463904 0.0003526057 0.2940572167 0.83803329 5 146146006 146146766 761 - 2.306 2.280 -0.085
ENSMUSG00000029634 E003 422.9068727 0.0001331991 0.5336215868 0.93660279 5 146146767 146148112 1346 - 2.623 2.632 0.030
ENSMUSG00000029634 E004 199.0148523 0.0001780485 0.1233161287 0.67408975 5 146148113 146148485 373 - 2.318 2.282 -0.120
ENSMUSG00000029634 E005 25.0066692 0.0007758778 0.5719441021 0.94460955 5 146148486 146148513 28 - 1.433 1.395 -0.133
ENSMUSG00000029634 E006 67.1327486 0.0004178782 0.0681820961 0.56367078 5 146148514 146148662 149 - 1.869 1.791 -0.260
ENSMUSG00000029634 E007 44.7155159 0.0005059752 0.4279951132 0.90623983 5 146148663 146148742 80 - 1.679 1.639 -0.139
ENSMUSG00000029634 E008 45.7720136 0.0005253758 0.2531211825 0.80699081 5 146152907 146152999 93 - 1.640 1.699 0.199
ENSMUSG00000029634 E009 21.5852641 0.0010416502 0.3297696927 0.86241242 5 146153000 146153002 3 - 1.317 1.389 0.249
ENSMUSG00000029634 E010 72.3757591 0.0003071924 0.0251293730 0.35460001 5 146154711 146154888 178 - 1.819 1.910 0.305
ENSMUSG00000029634 E011 13.6620839 0.0014081155 0.0005234816 0.02902222 5 146154889 146154906 18 - 0.982 1.302 1.147
ENSMUSG00000029634 E012 0.3326527 0.0276859682 0.9623056538   5 146156075 146156152 78 - 0.120 0.127 0.094
ENSMUSG00000029634 E013 32.2556708 0.0046498765 0.2965117557 0.84026030 5 146157212 146157294 83 - 1.486 1.557 0.243
ENSMUSG00000029634 E014 2.3175106 0.0085306269 0.3481633700 0.87469641 5 146157295 146157547 253 - 0.587 0.431 -0.753
ENSMUSG00000029634 E015 5.9354673 0.0030721673 0.4273169313 0.90589950 5 146157548 146157749 202 - 0.886 0.785 -0.391
ENSMUSG00000029634 E016 2.3107290 0.0075484981 0.5174794464 0.93149289 5 146157750 146158029 280 - 0.464 0.571 0.510
ENSMUSG00000029634 E017 32.9282681 0.0044004086 0.8314705590 0.98548395 5 146158030 146158365 336 - 1.537 1.523 -0.049

Help

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