ENSMUSG00000053559

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
ENSMUST00000066068 ENSMUSG00000053559 Control shVgll3 Smagp protein_coding protein_coding 1.984414 2.826704 1.142123 0.1333075 0.02817957 -1.299921 0.9224701 1.023036 0.8219040 0.04885733 0.1882445 -0.3124018 0.5387333 0.3648333 0.7126333 0.3478000 6.837757e-01 1.563192e-12   TRUE
ENSMUST00000172334 ENSMUSG00000053559 Control shVgll3 Smagp protein_coding protein_coding 1.984414 2.826704 1.142123 0.1333075 0.02817957 -1.299921 0.9018338 1.803668 0.0000000 0.17645615 0.0000000 -7.5027663 0.3175833 0.6351667 0.0000000 -0.6351667 1.563192e-12 1.563192e-12   TRUE
ENSMUST00000229965 ENSMUSG00000053559 Control shVgll3 Smagp protein_coding protein_coding 1.984414 2.826704 1.142123 0.1333075 0.02817957 -1.299921 0.1601096 0.000000 0.3202192 0.00000000 0.1606306 5.0453522 0.1436833 0.0000000 0.2873667 0.2873667 4.856202e-01 1.563192e-12   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
ENSMUSG00000053559 E001 0.3314605 0.363318252 0.7034670800   15 100519220 100519242 23 - 0.001 0.151 8.330
ENSMUSG00000053559 E002 4.4410881 0.004464716 0.1545674563 0.72356252 15 100519243 100519329 87 - 0.828 0.636 -0.783
ENSMUSG00000053559 E003 12.3136777 0.001809381 0.9694035842 1.00000000 15 100519330 100519519 190 - 1.077 1.088 0.039
ENSMUSG00000053559 E004 4.9232372 0.003987213 0.0002592131 0.01684597 15 100519520 100519599 80 - 0.182 0.847 3.535
ENSMUSG00000053559 E005 4.9418979 0.003866950 0.0130171520 0.24944177 15 100519600 100519649 50 - 0.409 0.821 1.847
ENSMUSG00000053559 E006 7.0801156 0.003175674 0.2603240586 0.81353043 15 100519650 100519839 190 - 0.755 0.907 0.594
ENSMUSG00000053559 E007 4.4410780 0.004338124 0.3109159252 0.84979533 15 100519840 100519907 68 - 0.793 0.657 -0.558
ENSMUSG00000053559 E008 7.2237301 0.002971406 0.5815578302 0.94816685 15 100520510 100520590 81 - 0.918 0.860 -0.224
ENSMUSG00000053559 E009 0.0000000       15 100533197 100533243 47 -      
ENSMUSG00000053559 E010 0.0000000       15 100533244 100533440 197 -      
ENSMUSG00000053559 E011 7.3964825 0.002952968 0.8146365961 0.98399344 15 100534068 100534136 69 - 0.860 0.896 0.136
ENSMUSG00000053559 E012 1.3200123 0.011790973 0.0062305042 0.16574688 15 100534440 100534629 190 - 0.615 0.151 -2.908
ENSMUSG00000053559 E013 16.7901738 0.001407068 0.1247102260 0.67632403 15 100534630 100534994 365 - 1.284 1.174 -0.387

Help

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