ENSMUSG00000070348

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
ENSMUST00000093962 ENSMUSG00000070348 Control shVgll3 Ccnd1 protein_coding protein_coding 88.14188 94.39553 81.88823 0.7852235 2.903291 -0.205039 66.02525 73.91231 58.13819 0.3057036 1.801656 -0.3462756 0.7467500 0.7831667 0.7103333 -0.07283333 0.03029945 0.03029945 FALSE  
MSTRG.21909.2 ENSMUSG00000070348 Control shVgll3 Ccnd1 protein_coding   88.14188 94.39553 81.88823 0.7852235 2.903291 -0.205039 20.33869 18.14171 22.53566 1.8160815 1.690470 0.3127441 0.2332833 0.1919000 0.2746667 0.08276667 0.25284126 0.03029945 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
ENSMUSG00000070348 E001 2587.01298 2.923499e-04 5.358706e-06 0.0006331933 7 144483668 144486398 2731 - 3.391 3.428 0.123
ENSMUSG00000070348 E002 328.70151 1.138281e-04 4.260723e-01 0.9054503823 7 144486399 144486508 110 - 2.522 2.512 -0.033
ENSMUSG00000070348 E003 22.68615 1.422787e-03 6.447667e-01 0.9566870527 7 144486509 144486574 66 - 1.389 1.360 -0.098
ENSMUSG00000070348 E004 12.85322 4.261149e-03 2.548497e-01 0.8074851423 7 144486935 144487752 818 - 1.193 1.089 -0.372
ENSMUSG00000070348 E005 564.41684 9.974029e-05 1.543801e-02 0.2802521180 7 144487753 144487901 149 - 2.767 2.737 -0.100
ENSMUSG00000070348 E006 193.39902 1.530955e-04 3.751979e-01 0.8790437186 7 144491031 144491031 1 - 2.297 2.280 -0.057
ENSMUSG00000070348 E007 706.55247 7.354970e-04 3.144213e-01 0.8521166522 7 144491032 144491190 159 - 2.855 2.843 -0.038
ENSMUSG00000070348 E008 612.47021 1.023832e-04 1.452348e-01 0.7100540283 7 144491624 144491839 216 - 2.795 2.780 -0.050
ENSMUSG00000070348 E009 2.64217 4.708867e-02 8.950708e-01 0.9956002734 7 144491840 144491934 95 - 0.543 0.573 0.141
ENSMUSG00000070348 E010 543.75596 5.389162e-04 1.491476e-02 0.2751713850 7 144493233 144493662 430 - 2.755 2.717 -0.126

Help

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