ENSMUSG00000034403

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
ENSMUST00000036354 ENSMUSG00000034403 Control shVgll3 Pja1 protein_coding protein_coding 37.27265 42.76332 31.78198 0.2940529 0.3395817 -0.4280483 5.084982 7.075295 3.094669 0.2621951 0.1895215 -1.19038842 0.1314167 0.1655000 0.09733333 -0.06816667 0.002117809 0.002117809 FALSE  
ENSMUST00000113797 ENSMUSG00000034403 Control shVgll3 Pja1 protein_coding protein_coding 37.27265 42.76332 31.78198 0.2940529 0.3395817 -0.4280483 21.429824 23.962812 18.896836 0.5836009 0.1674922 -0.34249126 0.5776500 0.5606000 0.59470000 0.03410000 0.970665669 0.002117809 FALSE  
ENSMUST00000167246 ENSMUSG00000034403 Control shVgll3 Pja1 protein_coding protein_coding 37.27265 42.76332 31.78198 0.2940529 0.3395817 -0.4280483 8.895457 9.163034 8.627879 0.8316319 0.3122393 -0.08672185 0.2427000 0.2140667 0.27133333 0.05726667 0.617440452 0.002117809 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
ENSMUSG00000034403 E001 0.3334988 0.3040234384 0.1893892831   X 98509340 98509343 4 - 0.248 0.000 -10.879
ENSMUSG00000034403 E002 1.6467492 0.0107921745 0.8731326751 0.990583458 X 98509344 98509373 30 - 0.404 0.430 0.143
ENSMUSG00000034403 E003 32.1064194 0.0006110692 0.8787600126 0.991895454 X 98509374 98509719 346 - 1.521 1.510 -0.040
ENSMUSG00000034403 E004 10.3604845 0.0018353651 0.0834583337 0.604290566 X 98509720 98509751 32 - 0.938 1.119 0.662
ENSMUSG00000034403 E005 1464.1782029 0.0009933735 0.7509708051 0.975413696 X 98509752 98511179 1428 - 3.164 3.159 -0.017
ENSMUSG00000034403 E006 30.9293056 0.0006010158 0.0784105656 0.591532544 X 98511180 98511188 9 - 1.433 1.542 0.377
ENSMUSG00000034403 E007 294.5669063 0.0001710092 0.4687085105 0.919580978 X 98511189 98511728 540 - 2.475 2.458 -0.057
ENSMUSG00000034403 E008 217.1681078 0.0001380992 0.7128747489 0.968197329 X 98511729 98511920 192 - 2.330 2.336 0.020
ENSMUSG00000034403 E009 19.8843278 0.0009392424 0.0001304873 0.009531121 X 98511921 98512206 286 - 1.110 1.422 1.095
ENSMUSG00000034403 E010 85.2351660 0.0029301303 0.2093317752 0.782866316 X 98514223 98514462 240 - 1.963 1.905 -0.196
ENSMUSG00000034403 E011 0.0000000       X 98514663 98514879 217 -      

Help

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