ENSMUSG00000027559

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
ENSMUST00000029076 ENSMUSG00000027559 Control shVgll3 Car3 protein_coding protein_coding 144.5697 44.87033 244.269 0.7767448 4.049875 2.444374 109.54087 21.37134 197.71040 1.164574 1.924710 3.2090379 0.6431 0.4766333 0.8095667 0.3329333 8.391249e-22 3.410627e-22 FALSE TRUE
ENSMUST00000195834 ENSMUSG00000027559 Control shVgll3 Car3 protein_coding retained_intron 144.5697 44.87033 244.269 0.7767448 4.049875 2.444374 31.93727 22.76201 41.11254 1.396709 2.706044 0.8526676 0.3375 0.5069667 0.1680333 -0.3389333 3.410627e-22 3.410627e-22 FALSE 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
ENSMUSG00000027559 E001 0.00000       3 14928572 14928597 26 +      
ENSMUSG00000027559 E002 0.00000       3 14928598 14928665 68 +      
ENSMUSG00000027559 E003 537.08909 0.0001088960 1.134223e-12 5.307254e-10 3 14929310 14929507 198 + 2.582 2.436 -0.488
ENSMUSG00000027559 E004 66.96556 0.0041117740 3.591688e-01 8.751770e-01 3 14929508 14930610 1103 + 1.674 1.630 -0.150
ENSMUSG00000027559 E005 474.31996 0.0009539610 8.496651e-10 2.424240e-07 3 14931863 14931981 119 + 2.529 2.373 -0.520
ENSMUSG00000027559 E006 278.35422 0.0001215825 4.289628e-07 6.969454e-05 3 14933409 14933501 93 + 2.298 2.152 -0.487
ENSMUSG00000027559 E007 19.76562 0.0010552717 3.060016e-10 9.178479e-08 3 14934238 14934294 57 + 1.031 1.586 1.946
ENSMUSG00000027559 E008 329.00465 0.0002643354 6.935594e-01 9.639881e-01 3 14934295 14934357 63 + 2.349 2.381 0.107
ENSMUSG00000027559 E009 711.83630 0.0001206767 3.720513e-03 1.186236e-01 3 14935102 14935257 156 + 2.677 2.750 0.243
ENSMUSG00000027559 E010 3548.66074 0.0007223485 4.176279e-07 6.880860e-05 3 14936602 14937583 982 + 3.376 3.435 0.195

Help

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