ENSMUSG00000029446

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
ENSMUST00000031399 ENSMUSG00000029446 Control shVgll3 Psph protein_coding protein_coding 9.239804 6.469809 12.0098 0.1278758 0.2639024 0.8913897 5.7116781 5.2084596 6.2148966 0.05177874 0.54142209 0.2544259 0.66276667 0.8059667 0.51956667 -0.28640000 6.844143e-03 3.776961e-09 FALSE TRUE
ENSMUST00000118268 ENSMUSG00000029446 Control shVgll3 Psph protein_coding protein_coding 9.239804 6.469809 12.0098 0.1278758 0.2639024 0.8913897 1.0761228 0.0000000 2.1522456 0.00000000 1.08308719 7.7563866 0.08770000 0.0000000 0.17540000 0.17540000 6.393618e-01 3.776961e-09 FALSE FALSE
ENSMUST00000136280 ENSMUSG00000029446 Control shVgll3 Psph protein_coding protein_coding_CDS_not_defined 9.239804 6.469809 12.0098 0.1278758 0.2639024 0.8913897 1.1442558 0.0000000 2.2885116 0.00000000 0.46900181 7.8445561 0.09456667 0.0000000 0.18913333 0.18913333 3.776961e-09 3.776961e-09   FALSE
MSTRG.18363.3 ENSMUSG00000029446 Control shVgll3 Psph protein_coding   9.239804 6.469809 12.0098 0.1278758 0.2639024 0.8913897 0.5299937 0.6179403 0.4420471 0.04242229 0.05430409 -0.4741544 0.06636667 0.0957000 0.03703333 -0.05866667 8.368624e-02 3.776961e-09 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
ENSMUSG00000029446 E001 0.0000000       5 129842622 129842625 4 -      
ENSMUSG00000029446 E002 49.7013394 0.0004449544 0.260174041 0.81353043 5 129842626 129842962 337 - 1.721 1.668 -0.178
ENSMUSG00000029446 E003 46.7769257 0.0004183252 0.673701553 0.96164256 5 129843483 129843631 149 - 1.664 1.686 0.074
ENSMUSG00000029446 E004 10.3870116 0.0018427165 0.907392516 0.99565900 5 129846303 129846306 4 - 1.045 1.058 0.047
ENSMUSG00000029446 E005 40.9923447 0.0004803966 0.359482066 0.87517695 5 129846307 129846382 76 - 1.637 1.589 -0.161
ENSMUSG00000029446 E006 36.9239933 0.0007022077 0.245225315 0.80442163 5 129846383 129846448 66 - 1.599 1.534 -0.220
ENSMUSG00000029446 E007 41.8151900 0.0004995738 0.235025106 0.80428340 5 129847670 129847763 94 - 1.651 1.589 -0.208
ENSMUSG00000029446 E008 21.5676854 0.0014834723 0.101456186 0.63901602 5 129847764 129847804 41 - 1.395 1.273 -0.423
ENSMUSG00000029446 E009 0.4943822 0.0219081671 0.765146432   5 129848051 129848219 169 - 0.193 0.142 -0.538
ENSMUSG00000029446 E010 0.3282956 0.0289112539 0.815655602   5 129848484 129848539 56 - 0.107 0.142 0.462
ENSMUSG00000029446 E011 34.4172702 0.0005970594 0.384772834 0.88471882 5 129848540 129848696 157 - 1.564 1.514 -0.169
ENSMUSG00000029446 E012 2.1510480 0.0086571762 0.790783762 0.98035062 5 129853894 129853929 36 - 0.511 0.467 -0.216
ENSMUSG00000029446 E013 2.3122379 0.0079471778 0.559041273 0.94110467 5 129853930 129854005 76 - 0.472 0.569 0.463
ENSMUSG00000029446 E014 10.0405068 0.0211986507 0.933701817 0.99963445 5 129854006 129856085 2080 - 1.034 1.043 0.032
ENSMUSG00000029446 E015 18.4647975 0.0013346449 0.727148738 0.97107356 5 129856086 129856125 40 - 1.271 1.299 0.100
ENSMUSG00000029446 E016 60.5027114 0.0003749904 0.620356472 0.95514198 5 129856126 129856312 187 - 1.773 1.795 0.075
ENSMUSG00000029446 E017 0.1613534 0.0357383435 0.645630108   5 129856313 129856425 113 - 0.107 0.000 -9.404
ENSMUSG00000029446 E018 14.3520518 0.0015710667 0.026070329 0.36219800 5 129856426 129856444 19 - 1.087 1.282 0.695
ENSMUSG00000029446 E019 20.7534407 0.0010547030 0.000337081 0.02131445 5 129856445 129856508 64 - 1.200 1.465 0.924
ENSMUSG00000029446 E020 0.4931798 0.0214946990 0.045388115   5 129863655 129863720 66 - 0.000 0.334 11.917
ENSMUSG00000029446 E021 6.5768531 0.0047963975 0.056814485 0.52249673 5 129864019 129864513 495 - 0.761 0.995 0.899

Help

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