ENSMUSG00000020088

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
ENSMUST00000020285 ENSMUSG00000020088 Control shVgll3 Sar1a protein_coding protein_coding 140.4342 155.9874 124.8809 4.82238 2.290934 -0.3208536 63.54885 76.005888 51.091804 1.1607155 0.9245028 -0.57292675 0.44858333 0.48776667 0.40940000 -0.07836667 0.01952779 0.01952779 FALSE  
ENSMUST00000218741 ENSMUSG00000020088 Control shVgll3 Sar1a protein_coding nonsense_mediated_decay 140.4342 155.9874 124.8809 4.82238 2.290934 -0.3208536 12.61630 9.023999 16.208611 5.2924176 2.1878189 0.84421357 0.09256667 0.05593333 0.12920000 0.07326667 0.61744045 0.01952779    
ENSMUST00000219055 ENSMUSG00000020088 Control shVgll3 Sar1a protein_coding protein_coding 140.4342 155.9874 124.8809 4.82238 2.290934 -0.3208536 11.96500 16.836713 7.093281 2.1389869 0.8368658 -1.24590967 0.08261667 0.10830000 0.05693333 -0.05136667 0.19738996 0.01952779    
ENSMUST00000220372 ENSMUSG00000020088 Control shVgll3 Sar1a protein_coding protein_coding 140.4342 155.9874 124.8809 4.82238 2.290934 -0.3208536 44.16865 44.844996 43.492298 0.9654884 2.1800181 -0.04417707 0.31803333 0.28823333 0.34783333 0.05960000 0.43074154 0.01952779 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
ENSMUSG00000020088 E001 0.8251697 0.0162961839 2.845497e-01 8.315494e-01 10 61516078 61516088 11 + 0.140 0.331 1.587
ENSMUSG00000020088 E002 4.4576223 0.0045661691 8.162985e-01 9.841109e-01 10 61516089 61516108 20 + 0.714 0.745 0.128
ENSMUSG00000020088 E003 72.7554580 0.0060400767 7.640536e-01 9.779907e-01 10 61516109 61516143 35 + 1.873 1.856 -0.058
ENSMUSG00000020088 E004 72.2531879 0.0056662150 6.938889e-01 9.639881e-01 10 61516144 61516145 2 + 1.873 1.851 -0.075
ENSMUSG00000020088 E005 218.1081127 0.0027466936 1.934258e-01 7.693626e-01 10 61516146 61516192 47 + 2.362 2.316 -0.154
ENSMUSG00000020088 E006 35.2350164 0.0121057767 6.923767e-03 1.787952e-01 10 61516390 61516676 287 + 1.416 1.636 0.754
ENSMUSG00000020088 E007 5.5989897 0.0032237825 3.692683e-01 8.756338e-01 10 61517878 61517927 50 + 0.745 0.862 0.462
ENSMUSG00000020088 E008 27.9731528 0.0006592341 9.664361e-02 6.317038e-01 10 61519840 61519966 127 + 1.517 1.407 -0.379
ENSMUSG00000020088 E009 5.5783823 0.0053888435 3.250781e-02 4.062682e-01 10 61520013 61520110 98 + 0.953 0.673 -1.105
ENSMUSG00000020088 E010 273.1216952 0.0003755896 1.480690e-02 2.743331e-01 10 61520659 61520732 74 + 2.465 2.408 -0.190
ENSMUSG00000020088 E011 118.8861937 0.0036338410 2.765918e-01 8.218390e-01 10 61520845 61520857 13 + 2.102 2.052 -0.165
ENSMUSG00000020088 E012 197.8984307 0.0042004297 3.469964e-01 8.743181e-01 10 61520858 61520880 23 + 2.317 2.276 -0.135
ENSMUSG00000020088 E013 489.5138619 0.0001253779 1.178461e-02 2.385058e-01 10 61520881 61520964 84 + 2.710 2.668 -0.141
ENSMUSG00000020088 E014 322.8348031 0.0044219550 9.132015e-02 6.235084e-01 10 61521333 61521398 66 + 2.542 2.477 -0.216
ENSMUSG00000020088 E015 0.3319899 0.0276216970 8.370200e-01   10 61521399 61521555 157 + 0.140 0.109 -0.413
ENSMUSG00000020088 E016 651.8910828 0.0021886397 1.866372e-01 7.639194e-01 10 61522154 61522257 104 + 2.830 2.795 -0.117
ENSMUSG00000020088 E017 3.4565639 0.0236097088 1.073833e-01 6.478444e-01 10 61525316 61525390 75 + 0.773 0.516 -1.112
ENSMUSG00000020088 E018 4.7806197 0.0181858294 3.945476e-01 8.876388e-01 10 61525391 61525466 76 + 0.681 0.808 0.514
ENSMUSG00000020088 E019 5.1012493 0.0142459349 1.335645e-01 6.913967e-01 10 61525467 61525552 86 + 0.645 0.862 0.877
ENSMUSG00000020088 E020 646.6731951 0.0003991081 1.612519e-03 6.960608e-02 10 61525553 61525684 132 + 2.836 2.784 -0.172
ENSMUSG00000020088 E021 2.6403503 0.0435421083 9.760649e-01 1.000000e+00 10 61526904 61527063 160 + 0.563 0.552 -0.050
ENSMUSG00000020088 E022 3071.7911874 0.0001210119 9.537226e-16 5.871919e-13 10 61527064 61529076 2013 + 3.459 3.501 0.139

Help

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