ENSMUSG00000060519

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
ENSMUST00000079625 ENSMUSG00000060519 Control shVgll3 Tor3a protein_coding protein_coding 14.9846 13.81905 16.15016 0.8980992 0.5877408 0.2247391 6.315441 6.873565 5.757318 0.3518445 0.1160560 -0.2552553 0.4277500 0.4985333 0.3569667 -0.14156667 0.004144603 0.004144603 FALSE TRUE
ENSMUST00000154353 ENSMUSG00000060519 Control shVgll3 Tor3a protein_coding protein_coding_CDS_not_defined 14.9846 13.81905 16.15016 0.8980992 0.5877408 0.2247391 2.674030 1.547787 3.800273 1.5477869 1.0083892 1.2903963 0.1655667 0.0998000 0.2313333 0.13153333 0.618162456 0.004144603 FALSE TRUE
ENSMUST00000188964 ENSMUSG00000060519 Control shVgll3 Tor3a protein_coding protein_coding 14.9846 13.81905 16.15016 0.8980992 0.5877408 0.2247391 5.697207 4.931234 6.463179 0.7123820 0.5727333 0.3896030 0.3848500 0.3658667 0.4038333 0.03796667 0.976512292 0.004144603 TRUE 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
ENSMUSG00000060519 E001 202.7037118 0.0002518413 5.759670e-07 8.865345e-05 1 156481187 156482592 1406 - 2.250 2.363 0.378
ENSMUSG00000060519 E002 52.4510382 0.0019793029 1.577830e-01 7.270506e-01 1 156482593 156482809 217 - 1.762 1.690 -0.246
ENSMUSG00000060519 E003 46.5363288 0.0004860451 4.890471e-01 9.257967e-01 1 156482810 156482896 87 - 1.694 1.659 -0.120
ENSMUSG00000060519 E004 142.1708890 0.0003453862 1.953927e-01 7.708254e-01 1 156482897 156483241 345 - 2.138 2.174 0.120
ENSMUSG00000060519 E005 144.1127318 0.0010138200 2.468464e-01 8.044216e-01 1 156483242 156483513 272 - 2.179 2.143 -0.118
ENSMUSG00000060519 E006 70.1167243 0.0003783181 1.422971e-01 7.077344e-01 1 156484042 156484166 125 - 1.881 1.820 -0.205
ENSMUSG00000060519 E007 0.4887934 0.0266781197 9.038414e-02   1 156485935 156486028 94 - 0.294 0.000 -12.691
ENSMUSG00000060519 E008 0.8289974 0.0639175430 1.915560e-02 3.134017e-01 1 156488499 156488650 152 - 0.000 0.428 13.539
ENSMUSG00000060519 E009 51.5476055 0.0004549606 3.498765e-02 4.232529e-01 1 156494169 156494261 93 - 1.767 1.665 -0.346
ENSMUSG00000060519 E010 43.8388961 0.0006068033 9.467788e-01 1.000000e+00 1 156494262 156494347 86 - 1.649 1.652 0.010
ENSMUSG00000060519 E011 0.1615462 0.0346202675 4.696783e-01   1 156496684 156496753 70 - 0.000 0.126 11.215
ENSMUSG00000060519 E012 102.5585975 0.0002715164 2.285009e-01 8.005513e-01 1 156496941 156497206 266 - 2.034 1.994 -0.137
ENSMUSG00000060519 E013 0.9829827 0.0143659278 8.960583e-03 2.047283e-01 1 156500809 156501099 291 - 0.468 0.000 -13.691
ENSMUSG00000060519 E014 38.3785579 0.0024305807 4.381557e-01 9.109772e-01 1 156501100 156501216 117 - 1.617 1.571 -0.157
ENSMUSG00000060519 E015 48.4316808 0.0004235827 3.982594e-01 8.901105e-01 1 156501656 156501926 271 - 1.714 1.671 -0.143

Help

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