ENSMUSG00000057113

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
ENSMUST00000075641 ENSMUSG00000057113 Control shVgll3 Npm1 protein_coding protein_coding 973.4332 773.5031 1173.363 12.33341 23.64663 0.6011643 75.24026 71.73556 78.74496 4.675486 1.637505 0.1344813 0.0799500 0.0927000 0.0672000 -0.02550000 6.704404e-02 2.119162e-44 FALSE TRUE
ENSMUST00000093201 ENSMUSG00000057113 Control shVgll3 Npm1 protein_coding protein_coding 973.4332 773.5031 1173.363 12.33341 23.64663 0.6011643 187.05654 171.58892 202.52415 7.178156 16.972516 0.2391247 0.1970333 0.2218667 0.1722000 -0.04966667 3.284114e-01 2.119162e-44 FALSE TRUE
ENSMUST00000101375 ENSMUSG00000057113 Control shVgll3 Npm1 protein_coding protein_coding 973.4332 773.5031 1173.363 12.33341 23.64663 0.6011643 199.17558 245.31372 153.03743 8.321083 8.807144 -0.6807079 0.2239167 0.3170667 0.1307667 -0.18630000 1.400227e-16 2.119162e-44 FALSE TRUE
ENSMUST00000109354 ENSMUSG00000057113 Control shVgll3 Npm1 protein_coding protein_coding 973.4332 773.5031 1173.363 12.33341 23.64663 0.6011643 488.52554 267.70796 709.34311 9.042400 16.046606 1.4057901 0.4753167 0.3461333 0.6045000 0.25836667 2.119162e-44 2.119162e-44 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
ENSMUSG00000057113 E001 9.378583 0.0283969626 6.879258e-01 9.629190e-01 11 33102287 33102509 223 - 0.979 1.044 0.241
ENSMUSG00000057113 E002 3.124000 0.0056996699 8.439330e-01 9.868692e-01 11 33102510 33102510 1 - 0.613 0.595 -0.077
ENSMUSG00000057113 E003 1371.853301 0.0003105476 2.264896e-20 1.766317e-17 11 33102511 33102852 342 - 3.073 3.198 0.416
ENSMUSG00000057113 E004 157.656747 0.0001632357 6.604947e-05 5.441174e-03 11 33103986 33104060 75 - 2.133 2.265 0.441
ENSMUSG00000057113 E005 105.555139 0.0051483193 9.102047e-03 2.055706e-01 11 33104061 33104465 405 - 2.055 1.940 -0.386
ENSMUSG00000057113 E006 651.285779 0.0001113175 5.625873e-75 1.645287e-71 11 33104927 33105220 294 - 2.885 2.618 -0.890
ENSMUSG00000057113 E007 54.474658 0.0003519293 3.044579e-03 1.029349e-01 11 33105328 33105431 104 - 1.777 1.645 -0.446
ENSMUSG00000057113 E008 75.608319 0.0002596710 4.399112e-07 7.049426e-05 11 33106003 33106025 23 - 1.938 1.735 -0.686
ENSMUSG00000057113 E009 474.826181 0.0024695070 4.523725e-01 9.134999e-01 11 33106026 33106104 79 - 2.666 2.663 -0.011
ENSMUSG00000057113 E010 1122.703677 0.0015447369 5.954537e-01 9.516577e-01 11 33106664 33106747 84 - 3.027 3.056 0.097
ENSMUSG00000057113 E011 290.492890 0.0011882278 5.127290e-01 9.308326e-01 11 33106991 33107048 58 - 2.452 2.452 0.002
ENSMUSG00000057113 E012 21.728143 0.0008940221 5.487858e-01 9.370703e-01 11 33107049 33107277 229 - 1.320 1.381 0.215
ENSMUSG00000057113 E013 890.634566 0.0011881807 6.348248e-01 9.566325e-01 11 33109934 33109995 62 - 2.934 2.943 0.030
ENSMUSG00000057113 E014 212.813285 0.0044402594 3.614271e-01 8.753500e-01 11 33110334 33110440 107 - 2.295 2.351 0.189
ENSMUSG00000057113 E015 840.900853 0.0002325049 1.397125e-01 7.026420e-01 11 33110828 33110921 94 - 2.913 2.911 -0.009
ENSMUSG00000057113 E016 726.146226 0.0003131597 1.048696e-01 6.422853e-01 11 33111106 33111225 120 - 2.851 2.844 -0.024
ENSMUSG00000057113 E017 15.776504 0.0058210520 9.358334e-02 6.286265e-01 11 33111548 33111627 80 - 1.262 1.119 -0.507
ENSMUSG00000057113 E018 2739.643997 0.0026704637 1.609787e-01 7.330201e-01 11 33112922 33113206 285 - 3.408 3.452 0.147

Help

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