ENSMUSG00000026404

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
ENSMUST00000027655 ENSMUSG00000026404 Control shVgll3 Ddx59 protein_coding protein_coding 9.821516 11.3426 8.300436 0.9398996 0.3964256 -0.4500262 5.5453633 5.293142 5.7975842 0.31897011 0.0708958 0.1310907 0.58531667 0.46923333 0.70140000 0.23216667 0.002461666 0.001908417 FALSE TRUE
ENSMUST00000122959 ENSMUSG00000026404 Control shVgll3 Ddx59 protein_coding protein_coding_CDS_not_defined 9.821516 11.3426 8.300436 0.9398996 0.3964256 -0.4500262 0.6044651 1.208930 0.0000000 0.70222348 0.0000000 -6.9294716 0.04978333 0.09956667 0.00000000 -0.09956667 0.622999521 0.001908417   FALSE
ENSMUST00000149783 ENSMUSG00000026404 Control shVgll3 Ddx59 protein_coding retained_intron 9.821516 11.3426 8.300436 0.9398996 0.3964256 -0.4500262 0.2225314 0.000000 0.4450628 0.00000000 0.1562609 5.5079937 0.02696667 0.00000000 0.05393333 0.05393333 0.001908417 0.001908417 FALSE FALSE
MSTRG.1135.3 ENSMUSG00000026404 Control shVgll3 Ddx59 protein_coding   9.821516 11.3426 8.300436 0.9398996 0.3964256 -0.4500262 1.4071460 2.216178 0.5981137 0.04633543 0.1983487 -1.8721561 0.13381667 0.19730000 0.07033333 -0.12696667 0.112822869 0.001908417 FALSE TRUE
MSTRG.1135.4 ENSMUSG00000026404 Control shVgll3 Ddx59 protein_coding   9.821516 11.3426 8.300436 0.9398996 0.3964256 -0.4500262 1.7631311 2.397621 1.1286413 0.57229366 0.3442937 -1.0802949 0.17555000 0.21560000 0.13550000 -0.08010000 0.970665669 0.001908417 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
ENSMUSG00000026404 E001 0.0000000       1 136343009 136343161 153 +      
ENSMUSG00000026404 E002 141.4565599 0.0002581082 1.136113e-05 1.242079e-03 1 136344320 136345134 815 + 2.206 2.101 -0.351
ENSMUSG00000026404 E003 2.8093349 0.0823051771 6.033093e-01 9.530216e-01 1 136345135 136345530 396 + 0.621 0.539 -0.372
ENSMUSG00000026404 E004 41.3526205 0.0006074797 9.797574e-01 1.000000e+00 1 136347148 136347315 168 + 1.623 1.627 0.016
ENSMUSG00000026404 E005 13.4782726 0.0014629607 1.206628e-01 6.680140e-01 1 136352533 136352622 90 + 1.077 1.221 0.515
ENSMUSG00000026404 E006 0.4846386 0.6587077510 3.267656e-01   1 136357630 136357691 62 + 0.000 0.282 9.768
ENSMUSG00000026404 E007 3.7897193 0.0051524482 4.919917e-02 4.873259e-01 1 136357921 136357951 31 + 0.494 0.793 1.300
ENSMUSG00000026404 E008 16.6102108 0.0011972107 2.901345e-07 5.221529e-05 1 136357952 136358110 159 + 0.943 1.402 1.641
ENSMUSG00000026404 E009 22.5034890 0.0119694037 9.629922e-02 6.317038e-01 1 136360050 136360139 90 + 1.287 1.432 0.505
ENSMUSG00000026404 E010 26.3540785 0.0016307412 7.431333e-01 9.729001e-01 1 136360140 136360301 162 + 1.422 1.447 0.086
ENSMUSG00000026404 E011 36.8932866 0.0006071791 9.694820e-01 1.000000e+00 1 136361451 136361603 153 + 1.577 1.578 0.003
ENSMUSG00000026404 E012 1.3203686 0.0116906429 1.560833e-02 2.809019e-01 1 136361604 136361804 201 + 0.541 0.116 -3.011
ENSMUSG00000026404 E013 26.5318706 0.0029728186 9.399643e-01 9.996345e-01 1 136362244 136362372 129 + 1.433 1.442 0.031
ENSMUSG00000026404 E014 92.0945485 0.0028878961 5.917008e-01 9.516577e-01 1 136367491 136367896 406 + 1.956 1.978 0.076

Help

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