ENSMUSG00000026456

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
ENSMUST00000027726 ENSMUSG00000026456 Control shVgll3 Cyb5r1 protein_coding protein_coding 31.98388 24.47448 39.49328 1.977253 0.884659 0.6901047 0.9822618 1.964524 0.000000 0.8774651 0.00000000 -7.6253608 0.04098333 0.08196667 0.00000000 -0.081966667 2.716090e-06 4.459967e-10 FALSE TRUE
ENSMUST00000130836 ENSMUSG00000026456 Control shVgll3 Cyb5r1 protein_coding protein_coding_CDS_not_defined 31.98388 24.47448 39.49328 1.977253 0.884659 0.6901047 2.5461600 3.404256 1.688064 0.7634987 0.92811694 -1.0076805 0.08981667 0.13676667 0.04286667 -0.093900000 9.410286e-01 4.459967e-10 FALSE FALSE
ENSMUST00000133686 ENSMUSG00000026456 Control shVgll3 Cyb5r1 protein_coding retained_intron 31.98388 24.47448 39.49328 1.977253 0.884659 0.6901047 1.7478740 1.395164 2.100584 0.1818206 0.09315221 0.5869034 0.05586667 0.05860000 0.05313333 -0.005466667 1.000000e+00 4.459967e-10 FALSE TRUE
ENSMUST00000154237 ENSMUSG00000026456 Control shVgll3 Cyb5r1 protein_coding nonsense_mediated_decay 31.98388 24.47448 39.49328 1.977253 0.884659 0.6901047 12.2407200 6.628845 17.852595 0.9770511 0.82677170 1.4279374 0.36413333 0.27610000 0.45216667 0.176066667 3.487412e-01 4.459967e-10 FALSE TRUE
MSTRG.1089.11 ENSMUSG00000026456 Control shVgll3 Cyb5r1 protein_coding   31.98388 24.47448 39.49328 1.977253 0.884659 0.6901047 4.9216196 5.533498 4.309741 0.5158211 0.61787555 -0.3598517 0.16833333 0.22756667 0.10910000 -0.118466667 1.730274e-02 4.459967e-10 FALSE TRUE
MSTRG.1089.8 ENSMUSG00000026456 Control shVgll3 Cyb5r1 protein_coding   31.98388 24.47448 39.49328 1.977253 0.884659 0.6901047 4.5252505 3.797043 5.253458 0.3905253 0.72987903 0.4673403 0.14461667 0.15556667 0.13366667 -0.021900000 9.706657e-01 4.459967e-10 FALSE TRUE
MSTRG.1089.9 ENSMUSG00000026456 Control shVgll3 Cyb5r1 protein_coding   31.98388 24.47448 39.49328 1.977253 0.884659 0.6901047 2.9526911 0.000000 5.905382 0.0000000 1.82776183 9.2083276 0.07460000 0.00000000 0.14920000 0.149200000 4.459967e-10 4.459967e-10 TRUE 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
ENSMUSG00000026456 E001 0.1660866 0.0347277553 9.465536e-01   1 134333297 134333518 222 + 0.093 0.000 -8.021
ENSMUSG00000026456 E002 0.0000000       1 134333519 134333537 19 +      
ENSMUSG00000026456 E003 2.1401615 0.0158996485 1.256689e-02 2.454215e-01 1 134333538 134333732 195 + 0.290 0.708 2.111
ENSMUSG00000026456 E004 2.7963868 0.0063464743 4.124069e-02 4.551166e-01 1 134333733 134333740 8 + 0.425 0.745 1.455
ENSMUSG00000026456 E005 2.7963868 0.0063464743 4.124069e-02 4.551166e-01 1 134333741 134333741 1 + 0.425 0.745 1.455
ENSMUSG00000026456 E006 10.0267728 0.0056249594 5.826716e-01 9.485549e-01 1 134333742 134333757 16 + 1.001 1.060 0.216
ENSMUSG00000026456 E007 31.0731972 0.0008303875 8.276568e-01 9.854840e-01 1 134333758 134333765 8 + 1.480 1.493 0.043
ENSMUSG00000026456 E008 42.8942834 0.0078692982 7.889736e-01 9.802040e-01 1 134333766 134333791 26 + 1.614 1.633 0.063
ENSMUSG00000026456 E009 9.5105752 0.0977927808 9.368939e-01 9.996345e-01 1 134333792 134334018 227 + 0.980 1.041 0.224
ENSMUSG00000026456 E010 4.5865222 0.0090326287 3.579720e-01 8.751770e-01 1 134334019 134334050 32 + 0.681 0.811 0.526
ENSMUSG00000026456 E011 96.0383953 0.0008101478 6.433397e-01 9.566871e-01 1 134334051 134334130 80 + 1.959 1.975 0.054
ENSMUSG00000026456 E012 52.4746611 0.0004104232 5.543634e-01 9.388808e-01 1 134334131 134334146 16 + 1.696 1.724 0.094
ENSMUSG00000026456 E013 80.1926140 0.0004188874 2.633137e-02 3.636651e-01 1 134334147 134334200 54 + 1.855 1.943 0.296
ENSMUSG00000026456 E014 70.0503328 0.0132447434 5.069782e-01 9.302983e-01 1 134334337 134334409 73 + 1.813 1.858 0.154
ENSMUSG00000026456 E015 0.6597561 0.0225755275 1.005274e-01   1 134334599 134334704 106 + 0.093 0.374 2.526
ENSMUSG00000026456 E016 108.9755178 0.0002148184 6.026169e-02 5.320311e-01 1 134334784 134334890 107 + 1.996 2.059 0.211
ENSMUSG00000026456 E017 39.0215898 0.0006353477 2.289088e-02 3.398192e-01 1 134335312 134335324 13 + 1.532 1.660 0.437
ENSMUSG00000026456 E018 109.9725619 0.0002972621 7.909668e-03 1.944692e-01 1 134335325 134335441 117 + 1.990 2.079 0.300
ENSMUSG00000026456 E019 121.7673395 0.0002089534 5.949678e-03 1.603671e-01 1 134335555 134335743 189 + 2.097 2.002 -0.319
ENSMUSG00000026456 E020 295.9524423 0.0009495519 1.640115e-11 6.395355e-09 1 134335744 134336141 398 + 2.501 2.330 -0.569
ENSMUSG00000026456 E021 95.2494679 0.0002618729 1.161365e-01 6.617461e-01 1 134336142 134336225 84 + 1.981 1.919 -0.208
ENSMUSG00000026456 E022 20.0971774 0.0111007620 5.724709e-01 9.446095e-01 1 134336226 134336673 448 + 1.285 1.333 0.165
ENSMUSG00000026456 E023 34.7504982 0.0009356677 2.617375e-01 8.143369e-01 1 134336674 134337338 665 + 1.507 1.574 0.229
ENSMUSG00000026456 E024 112.2924126 0.0002111701 8.764515e-01 9.907933e-01 1 134337339 134337424 86 + 2.034 2.027 -0.024
ENSMUSG00000026456 E025 8.7127348 0.0022064809 9.767973e-01 1.000000e+00 1 134337425 134337737 313 + 0.969 0.964 -0.019
ENSMUSG00000026456 E026 128.5752392 0.0001836726 2.767785e-01 8.218390e-01 1 134338231 134338330 100 + 2.078 2.111 0.109
ENSMUSG00000026456 E027 86.7827815 0.0015729544 3.765693e-06 4.588653e-04 1 134338331 134338644 314 + 1.982 1.770 -0.714
ENSMUSG00000026456 E028 453.7635351 0.0004184911 6.187139e-04 3.366379e-02 1 134338645 134339478 834 + 2.615 2.671 0.187

Help

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