ENSMUSG00000053080

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
ENSMUST00000159348 ENSMUSG00000053080 Control shVgll3 Zfta protein_coding protein_coding 20.40151 20.23759 20.56544 0.7564623 0.3086988 0.02317345 3.870510 4.213451 3.527568 0.4604869 0.17354927 -0.2556647 0.1895167 0.20733333 0.1717000 -0.035633333 9.706657e-01 9.110109e-09 FALSE TRUE
ENSMUST00000160561 ENSMUSG00000053080 Control shVgll3 Zfta protein_coding retained_intron 20.40151 20.23759 20.56544 0.7564623 0.3086988 0.02317345 6.697447 6.056826 7.338067 0.3838754 0.33911442 0.2764229 0.3287000 0.30056667 0.3568333 0.056266667 9.129458e-01 9.110109e-09 FALSE TRUE
ENSMUST00000189779 ENSMUSG00000053080 Control shVgll3 Zfta protein_coding retained_intron 20.40151 20.23759 20.56544 0.7564623 0.3086988 0.02317345 2.342589 1.984657 2.700522 0.5218217 0.30428877 0.4424304 0.1140167 0.09673333 0.1313000 0.034566667 9.706657e-01 9.110109e-09 FALSE TRUE
ENSMUST00000191580 ENSMUSG00000053080 Control shVgll3 Zfta protein_coding nonsense_mediated_decay 20.40151 20.23759 20.56544 0.7564623 0.3086988 0.02317345 1.179344 2.358689 0.000000 0.7242035 0.00000000 -7.8879447 0.0571000 0.11420000 0.0000000 -0.114200000 9.110109e-09 9.110109e-09 FALSE TRUE
MSTRG.11572.2 ENSMUSG00000053080 Control shVgll3 Zfta protein_coding   20.40151 20.23759 20.56544 0.7564623 0.3086988 0.02317345 4.053556 3.389101 4.718011 0.2074518 0.09783743 0.4760803 0.1989333 0.16846667 0.2294000 0.060933333 4.786005e-01 9.110109e-09 FALSE TRUE
MSTRG.11572.3 ENSMUSG00000053080 Control shVgll3 Zfta protein_coding   20.40151 20.23759 20.56544 0.7564623 0.3086988 0.02317345 2.258069 2.234864 2.281274 0.5918153 0.18404681 0.0295221 0.1117333 0.11266667 0.1108000 -0.001866667 1.000000e+00 9.110109e-09 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
ENSMUSG00000053080 E001 32.712013 0.0007359636 4.385897e-01 0.9109772136 19 7394990 7395282 293 + 1.504 1.552 0.164
ENSMUSG00000053080 E002 94.940029 0.0002346104 3.478064e-05 0.0033349501 19 7395523 7396081 559 + 2.048 1.898 -0.502
ENSMUSG00000053080 E003 163.286645 0.0032760146 3.980153e-02 0.4493363317 19 7396082 7397046 965 + 2.251 2.174 -0.256
ENSMUSG00000053080 E004 99.220675 0.0002429967 4.045157e-02 0.4515290459 19 7397047 7397431 385 + 2.034 1.962 -0.240
ENSMUSG00000053080 E005 17.914611 0.0142873322 3.717669e-01 0.8768395955 19 7397432 7397454 23 + 1.317 1.230 -0.307
ENSMUSG00000053080 E006 132.433907 0.0001809491 7.713361e-01 0.9779906794 19 7397455 7397773 319 + 2.129 2.121 -0.027
ENSMUSG00000053080 E007 5.582551 0.0037491180 6.087476e-01 0.9533477035 19 7397774 7397783 10 + 0.785 0.852 0.261
ENSMUSG00000053080 E008 2.297628 0.0074767504 3.442361e-01 0.8719953121 19 7397784 7397850 67 + 0.588 0.431 -0.756
ENSMUSG00000053080 E009 5.908007 0.0066226578 8.890917e-01 0.9945296271 19 7397851 7397926 76 + 0.849 0.831 -0.068
ENSMUSG00000053080 E010 24.195705 0.0241111469 2.387899e-01 0.8044216279 19 7397927 7398392 466 + 1.453 1.337 -0.402
ENSMUSG00000053080 E011 43.157714 0.0005232065 2.034214e-02 0.3233184194 19 7398393 7398619 227 + 1.700 1.576 -0.420
ENSMUSG00000053080 E012 58.427322 0.0008744748 3.565013e-01 0.8751769517 19 7398620 7398761 142 + 1.794 1.751 -0.145
ENSMUSG00000053080 E013 46.730261 0.0028429911 1.479401e-01 0.7157110082 19 7398762 7398834 73 + 1.716 1.635 -0.276
ENSMUSG00000053080 E014 72.534035 0.0003062811 9.019504e-01 0.9956322532 19 7398835 7398957 123 + 1.864 1.869 0.020
ENSMUSG00000053080 E015 47.547110 0.0004145569 4.183024e-01 0.9016081508 19 7398958 7399009 52 + 1.665 1.707 0.142
ENSMUSG00000053080 E016 159.272133 0.0002480940 9.532950e-01 1.0000000000 19 7399279 7399827 549 + 2.203 2.206 0.008
ENSMUSG00000053080 E017 1571.701144 0.0001427513 4.849613e-07 0.0000766632 19 7400008 7403269 3262 + 3.181 3.212 0.103

Help

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