ENSMUSG00000028766

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
ENSMUST00000030551 ENSMUSG00000028766 Control shVgll3 Alpl protein_coding protein_coding 71.30295 131.5015 11.10442 1.509945 0.3882752 -3.564684 58.213185 111.128253 5.2981161 0.35408904 0.26913247 -4.3880117 0.6610000 0.84533333 0.47666667 -0.36866667 2.370491e-22 7.844963e-25 FALSE TRUE
MSTRG.16737.2 ENSMUSG00000028766 Control shVgll3 Alpl protein_coding   71.30295 131.5015 11.10442 1.509945 0.3882752 -3.564684 1.835643 2.234654 1.4366321 0.07747012 0.05597384 -0.6337948 0.0733500 0.01703333 0.12966667 0.11263333 7.844963e-25 7.844963e-25 FALSE TRUE
MSTRG.16737.3 ENSMUSG00000028766 Control shVgll3 Alpl protein_coding   71.30295 131.5015 11.10442 1.509945 0.3882752 -3.564684 3.112325 5.307494 0.9171551 0.76453735 0.32875141 -2.5198640 0.0605000 0.04023333 0.08076667 0.04053333 8.709291e-01 7.844963e-25 FALSE TRUE
MSTRG.16737.4 ENSMUSG00000028766 Control shVgll3 Alpl protein_coding   71.30295 131.5015 11.10442 1.509945 0.3882752 -3.564684 6.840910 10.386146 3.2956736 0.70336010 0.11573342 -1.6530327 0.1885667 0.07890000 0.29823333 0.21933333 6.893516e-18 7.844963e-25 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
ENSMUSG00000028766 E001 1.9732385 0.0949632987 4.447656e-01 9.133596e-01 4 137469044 137469051 8 - 0.001 0.317 9.575
ENSMUSG00000028766 E002 5.5912077 0.0059839000 2.753002e-01 8.207088e-01 4 137469052 137469064 13 - 0.344 0.598 1.293
ENSMUSG00000028766 E003 2062.3680508 0.0009774805 5.184102e-12 2.165844e-09 4 137469065 137469996 932 - 3.132 3.011 -0.404
ENSMUSG00000028766 E004 77.1154680 0.0002675401 3.082824e-02 3.962954e-01 4 137469997 137470013 17 - 1.762 1.589 -0.585
ENSMUSG00000028766 E005 57.5838649 0.0003784379 9.963674e-04 4.836309e-02 4 137470014 137470495 482 - 1.724 1.455 -0.915
ENSMUSG00000028766 E006 218.9215988 0.0003716148 6.436403e-03 1.699617e-01 4 137470496 137470615 120 - 2.178 2.038 -0.468
ENSMUSG00000028766 E007 413.2653027 0.0004262246 1.213388e-02 2.410101e-01 4 137470946 137471137 192 - 2.420 2.316 -0.348
ENSMUSG00000028766 E008 24.7025752 0.0018759293 2.362886e-15 1.382052e-12 4 137471138 137471305 168 - 1.733 1.021 -2.482
ENSMUSG00000028766 E009 141.7260504 0.0001724085 1.393968e-01 7.025695e-01 4 137473704 137473730 27 - 1.805 1.867 0.210
ENSMUSG00000028766 E010 333.1321526 0.0001322031 1.154272e-03 5.358205e-02 4 137473731 137473838 108 - 2.134 2.237 0.344
ENSMUSG00000028766 E011 10.1961899 0.0019612693 7.950896e-01 9.810080e-01 4 137473961 137474458 498 - 0.766 0.792 0.107
ENSMUSG00000028766 E012 209.4793268 0.0041621668 2.120343e-02 3.297862e-01 4 137475070 137475139 70 - 1.926 2.038 0.376
ENSMUSG00000028766 E013 295.8392897 0.0003545303 2.180921e-01 7.910826e-01 4 137476860 137477003 144 - 2.157 2.181 0.082
ENSMUSG00000028766 E014 234.8663918 0.0004765548 2.490664e-08 5.497319e-06 4 137479863 137480038 176 - 1.821 2.094 0.919
ENSMUSG00000028766 E015 0.4930067 0.0275022111 1.000000e+00   4 137481178 137481178 1 - 0.000 0.103 9.509
ENSMUSG00000028766 E016 252.0251533 0.0001415037 2.615909e-07 4.781391e-05 4 137481179 137481353 175 - 1.894 2.123 0.770
ENSMUSG00000028766 E017 57.7372972 0.0003411549 1.954876e-03 7.778280e-02 4 137482396 137482396 1 - 1.190 1.497 1.069
ENSMUSG00000028766 E018 210.4806306 0.0021267084 6.912430e-07 1.050151e-04 4 137482397 137482511 115 - 1.771 2.047 0.930
ENSMUSG00000028766 E019 246.4444394 0.0014907710 7.275408e-03 1.858247e-01 4 137482941 137483060 120 - 2.000 2.108 0.361
ENSMUSG00000028766 E020 222.4721872 0.0016905555 2.622701e-02 3.632708e-01 4 137485883 137485986 104 - 1.973 2.063 0.301
ENSMUSG00000028766 E021 74.8484850 0.0019457474 5.964443e-02 5.297753e-01 4 137485987 137486015 29 - 1.459 1.599 0.481
ENSMUSG00000028766 E022 89.1489623 0.0007135668 1.950103e-04 1.341900e-02 4 137486016 137486043 28 - 1.379 1.680 1.032
ENSMUSG00000028766 E023 0.0000000       4 137493619 137493786 168 -      
ENSMUSG00000028766 E024 0.4933529 0.0263709742 1.000000e+00   4 137496833 137496840 8 - 0.000 0.103 9.522
ENSMUSG00000028766 E025 15.9673927 0.0051522678 8.049176e-03 1.949467e-01 4 137496841 137497131 291 - 1.281 0.922 -1.300
ENSMUSG00000028766 E026 0.0000000       4 137509472 137509502 31 -      
ENSMUSG00000028766 E027 0.3318067 0.3183758169 8.161160e-01   4 137512607 137512682 76 - 0.000 0.072 8.151
ENSMUSG00000028766 E028 6.5878677 0.0027751599 9.123196e-09 2.223399e-06 4 137521052 137521287 236 - 1.308 0.499 -3.166
ENSMUSG00000028766 E029 2.1395083 0.1040074485 3.523835e-01 8.751770e-01 4 137523104 137523552 449 - 0.534 0.298 -1.293
ENSMUSG00000028766 E030 94.3779715 0.0012382417 1.233424e-07 2.487688e-05 4 137523553 137523695 143 - 1.223 1.710 1.680

Help

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