ENSMUSG00000028086

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
ENSMUST00000029727 ENSMUSG00000028086 Control shVgll3 Fbxw7 protein_coding protein_coding 4.3799 2.902723 5.857077 0.1183621 0.3624107 1.010273 3.1816133 1.7841663 4.5790602 0.05891527 0.42415590 1.3548851 0.69703333 0.61510000 0.7789667 0.163866667 0.22050616 0.01832852 FALSE TRUE
ENSMUST00000151410 ENSMUSG00000028086 Control shVgll3 Fbxw7 protein_coding retained_intron 4.3799 2.902723 5.857077 0.1183621 0.3624107 1.010273 0.3250160 0.2075259 0.4425061 0.05627788 0.02900773 1.0567505 0.07316667 0.07023333 0.0761000 0.005866667 0.99735446 0.01832852 TRUE TRUE
MSTRG.14697.1 ENSMUSG00000028086 Control shVgll3 Fbxw7 protein_coding   4.3799 2.902723 5.857077 0.1183621 0.3624107 1.010273 0.8278533 0.8886910 0.7670156 0.06120871 0.08610618 -0.2098815 0.21925000 0.30690000 0.1316000 -0.175300000 0.01832852 0.01832852 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
ENSMUSG00000028086 E001 5.7603335 0.0033362436 0.0048213840 0.13960532 3 84722422 84722574 153 + 0.655 1.011 1.396
ENSMUSG00000028086 E002 6.4029281 0.0031077940 0.0038629173 0.12050242 3 84722575 84722784 210 + 0.697 1.048 1.352
ENSMUSG00000028086 E003 6.7170351 0.0184244872 0.4937716855 0.92674629 3 84722785 84723072 288 + 0.836 0.924 0.337
ENSMUSG00000028086 E004 0.8159063 0.0283548687 0.0365437425 0.43139874 3 84723073 84723076 4 + 0.091 0.455 2.981
ENSMUSG00000028086 E005 1.9782691 0.0084313903 0.0211280623 0.32978625 3 84771271 84771318 48 + 0.287 0.672 1.981
ENSMUSG00000028086 E006 0.3318067 0.2707112260 0.1121480027   3 84771444 84771451 8 + 0.000 0.285 10.659
ENSMUSG00000028086 E007 0.9863303 0.0166604143 0.4144742877 0.89831921 3 84771452 84771507 56 + 0.231 0.378 0.981
ENSMUSG00000028086 E008 0.3321731 0.4012070491 0.5641176922   3 84797402 84797559 158 + 0.167 0.000 -9.820
ENSMUSG00000028086 E009 1.6513394 0.0277449332 0.8112436567 0.98376893 3 84810808 84810811 4 + 0.422 0.378 -0.242
ENSMUSG00000028086 E010 17.1448131 0.0013632218 0.0002774607 0.01793224 3 84810812 84811386 575 + 1.112 1.407 1.036
ENSMUSG00000028086 E011 0.0000000       3 84832787 84833106 320 +      
ENSMUSG00000028086 E012 30.4770887 0.0008091572 0.2014799113 0.77686960 3 84859453 84859946 494 + 1.501 1.414 -0.298
ENSMUSG00000028086 E013 13.6594729 0.0015789996 0.2379535813 0.80442163 3 84862182 84862264 83 + 1.104 1.211 0.381
ENSMUSG00000028086 E014 21.8792745 0.0009350324 0.1769205311 0.75677617 3 84865811 84865952 142 + 1.300 1.399 0.341
ENSMUSG00000028086 E015 20.5154437 0.0287756244 0.7514528049 0.97541370 3 84872555 84872689 135 + 1.325 1.279 -0.159
ENSMUSG00000028086 E016 22.7115598 0.0008424848 0.0132216709 0.25232082 3 84874747 84874870 124 + 1.408 1.211 -0.689
ENSMUSG00000028086 E017 16.1428972 0.0013708833 0.4036755831 0.89258252 3 84874871 84876471 1601 + 1.235 1.159 -0.270
ENSMUSG00000028086 E018 22.2290709 0.0009055148 0.4304908620 0.90756311 3 84876472 84876608 137 + 1.362 1.300 -0.217
ENSMUSG00000028086 E019 20.7514546 0.0010187645 0.5351825497 0.93662476 3 84878103 84878216 114 + 1.330 1.279 -0.177
ENSMUSG00000028086 E020 36.1446578 0.0120434749 0.0407161287 0.45275406 3 84879682 84879863 182 + 1.594 1.430 -0.562
ENSMUSG00000028086 E021 33.8614881 0.0007116535 0.5403051444 0.93662476 3 84881710 84881935 226 + 1.532 1.492 -0.137
ENSMUSG00000028086 E022 32.4111631 0.0005890014 0.4347472224 0.90880504 3 84883481 84883691 211 + 1.517 1.465 -0.176
ENSMUSG00000028086 E023 212.8389200 0.0001765413 0.7375785628 0.97290014 3 84884580 84886505 1926 + 2.304 2.308 0.015

Help

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