ENSMUSG00000003352

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
ENSMUST00000003442 ENSMUSG00000003352 Control shVgll3 Cacnb3 protein_coding protein_coding 24.01587 33.17978 14.85195 0.638332 0.4413402 -1.159116 4.107092 4.440780 3.773404 0.1483319 0.3864146 -0.2343734 0.1940667 0.13380000 0.2543333 0.12053333 0.00315275 0.002556771 FALSE TRUE
ENSMUST00000109150 ENSMUSG00000003352 Control shVgll3 Cacnb3 protein_coding protein_coding 24.01587 33.17978 14.85195 0.638332 0.4413402 -1.159116 12.211044 19.681478 4.740610 0.6891564 2.4339376 -2.0513868 0.4533833 0.59366667 0.3131000 -0.28056667 0.97066567 0.002556771 FALSE TRUE
ENSMUST00000230064 ENSMUSG00000003352 Control shVgll3 Cacnb3 protein_coding retained_intron 24.01587 33.17978 14.85195 0.638332 0.4413402 -1.159116 3.162854 4.587267 1.738441 0.2744396 0.1960671 -1.3947072 0.1281667 0.13830000 0.1180333 -0.02026667 0.97066567 0.002556771 FALSE TRUE
ENSMUST00000230490 ENSMUSG00000003352 Control shVgll3 Cacnb3 protein_coding protein_coding 24.01587 33.17978 14.85195 0.638332 0.4413402 -1.159116 3.248193 2.218449 4.277937 1.1473938 2.4266294 0.9442438 0.1793667 0.06616667 0.2925667 0.22640000 0.97066567 0.002556771 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
ENSMUSG00000003352 E001 0.3319899 0.0286318745 5.868398e-01   15 98528721 98528884 164 + 0.169 0.089 -1.058
ENSMUSG00000003352 E002 0.0000000       15 98529155 98529307 153 +      
ENSMUSG00000003352 E003 0.1657302 0.0345647451 1.000000e+00   15 98529686 98529812 127 + 0.000 0.089 9.739
ENSMUSG00000003352 E004 0.9736344 0.3649026821 1.777346e-01 0.7567761689 15 98530251 98530256 6 + 0.000 0.373 11.543
ENSMUSG00000003352 E005 1.1393647 0.1310239289 6.371202e-02 0.5476144021 15 98530257 98530261 5 + 0.000 0.414 12.085
ENSMUSG00000003352 E006 21.3217924 0.3274338401 2.409797e-01 0.8044216279 15 98530262 98530401 140 + 1.139 1.388 0.877
ENSMUSG00000003352 E007 0.8120882 0.2591449365 1.772677e-01 0.7567761689 15 98532029 98532072 44 + 0.000 0.330 11.394
ENSMUSG00000003352 E008 1.4803855 0.0106434659 1.425940e-01 0.7089097697 15 98532073 98532132 60 + 0.169 0.451 1.942
ENSMUSG00000003352 E009 3.9652515 0.1538604649 4.812427e-02 0.4836406842 15 98532133 98532316 184 + 0.290 0.780 2.403
ENSMUSG00000003352 E010 9.6821197 0.0064024826 4.855863e-06 0.0005796314 15 98532317 98532632 316 + 0.462 1.132 2.723
ENSMUSG00000003352 E011 0.9863697 0.0562818648 4.118694e-01 0.8968300992 15 98532633 98532647 15 + 0.169 0.330 1.263
ENSMUSG00000003352 E012 27.7983686 0.0118220988 2.540388e-02 0.3575910076 15 98532648 98532985 338 + 1.546 1.364 -0.628
ENSMUSG00000003352 E013 28.1524441 0.0006674165 5.468971e-06 0.0006397602 15 98532986 98533094 109 + 1.612 1.319 -1.008
ENSMUSG00000003352 E014 18.5712598 0.0011512733 7.001140e-04 0.0367256115 15 98537369 98537369 1 + 1.426 1.160 -0.930
ENSMUSG00000003352 E015 62.0116606 0.0003044596 4.197021e-02 0.4604457932 15 98537370 98537491 122 + 1.829 1.741 -0.299
ENSMUSG00000003352 E016 74.2693485 0.0005986185 7.252538e-01 0.9710735626 15 98537695 98537817 123 + 1.835 1.855 0.068
ENSMUSG00000003352 E017 60.5334773 0.0003281082 6.952561e-01 0.9646063242 15 98538220 98538335 116 + 1.770 1.757 -0.046
ENSMUSG00000003352 E018 18.2553661 0.0101318897 3.592328e-01 0.8751769517 15 98538567 98538569 3 + 1.311 1.230 -0.286
ENSMUSG00000003352 E019 43.6343854 0.0118438198 8.488222e-01 0.9870300453 15 98538570 98538631 62 + 1.626 1.619 -0.025
ENSMUSG00000003352 E020 26.3763764 0.0091435294 3.634025e-01 0.8754022310 15 98538840 98538859 20 + 1.456 1.385 -0.244
ENSMUSG00000003352 E021 48.3322944 0.0043504750 7.067685e-01 0.9660361428 15 98539058 98539138 81 + 1.677 1.660 -0.059
ENSMUSG00000003352 E022 47.5553723 0.0004264568 7.960974e-01 0.9810079907 15 98539281 98539339 59 + 1.646 1.664 0.063
ENSMUSG00000003352 E023 15.8041096 0.0202648074 4.903191e-01 0.9261797087 15 98539340 98539496 157 + 1.141 1.224 0.295
ENSMUSG00000003352 E024 81.2300358 0.0002766514 7.660758e-01 0.9779906794 15 98539497 98539606 110 + 1.875 1.893 0.057
ENSMUSG00000003352 E025 23.8298445 0.0038445873 7.831319e-01 0.9790321967 15 98539607 98539819 213 + 1.350 1.377 0.093
ENSMUSG00000003352 E026 125.8555651 0.0001869494 8.551101e-01 0.9886727128 15 98539820 98539971 152 + 2.068 2.078 0.036
ENSMUSG00000003352 E027 68.5862072 0.0003897066 5.790319e-01 0.9473736526 15 98540190 98540285 96 + 1.794 1.824 0.100
ENSMUSG00000003352 E028 110.4574431 0.0009526379 8.089502e-01 0.9830417642 15 98540383 98540532 150 + 2.009 2.023 0.046
ENSMUSG00000003352 E029 747.2691046 0.0003715070 1.993168e-01 0.7751356392 15 98541138 98542410 1273 + 2.832 2.852 0.066

Help

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