ENSMUSG00000019763

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
ENSMUST00000128434 ENSMUSG00000019763 Control shVgll3 Rmnd1 protein_coding protein_coding 28.66847 24.67165 32.66529 0.6175713 0.4356018 0.4047612 1.514469 1.474215 1.554722 0.02977317 0.27852912 0.076206101 0.05363333 0.05976667 0.04750000 -0.012266667 0.97066567 0.02176738    
ENSMUST00000137429 ENSMUSG00000019763 Control shVgll3 Rmnd1 protein_coding retained_intron 28.66847 24.67165 32.66529 0.6175713 0.4356018 0.4047612 3.146228 3.148181 3.144275 0.34757043 0.37568888 -0.001785394 0.11190000 0.12773333 0.09606667 -0.031666667 0.90194485 0.02176738    
ENSMUST00000140660 ENSMUSG00000019763 Control shVgll3 Rmnd1 protein_coding retained_intron 28.66847 24.67165 32.66529 0.6175713 0.4356018 0.4047612 2.143150 2.075305 2.210995 0.09653019 0.02656385 0.090947688 0.07601667 0.08433333 0.06770000 -0.016633333 0.96691930 0.02176738    
ENSMUST00000155172 ENSMUSG00000019763 Control shVgll3 Rmnd1 protein_coding protein_coding 28.66847 24.67165 32.66529 0.6175713 0.4356018 0.4047612 5.744328 5.485536 6.003120 0.53333005 0.47844236 0.129853416 0.20300000 0.22193333 0.18406667 -0.037866667 0.97066567 0.02176738    
MSTRG.1757.2 ENSMUSG00000019763 Control shVgll3 Rmnd1 protein_coding   28.66847 24.67165 32.66529 0.6175713 0.4356018 0.4047612 5.535618 3.804065 7.267171 0.13141070 0.04561947 0.932048316 0.18840000 0.15420000 0.22260000 0.068400000 0.02176738 0.02176738 FALSE  
MSTRG.1757.3 ENSMUSG00000019763 Control shVgll3 Rmnd1 protein_coding   28.66847 24.67165 32.66529 0.6175713 0.4356018 0.4047612 7.457314 6.434094 8.480533 0.11824083 0.68685765 0.397877512 0.26031667 0.26123333 0.25940000 -0.001833333 1.00000000 0.02176738 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
ENSMUSG00000019763 E001 12.9907463 0.0015299119 3.787895e-03 0.1194361140 10 4351915 4353170 1256 - 1.012 1.275 0.943
ENSMUSG00000019763 E002 49.8844647 0.0005863584 1.014812e-01 0.6390160184 10 4353171 4353501 331 - 1.666 1.743 0.262
ENSMUSG00000019763 E003 10.1985741 0.0023422026 3.359129e-01 0.8664850438 10 4353546 4353873 328 - 1.000 1.097 0.352
ENSMUSG00000019763 E004 16.6404268 0.0012062825 4.672185e-02 0.4781733713 10 4353874 4353983 110 - 1.166 1.327 0.567
ENSMUSG00000019763 E005 16.3138730 0.0012149293 2.425927e-01 0.8044216279 10 4353984 4353990 7 - 1.190 1.284 0.334
ENSMUSG00000019763 E006 0.3328359 0.0258479936 3.225642e-01   10 4357576 4357609 34 - 0.189 0.001 -8.611
ENSMUSG00000019763 E007 51.0235429 0.0004139329 4.792824e-03 0.1391227052 10 4357805 4357925 121 - 1.650 1.782 0.445
ENSMUSG00000019763 E008 53.8565032 0.0003607954 7.985718e-03 0.1949467196 10 4357926 4359022 1097 - 1.678 1.798 0.406
ENSMUSG00000019763 E009 0.0000000       10 4360713 4360789 77 -      
ENSMUSG00000019763 E010 21.4357537 0.0009279862 9.741739e-01 1.0000000000 10 4361667 4361731 65 - 1.343 1.343 0.000
ENSMUSG00000019763 E011 38.2232952 0.0049129200 2.961299e-01 0.8395849014 10 4363309 4363415 107 - 1.559 1.622 0.213
ENSMUSG00000019763 E012 33.8875506 0.0011399854 1.071663e-02 0.2234638016 10 4363416 4363745 330 - 1.468 1.618 0.511
ENSMUSG00000019763 E013 8.7184762 0.0022861071 4.969007e-01 0.9271499049 10 4364543 4364643 101 - 0.950 1.022 0.265
ENSMUSG00000019763 E014 6.6093539 0.0366081935 9.235862e-01 0.9985315478 10 4367153 4367192 40 - 0.878 0.866 -0.047
ENSMUSG00000019763 E015 6.2660041 0.0054012882 6.449201e-01 0.9566870527 10 4368556 4368631 76 - 0.878 0.816 -0.239
ENSMUSG00000019763 E016 2.9775439 0.0130871796 5.365420e-01 0.9366247565 10 4369807 4369902 96 - 0.631 0.529 -0.461
ENSMUSG00000019763 E017 0.0000000       10 4372082 4372190 109 -      
ENSMUSG00000019763 E018 2.2976086 0.0079568522 3.547977e-01 0.8751769517 10 4376094 4377170 1077 - 0.572 0.413 -0.783
ENSMUSG00000019763 E019 28.0195030 0.0007189411 7.445180e-01 0.9730331937 10 4377171 4377242 72 - 1.464 1.440 -0.082
ENSMUSG00000019763 E020 41.8500076 0.0004908838 5.847442e-01 0.9493189345 10 4377243 4377444 202 - 1.637 1.605 -0.108
ENSMUSG00000019763 E021 0.0000000       10 4377445 4377522 78 -      
ENSMUSG00000019763 E022 24.1749825 0.0008844180 9.023331e-01 0.9956322532 10 4377523 4377691 169 - 1.398 1.387 -0.038
ENSMUSG00000019763 E023 77.1473872 0.0013565054 1.783314e-07 0.0000341987 10 4377692 4378368 677 - 1.965 1.737 -0.768
ENSMUSG00000019763 E024 7.5678745 0.0031403400 2.687821e-01 0.8179193056 10 4378369 4378408 40 - 0.976 0.842 -0.508
ENSMUSG00000019763 E025 9.2001443 0.0520087277 7.267238e-02 0.5796801067 10 4378409 4378465 57 - 1.095 0.816 -1.044
ENSMUSG00000019763 E026 6.2677344 0.0031251932 6.371609e-01 0.9566870527 10 4378466 4378535 70 - 0.878 0.816 -0.239
ENSMUSG00000019763 E027 72.7689222 0.0003134007 1.280508e-02 0.2480029934 10 4378536 4379076 541 - 1.900 1.796 -0.350
ENSMUSG00000019763 E028 44.1725048 0.0004846538 3.173586e-01 0.8533737809 10 4379077 4379171 95 - 1.668 1.613 -0.187
ENSMUSG00000019763 E029 14.1526777 0.0105003345 7.168404e-01 0.9691201537 10 4382064 4382265 202 - 1.189 1.149 -0.145
ENSMUSG00000019763 E030 14.1752710 0.0014320729 1.257973e-01 0.6779968726 10 4382266 4382388 123 - 1.226 1.083 -0.512

Help

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