ENSMUSG00000029178

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
ENSMUST00000165536 ENSMUSG00000029178 Control shVgll3 Klf3 protein_coding protein_coding 15.0021 13.79066 16.21353 0.4916622 2.002781 0.2333502 7.105892 7.0788173 7.132968 0.3072436 0.6223698 0.01097862 0.48063333 0.516100000 0.4451667 -0.07093333 0.9706657 0.0177027 FALSE TRUE
ENSMUST00000166409 ENSMUSG00000029178 Control shVgll3 Klf3 protein_coding protein_coding 15.0021 13.79066 16.21353 0.4916622 2.002781 0.2333502 1.212736 2.4254720 0.000000 1.6648795 0.0000000 -7.92805757 0.08461667 0.169233333 0.0000000 -0.16923333 0.6174405 0.0177027 FALSE TRUE
ENSMUST00000197879 ENSMUSG00000029178 Control shVgll3 Klf3 protein_coding protein_coding 15.0021 13.79066 16.21353 0.4916622 2.002781 0.2333502 1.382485 0.1286530 2.636317 0.1286530 0.5139767 4.25443466 0.08423333 0.008733333 0.1597333 0.15100000 0.0177027 0.0177027 FALSE FALSE
ENSMUST00000200384 ENSMUSG00000029178 Control shVgll3 Klf3 protein_coding nonsense_mediated_decay 15.0021 13.79066 16.21353 0.4916622 2.002781 0.2333502 1.795688 0.4704946 3.120882 0.4704946 1.2544921 2.70397676 0.10468333 0.031900000 0.1774667 0.14556667 0.6126783 0.0177027   FALSE
MSTRG.17605.4 ENSMUSG00000029178 Control shVgll3 Klf3 protein_coding   15.0021 13.79066 16.21353 0.4916622 2.002781 0.2333502 2.316166 2.6904686 1.941864 1.4744118 0.4569832 -0.46835734 0.16661667 0.201300000 0.1319333 -0.06936667 1.0000000 0.0177027 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
ENSMUSG00000029178 E001 0.0000000       5 64960731 64960919 189 +      
ENSMUSG00000029178 E002 0.0000000       5 64960920 64960964 45 +      
ENSMUSG00000029178 E003 0.0000000       5 64960965 64961134 170 +      
ENSMUSG00000029178 E004 0.1667494 0.0341615183 0.389007769   5 64969649 64969681 33 + 0.137 0.000 -10.024
ENSMUSG00000029178 E005 0.1667494 0.0341615183 0.389007769   5 64969682 64969682 1 + 0.137 0.000 -11.281
ENSMUSG00000029178 E006 0.3326527 0.0276115701 0.861656294   5 64969683 64969726 44 + 0.137 0.112 -0.337
ENSMUSG00000029178 E007 3.6225661 0.0048581508 0.580244348 0.94771568 5 64969727 64969846 120 + 0.705 0.625 -0.337
ENSMUSG00000029178 E008 0.3318067 0.2998335773 0.347247908   5 64969847 64969850 4 + 0.000 0.200 10.499
ENSMUSG00000029178 E009 1.9803175 0.0084678461 0.328022189 0.86229294 5 64973193 64974077 885 + 0.555 0.392 -0.823
ENSMUSG00000029178 E010 1.4773942 0.0125168000 0.494919395 0.92674629 5 64974078 64974078 1 + 0.455 0.337 -0.659
ENSMUSG00000029178 E011 29.2903262 0.0006539949 0.113444222 0.65761670 5 64974079 64974173 95 + 1.530 1.432 -0.337
ENSMUSG00000029178 E012 2.7997152 0.0062740997 0.805634195 0.98210805 5 64974174 64975967 1794 + 0.598 0.561 -0.167
ENSMUSG00000029178 E013 1.1538120 0.0137146740 0.148750269 0.71578801 5 64975968 64976050 83 + 0.455 0.200 -1.659
ENSMUSG00000029178 E014 1.4656573 0.6264760325 0.781909271 0.97903220 5 64976051 64976662 612 + 0.504 0.274 -1.316
ENSMUSG00000029178 E015 234.3658895 0.0001771426 0.002392956 0.08802766 5 64979217 64979690 474 + 2.403 2.340 -0.213
ENSMUSG00000029178 E016 31.2465281 0.0006211770 0.264432206 0.81433690 5 64979691 64979700 10 + 1.464 1.536 0.248
ENSMUSG00000029178 E017 92.9309407 0.0002440128 0.595927230 0.95169375 5 64980222 64980372 151 + 1.979 1.963 -0.055
ENSMUSG00000029178 E018 40.6644115 0.0009592914 0.729907836 0.97107356 5 64980373 64982772 2400 + 1.604 1.626 0.075
ENSMUSG00000029178 E019 1.4809053 0.0105798454 0.980305132 1.00000000 5 64984147 64984151 5 + 0.394 0.392 -0.015
ENSMUSG00000029178 E020 3.6092821 0.0050865161 0.163625028 0.73703719 5 64984152 64984225 74 + 0.764 0.560 -0.868
ENSMUSG00000029178 E021 90.5174269 0.0003526374 0.236504848 0.80442163 5 64984453 64984613 161 + 1.981 1.940 -0.137
ENSMUSG00000029178 E022 1061.8837060 0.0002314300 0.000496096 0.02817151 5 64986320 64990244 3925 + 3.009 3.035 0.088

Help

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