ENSMUSG00000011960

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
ENSMUST00000012104 ENSMUSG00000011960 Control shVgll3 Ccnt1 protein_coding protein_coding 4.913227 4.699128 5.127325 0.271958 0.3749035 0.1255576 0.1751429 0.0000000 0.3502858 0.00000000 0.3502858 5.1710698 0.02995000 0.00000000 0.05990000 0.059900000 0.9706656688 0.0001564786 FALSE TRUE
ENSMUST00000130921 ENSMUSG00000011960 Control shVgll3 Ccnt1 protein_coding retained_intron 4.913227 4.699128 5.127325 0.271958 0.3749035 0.1255576 0.2456656 0.2724838 0.2188473 0.01557395 0.0332514 -0.3037827 0.05063333 0.05873333 0.04253333 -0.016200000 0.9706656688 0.0001564786 FALSE FALSE
ENSMUST00000168928 ENSMUSG00000011960 Control shVgll3 Ccnt1 protein_coding nonsense_mediated_decay 4.913227 4.699128 5.127325 0.271958 0.3749035 0.1255576 0.2504875 0.5009750 0.0000000 0.16391590 0.0000000 -5.6751807 0.05176667 0.10353333 0.00000000 -0.103533333 0.0001564786 0.0001564786 FALSE TRUE
ENSMUST00000169707 ENSMUSG00000011960 Control shVgll3 Ccnt1 protein_coding protein_coding 4.913227 4.699128 5.127325 0.271958 0.3749035 0.1255576 3.8711498 3.7053854 4.0369142 0.03542774 0.2245141 0.1233104 0.79690000 0.79393333 0.79986667 0.005933333 1.0000000000 0.0001564786 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
ENSMUSG00000011960 E001 0.4983830 0.0219470095 0.503761024   15 98436570 98436579 10 - 0.118 0.230 1.164
ENSMUSG00000011960 E002 67.8000654 0.0003228546 0.446824681 0.91335964 15 98436580 98436996 417 - 1.851 1.820 -0.103
ENSMUSG00000011960 E003 379.0191735 0.0002922073 0.180828756 0.76033243 15 98436997 98440635 3639 - 2.569 2.589 0.066
ENSMUSG00000011960 E004 34.8798244 0.0005416042 0.262660508 0.81433690 15 98440636 98441091 456 - 1.583 1.519 -0.219
ENSMUSG00000011960 E005 196.0411446 0.0003040792 0.126313175 0.67814909 15 98441092 98442019 928 - 2.277 2.313 0.120
ENSMUSG00000011960 E006 24.0151327 0.0067722908 0.140973868 0.70474885 15 98442020 98442220 201 - 1.448 1.333 -0.397
ENSMUSG00000011960 E007 21.8903066 0.0008789223 0.405716854 0.89347807 15 98442221 98442447 227 - 1.386 1.326 -0.207
ENSMUSG00000011960 E008 11.8389165 0.0016474386 0.059761910 0.52977533 15 98442448 98442489 42 - 1.185 1.002 -0.659
ENSMUSG00000011960 E009 11.6754424 0.0016434402 0.002729347 0.09645893 15 98444405 98444475 71 - 1.219 0.920 -1.088
ENSMUSG00000011960 E010 20.7001342 0.0012556905 0.092171809 0.62687548 15 98444626 98444789 164 - 1.391 1.265 -0.440
ENSMUSG00000011960 E011 1.6540799 0.0830560793 0.334472242 0.86618188 15 98444790 98444901 112 - 0.502 0.311 -1.062
ENSMUSG00000011960 E012 0.8260158 0.0158136742 0.571173590 0.94412726 15 98446533 98446546 14 - 0.210 0.311 0.749
ENSMUSG00000011960 E013 13.5281231 0.0035440289 0.782433552 0.97903220 15 98446547 98446592 46 - 1.148 1.174 0.094
ENSMUSG00000011960 E014 13.3598994 0.0437048451 0.841165974 0.98677151 15 98449795 98449857 63 - 1.138 1.175 0.132
ENSMUSG00000011960 E015 7.8936909 0.0065716055 0.853854152 0.98836106 15 98452482 98452542 61 - 0.958 0.938 -0.077
ENSMUSG00000011960 E016 0.3230924 0.2844270124 0.234369009   15 98452543 98452566 24 - 0.000 0.229 9.383
ENSMUSG00000011960 E017 5.7536820 0.0060346670 0.626663969 0.95514198 15 98456479 98458077 1599 - 0.798 0.862 0.247
ENSMUSG00000011960 E018 18.9140277 0.0010484814 0.214893880 0.78796646 15 98458078 98458206 129 - 1.250 1.347 0.340
ENSMUSG00000011960 E019 8.2215066 0.0022892615 0.698187920 0.96475394 15 98462928 98463009 82 - 0.943 0.987 0.164
ENSMUSG00000011960 E020 0.8260061 0.0156311550 0.210531899 0.78308495 15 98463010 98463020 11 - 0.351 0.130 -1.836
ENSMUSG00000011960 E021 0.0000000       15 98465357 98466164 808 -      
ENSMUSG00000011960 E022 0.0000000       15 98468752 98468804 53 -      

Help

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