ENSMUSG00000031523

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
ENSMUST00000033923 ENSMUSG00000031523 Control shVgll3 Dlc1 protein_coding protein_coding 6.962979 7.679641 6.246318 0.2959932 0.2415695 -0.2976025 5.0906350 6.2141401 3.9671298 0.2119108 0.05272525 -0.6461469 0.7233833 0.80950000 0.63726667 -0.17223333 0.007672991 0.007672991 FALSE TRUE
ENSMUST00000163663 ENSMUSG00000031523 Control shVgll3 Dlc1 protein_coding protein_coding 6.962979 7.679641 6.246318 0.2959932 0.2415695 -0.2976025 1.0950309 0.8903802 1.2996815 0.2021188 0.22333126 0.5406098 0.1628167 0.11656667 0.20906667 0.09250000 0.663084776 0.007672991 FALSE TRUE
ENSMUST00000178717 ENSMUSG00000031523 Control shVgll3 Dlc1 protein_coding retained_intron 6.962979 7.679641 6.246318 0.2959932 0.2415695 -0.2976025 0.3588671 0.2785696 0.4391645 0.2785696 0.22700230 0.6383242 0.0522000 0.03393333 0.07046667 0.03653333 0.970665669 0.007672991 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
ENSMUSG00000031523 E001 368.7245987 0.0037300937 1.142722e-01 6.584532e-01 8 37034905 37037402 2498 - 2.534 2.585 0.168
ENSMUSG00000031523 E002 18.2707437 0.0010758825 8.034036e-01 9.818626e-01 8 37037403 37037557 155 - 1.264 1.293 0.100
ENSMUSG00000031523 E003 27.7717359 0.0007177504 5.422332e-01 9.368818e-01 8 37038419 37038592 174 - 1.473 1.442 -0.107
ENSMUSG00000031523 E004 0.1659033 0.0345949362 6.350071e-01   8 37039299 37039821 523 - 0.000 0.109 10.774
ENSMUSG00000031523 E005 35.4854131 0.0084167666 4.450167e-01 9.133596e-01 8 37039822 37040039 218 - 1.584 1.538 -0.157
ENSMUSG00000031523 E006 34.9923396 0.0009469111 8.031406e-01 9.818626e-01 8 37041109 37041327 219 - 1.539 1.563 0.080
ENSMUSG00000031523 E007 29.7646997 0.0006383932 8.992163e-01 9.956323e-01 8 37041961 37042075 115 - 1.484 1.485 0.002
ENSMUSG00000031523 E008 4.9438780 0.0038520377 6.601231e-01 9.580389e-01 8 37042076 37044188 2113 - 0.799 0.747 -0.206
ENSMUSG00000031523 E009 62.6334516 0.0062172305 2.723654e-01 8.182921e-01 8 37044189 37044402 214 - 1.758 1.829 0.239
ENSMUSG00000031523 E010 0.3318168 0.0284801920 8.282447e-01   8 37044403 37044423 21 - 0.139 0.109 -0.399
ENSMUSG00000031523 E011 59.9957881 0.0003445685 7.485406e-02 5.842661e-01 8 37046378 37046576 199 - 1.728 1.818 0.303
ENSMUSG00000031523 E012 34.2279437 0.0005414038 3.499376e-01 8.751770e-01 8 37046701 37046860 160 - 1.505 1.570 0.221
ENSMUSG00000031523 E013 31.9274538 0.0023018014 3.156466e-01 8.526612e-01 8 37049855 37050031 177 - 1.544 1.489 -0.190
ENSMUSG00000031523 E014 244.3298121 0.0001658115 6.847052e-01 9.629190e-01 8 37050695 37052121 1427 - 2.385 2.386 0.002
ENSMUSG00000031523 E015 12.3104612 0.0057858537 5.108277e-01 9.308326e-01 8 37053830 37053893 64 - 1.153 1.096 -0.206
ENSMUSG00000031523 E016 0.0000000       8 37060385 37060530 146 -      
ENSMUSG00000031523 E017 9.0348844 0.0020798265 5.082645e-01 9.308299e-01 8 37060531 37060612 82 - 0.951 1.031 0.296
ENSMUSG00000031523 E018 9.0515758 0.0024009276 2.285041e-01 8.005513e-01 8 37066523 37066594 72 - 0.913 1.054 0.523
ENSMUSG00000031523 E019 33.4012768 0.0005524544 7.032430e-04 3.672561e-02 8 37080713 37081097 385 - 1.395 1.614 0.753
ENSMUSG00000031523 E020 0.0000000       8 37199742 37200208 467 -      
ENSMUSG00000031523 E021 2.1354390 0.0191131223 1.876922e-01 7.658262e-01 8 37230799 37230832 34 - 0.604 0.386 -1.077
ENSMUSG00000031523 E022 0.1615462 0.0350098055 6.347217e-01   8 37316280 37317317 1038 - 0.000 0.109 10.767
ENSMUSG00000031523 E023 8.8876975 0.0079232943 4.392413e-01 9.111304e-01 8 37317318 37317449 132 - 1.034 0.955 -0.292
ENSMUSG00000031523 E024 0.1660866 0.0347334695 3.679252e-01   8 37324865 37325079 215 - 0.139 0.000 -11.837
ENSMUSG00000031523 E025 10.5459166 0.0056216689 2.032227e-02 3.233184e-01 8 37325080 37325229 150 - 1.176 0.941 -0.853
ENSMUSG00000031523 E026 0.1667494 0.0348311756 3.678715e-01   8 37402738 37404713 1976 - 0.139 0.000 -11.835
ENSMUSG00000031523 E027 48.2011973 0.0005851502 1.919999e-08 4.403950e-06 8 37404714 37405708 995 - 1.822 1.549 -0.926
ENSMUSG00000031523 E028 11.8219669 0.0017001616 5.182769e-05 4.490965e-03 8 37405709 37405912 204 - 1.282 0.896 -1.399
ENSMUSG00000031523 E029 9.2329770 0.0135321923 4.859581e-02 4.839731e-01 8 37419275 37419596 322 - 1.117 0.897 -0.813
ENSMUSG00000031523 E030 0.9819636 0.0352322386 4.702843e-02 4.787977e-01 8 37420099 37420310 212 - 0.461 0.109 -2.720

Help

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