ENSMUSG00000028479

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
ENSMUST00000030201 ENSMUSG00000028479 Control shVgll3 Gne protein_coding protein_coding 14.30136 18.83293 9.769778 0.7574456 0.2158783 -0.9461499 1.1722978 1.7794636 0.5651320 0.0225864 0.01932057 -1.6375623 0.07631667 0.09476667 0.05786667 -0.03690000 0.48417356 0.0003697422 FALSE  
ENSMUST00000102936 ENSMUSG00000028479 Control shVgll3 Gne protein_coding protein_coding 14.30136 18.83293 9.769778 0.7574456 0.2158783 -0.9461499 5.6523394 6.4711834 4.8334953 0.4639236 0.37803309 -0.4202087 0.42016667 0.34496667 0.49536667 0.15040000 0.41056334 0.0003697422 FALSE  
ENSMUST00000173274 ENSMUSG00000028479 Control shVgll3 Gne protein_coding protein_coding 14.30136 18.83293 9.769778 0.7574456 0.2158783 -0.9461499 1.1805634 2.0091929 0.3519339 1.1920083 0.35193392 -2.4799805 0.06900000 0.10290000 0.03510000 -0.06780000 0.86306937 0.0003697422 FALSE  
ENSMUST00000174522 ENSMUSG00000028479 Control shVgll3 Gne protein_coding nonsense_mediated_decay 14.30136 18.83293 9.769778 0.7574456 0.2158783 -0.9461499 0.7360364 1.4720727 0.0000000 0.7390196 0.00000000 -7.2114724 0.03806667 0.07613333 0.00000000 -0.07613333 0.67066251 0.0003697422 FALSE  
MSTRG.15870.2 ENSMUSG00000028479 Control shVgll3 Gne protein_coding   14.30136 18.83293 9.769778 0.7574456 0.2158783 -0.9461499 2.2675685 2.6818671 1.8532698 1.3928694 0.01147318 -0.5307706 0.16680000 0.14370000 0.18990000 0.04620000 0.97066567 0.0003697422 FALSE  
MSTRG.15870.8 ENSMUSG00000028479 Control shVgll3 Gne protein_coding   14.30136 18.83293 9.769778 0.7574456 0.2158783 -0.9461499 0.8553232 0.6253328 1.0853137 0.1465837 0.12792969 0.7857596 0.07285000 0.03390000 0.11180000 0.07790000 0.02266867 0.0003697422 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
ENSMUSG00000028479 E001 83.2377066 0.0002728468 2.517663e-11 8.924735e-09 4 44034075 44036809 2735 - 1.716 1.997 0.944
ENSMUSG00000028479 E002 0.8118954 0.1102330088 4.470496e-01 9.133596e-01 4 44036810 44036825 16 - 0.154 0.305 1.258
ENSMUSG00000028479 E003 1.7980723 0.0106895112 4.856813e-01 9.253847e-01 4 44036826 44036829 4 - 0.357 0.482 0.674
ENSMUSG00000028479 E004 24.4932117 0.0007795012 9.620986e-01 1.000000e+00 4 44036830 44036957 128 - 1.395 1.392 -0.010
ENSMUSG00000028479 E005 132.6072659 0.0002378010 6.826825e-01 9.629190e-01 4 44036958 44037353 396 - 2.104 2.117 0.043
ENSMUSG00000028479 E006 42.1716583 0.0120500250 1.116808e-01 6.545303e-01 4 44038947 44039063 117 - 1.539 1.664 0.424
ENSMUSG00000028479 E007 5.2640636 0.0036858043 1.492566e-03 6.655864e-02 4 44039986 44040253 268 - 0.997 0.580 -1.674
ENSMUSG00000028479 E008 51.3735993 0.0061643449 6.004632e-01 9.525881e-01 4 44040254 44040436 183 - 1.723 1.694 -0.101
ENSMUSG00000028479 E009 86.1380869 0.0031034628 2.101963e-01 7.828663e-01 4 44041663 44041884 222 - 1.960 1.904 -0.189
ENSMUSG00000028479 E010 0.4973638 0.0255263402 1.967973e-01   4 44041885 44041889 5 - 0.000 0.246 10.109
ENSMUSG00000028479 E011 48.6643105 0.0004204219 7.459310e-01 9.731474e-01 4 44042163 44042292 130 - 1.672 1.689 0.058
ENSMUSG00000028479 E012 63.8347404 0.0003472658 9.114805e-03 2.055706e-01 4 44044759 44044969 211 - 1.865 1.752 -0.383
ENSMUSG00000028479 E013 38.8102895 0.0005421021 6.167526e-01 9.543274e-01 4 44045903 44045954 52 - 1.604 1.576 -0.095
ENSMUSG00000028479 E014 37.6430798 0.0006855225 6.497955e-01 9.566871e-01 4 44045955 44045990 36 - 1.590 1.564 -0.088
ENSMUSG00000028479 E015 58.2384341 0.0003319248 5.513074e-01 9.376554e-01 4 44052771 44052874 104 - 1.741 1.769 0.096
ENSMUSG00000028479 E016 61.6131179 0.0025378104 7.078226e-01 9.661215e-01 4 44052875 44052979 105 - 1.794 1.776 -0.060
ENSMUSG00000028479 E017 25.3091195 0.0008320162 6.908418e-01 9.629190e-01 4 44052980 44052983 4 - 1.424 1.397 -0.094
ENSMUSG00000028479 E018 50.5305732 0.0004081438 2.788976e-01 8.238748e-01 4 44055205 44055304 100 - 1.730 1.677 -0.180
ENSMUSG00000028479 E019 22.7227921 0.0016163667 4.548414e-01 9.140174e-01 4 44055305 44055357 53 - 1.395 1.340 -0.191
ENSMUSG00000028479 E020 0.8206395 0.0191067120 4.079866e-01 8.946505e-01 4 44059700 44059775 76 - 0.154 0.305 1.258
ENSMUSG00000028479 E021 27.1184220 0.0008662270 7.859605e-01 9.794573e-01 4 44059776 44059867 92 - 1.424 1.443 0.066
ENSMUSG00000028479 E022 44.2277526 0.0004404081 7.617173e-01 9.779031e-01 4 44059868 44059971 104 - 1.652 1.636 -0.053
ENSMUSG00000028479 E023 19.2504193 0.0009733812 2.277904e-02 3.386256e-01 4 44059972 44059990 19 - 1.165 1.355 0.668
ENSMUSG00000028479 E024 43.5844912 0.0006511098 6.056517e-01 9.530216e-01 4 44059991 44060102 112 - 1.617 1.646 0.098
ENSMUSG00000028479 E025 16.4465930 0.0013751775 1.821079e-01 7.608225e-01 4 44060103 44060111 9 - 1.295 1.183 -0.394
ENSMUSG00000028479 E026 51.8201273 0.0003596121 4.011839e-01 8.909102e-01 4 44060112 44060227 116 - 1.734 1.693 -0.137
ENSMUSG00000028479 E027 2.6408797 0.0907542594 4.007230e-01 8.906938e-01 4 44063087 44063146 60 - 0.644 0.482 -0.742
ENSMUSG00000028479 E028 1.1429702 0.1229172184 8.235592e-01 9.841109e-01 4 44063147 44063206 60 - 0.357 0.305 -0.323
ENSMUSG00000028479 E029 103.2063826 0.0002298238 8.965877e-01 9.956323e-01 4 44066755 44066960 206 - 2.006 2.002 -0.013
ENSMUSG00000028479 E030 0.9912563 0.0160593828 8.363537e-01 9.862613e-01 4 44066961 44067061 101 - 0.267 0.305 0.259
ENSMUSG00000028479 E031 14.9931293 0.0027407045 5.220800e-01 9.336068e-01 4 44072362 44072387 26 - 1.152 1.211 0.211
ENSMUSG00000028479 E032 24.6612520 0.0013096728 3.321741e-01 8.638889e-01 4 44072388 44072436 49 - 1.437 1.369 -0.236
ENSMUSG00000028479 E033 44.5342749 0.0004700105 3.825879e-02 4.417240e-01 4 44072437 44072778 342 - 1.709 1.601 -0.367
ENSMUSG00000028479 E034 0.0000000       4 44072830 44072891 62 -      
ENSMUSG00000028479 E035 0.4931798 0.0214633669 1.956908e-01   4 44072892 44072931 40 - 0.000 0.246 10.139
ENSMUSG00000028479 E036 0.9919191 0.0143509071 8.372922e-01 9.866671e-01 4 44072932 44073018 87 - 0.267 0.305 0.258
ENSMUSG00000028479 E037 0.0000000       4 44083825 44084047 223 -      
ENSMUSG00000028479 E038 0.0000000       4 44084048 44084177 130 -      

Help

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