ENSMUSG00000012117

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
ENSMUST00000105887 ENSMUSG00000012117 Control shVgll3 Dhdds protein_coding protein_coding 8.33007 9.016463 7.643677 0.4413601 0.3745888 -0.2380077 2.1163289 1.603036 2.6296219 0.3564415 0.3310161 0.7105528 0.25921667 0.1761667 0.3422667 0.1661000 0.29558508 0.04188963 FALSE TRUE
ENSMUST00000144668 ENSMUSG00000012117 Control shVgll3 Dhdds protein_coding protein_coding 8.33007 9.016463 7.643677 0.4413601 0.3745888 -0.2380077 4.5455265 6.113539 2.9775139 0.2706765 0.1891049 -1.0354203 0.53786667 0.6834000 0.3923333 -0.2910667 0.04188963 0.04188963 FALSE TRUE
ENSMUST00000146241 ENSMUSG00000012117 Control shVgll3 Dhdds protein_coding protein_coding_CDS_not_defined 8.33007 9.016463 7.643677 0.4413601 0.3745888 -0.2380077 0.5900827 0.238293 0.9418723 0.1615589 0.4952512 1.9387245 0.07753333 0.0270000 0.1280667 0.1010667 0.97066567 0.04188963 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
ENSMUSG00000012117 E001 0.4844458 0.1404912882 0.721841753   4 133696339 133696367 29 - 0.135 0.202 0.706
ENSMUSG00000012117 E002 0.3230924 0.2675176930 0.327652135   4 133696368 133696368 1 - 0.000 0.202 10.263
ENSMUSG00000012117 E003 0.4889958 0.0258001823 0.120591159   4 133696369 133696373 5 - 0.000 0.277 11.676
ENSMUSG00000012117 E004 6.8836893 0.0142594583 0.420312835 0.90331353 4 133696374 133696485 112 - 0.834 0.941 0.406
ENSMUSG00000012117 E005 147.0662638 0.0029910354 0.001283137 0.05842267 4 133696486 133697503 1018 - 2.104 2.215 0.372
ENSMUSG00000012117 E006 142.6923090 0.0003970223 0.011914593 0.23865824 4 133697504 133698231 728 - 2.115 2.186 0.237
ENSMUSG00000012117 E007 15.9493733 0.0011884894 0.190763746 0.76590946 4 133698232 133698259 28 - 1.284 1.175 -0.383
ENSMUSG00000012117 E008 19.4616613 0.0047161391 0.083995987 0.60541285 4 133698260 133698291 32 - 1.379 1.239 -0.490
ENSMUSG00000012117 E009 86.1835896 0.0075842280 0.123996407 0.67465267 4 133698292 133698553 262 - 1.980 1.900 -0.266
ENSMUSG00000012117 E010 16.8172152 0.0249950266 0.546631361 0.93707028 4 133698554 133698564 11 - 1.284 1.216 -0.238
ENSMUSG00000012117 E011 2.9682161 0.0063232763 0.173934167 0.75582537 4 133698565 133698567 3 - 0.700 0.489 -0.946
ENSMUSG00000012117 E012 28.0033158 0.0007717783 0.674595590 0.96164256 4 133707435 133707504 70 - 1.474 1.448 -0.090
ENSMUSG00000012117 E013 17.9598978 0.0286244056 0.931889492 0.99930331 4 133707505 133707542 38 - 1.267 1.282 0.053
ENSMUSG00000012117 E014 0.8266786 0.0179953282 0.828590426 0.98548395 4 133707543 133707921 379 - 0.238 0.277 0.291
ENSMUSG00000012117 E015 33.4379311 0.0157101532 0.223110405 0.79803804 4 133710111 133710225 115 - 1.586 1.488 -0.334
ENSMUSG00000012117 E016 30.4035170 0.0030419023 0.098155591 0.63317139 4 133718590 133718691 102 - 1.551 1.443 -0.371
ENSMUSG00000012117 E017 27.9796086 0.0006935113 0.015531295 0.28025212 4 133719775 133719891 117 - 1.538 1.384 -0.532
ENSMUSG00000012117 E018 42.8966808 0.0004989415 0.520814610 0.93245373 4 133721473 133721615 143 - 1.621 1.656 0.118
ENSMUSG00000012117 E019 0.0000000       4 133721616 133721640 25 -      
ENSMUSG00000012117 E020 1.3168671 0.0175566154 0.089524879 0.61903982 4 133723917 133724042 126 - 0.503 0.203 -1.879
ENSMUSG00000012117 E021 0.3328359 0.0260715140 0.149674440   4 133724043 133724046 4 - 0.238 0.000 -12.394
ENSMUSG00000012117 E022 33.3643472 0.0005856045 0.662275122 0.95817326 4 133724133 133724249 117 - 1.519 1.546 0.092
ENSMUSG00000012117 E023 26.1666672 0.0007594709 0.090471419 0.62108841 4 133727580 133727650 71 - 1.490 1.378 -0.384
ENSMUSG00000012117 E024 19.7720958 0.0009996314 0.833017748 0.98548395 4 133727651 133727704 54 - 1.323 1.308 -0.053
ENSMUSG00000012117 E025 22.3763558 0.0009311899 0.860891066 0.98884244 4 133728036 133728177 142 - 1.359 1.373 0.047
ENSMUSG00000012117 E026 0.3319899 0.0283631824 0.881641356   4 133728178 133728229 52 - 0.135 0.113 -0.294

Help

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