ENSMUSG00000028580

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
ENSMUST00000030315 ENSMUSG00000028580 Control shVgll3 Pum1 protein_coding protein_coding 8.876968 9.425994 8.327942 0.1690256 0.2847161 -0.1784831 1.1591671 2.318334 0.0000000 0.2526190 0.0000000 -7.8631543 0.12263333 0.2452667 0.0000000 -0.24526667 1.993195e-19 1.993195e-19 FALSE TRUE
ENSMUST00000097862 ENSMUSG00000028580 Control shVgll3 Pum1 protein_coding protein_coding 8.876968 9.425994 8.327942 0.1690256 0.2847161 -0.1784831 0.3658849 0.000000 0.7317697 0.0000000 0.7317697 6.2128995 0.04300000 0.0000000 0.0860000 0.08600000 9.706657e-01 1.993195e-19 FALSE TRUE
ENSMUST00000105991 ENSMUSG00000028580 Control shVgll3 Pum1 protein_coding protein_coding 8.876968 9.425994 8.327942 0.1690256 0.2847161 -0.1784831 3.0060246 3.452939 2.5591100 0.3279246 0.3279160 -0.4307283 0.33748333 0.3677667 0.3072000 -0.06056667 9.706657e-01 1.993195e-19 FALSE TRUE
ENSMUST00000105992 ENSMUSG00000028580 Control shVgll3 Pum1 protein_coding protein_coding 8.876968 9.425994 8.327942 0.1690256 0.2847161 -0.1784831 0.5599455 0.000000 1.1198909 0.0000000 0.3866418 6.8200397 0.06743333 0.0000000 0.1348667 0.13486667 1.775336e-04 1.993195e-19 FALSE TRUE
MSTRG.16594.1 ENSMUSG00000028580 Control shVgll3 Pum1 protein_coding   8.876968 9.425994 8.327942 0.1690256 0.2847161 -0.1784831 3.6637785 3.410385 3.9171716 0.4028151 0.6233719 0.1993317 0.41630000 0.3607000 0.4719000 0.11120000 9.706657e-01 1.993195e-19 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
ENSMUSG00000028580 E001 0.3276328 0.0284275938 0.944472071   4 130390607 130390631 25 + 0.129 0.119 -0.138
ENSMUSG00000028580 E002 0.6505324 0.0442445065 0.923474873   4 130390632 130390669 38 + 0.228 0.211 -0.138
ENSMUSG00000028580 E003 0.4889862 0.0218708605 0.513552416   4 130390670 130390676 7 + 0.228 0.119 -1.137
ENSMUSG00000028580 E004 0.3228996 0.0283029039 0.944817009   4 130390677 130390677 1 + 0.129 0.119 -0.137
ENSMUSG00000028580 E005 1.6325055 0.0125529603 0.883734394 0.99307636 4 130390678 130390696 19 + 0.435 0.410 -0.137
ENSMUSG00000028580 E006 2.2961194 0.0130147220 0.491801347 0.92674629 4 130390697 130390705 9 + 0.575 0.460 -0.552
ENSMUSG00000028580 E007 2.6210771 0.0071661852 0.240229323 0.80442163 4 130390706 130390716 11 + 0.648 0.460 -0.874
ENSMUSG00000028580 E008 12.3120778 0.0017965469 0.868937224 0.98919635 4 130390717 130390778 62 + 1.117 1.132 0.055
ENSMUSG00000028580 E009 80.9835295 0.0009115671 0.166247553 0.74170134 4 130396236 130396609 374 + 1.884 1.939 0.186
ENSMUSG00000028580 E010 20.2035391 0.0009552434 0.430506725 0.90756311 4 130428353 130428421 69 + 1.357 1.297 -0.208
ENSMUSG00000028580 E011 19.0572046 0.0009951133 0.963824751 1.00000000 4 130445465 130445573 109 + 1.301 1.304 0.012
ENSMUSG00000028580 E012 0.0000000       4 130445574 130446192 619 +      
ENSMUSG00000028580 E013 33.8873618 0.0005491147 0.793016563 0.98058592 4 130446484 130446662 179 + 1.550 1.535 -0.053
ENSMUSG00000028580 E014 29.9424456 0.0006084026 0.524481703 0.93441775 4 130455309 130455475 167 + 1.511 1.471 -0.137
ENSMUSG00000028580 E015 43.4034143 0.0077626910 0.895528239 0.99560027 4 130457589 130457859 271 + 1.651 1.643 -0.027
ENSMUSG00000028580 E016 32.8856566 0.0008332449 0.308634771 0.84753465 4 130468774 130468867 94 + 1.496 1.558 0.211
ENSMUSG00000028580 E017 7.3950588 0.0030999839 0.001698842 0.07122958 4 130471001 130471003 3 + 0.681 1.067 1.491
ENSMUSG00000028580 E018 34.3800655 0.0013763518 0.379572949 0.88024846 4 130471004 130471105 102 + 1.520 1.573 0.182
ENSMUSG00000028580 E019 37.7874807 0.0027718959 0.363028127 0.87540223 4 130474289 130474440 152 + 1.617 1.562 -0.187
ENSMUSG00000028580 E020 25.9666444 0.0068444185 0.102673410 0.63998251 4 130476723 130476852 130 + 1.492 1.367 -0.431
ENSMUSG00000028580 E021 4.9191557 0.0038727356 0.014821209 0.27433307 4 130476853 130476861 9 + 0.916 0.582 -1.360
ENSMUSG00000028580 E022 30.2286343 0.0029002726 0.152682083 0.72005774 4 130478737 130478880 144 + 1.542 1.447 -0.326
ENSMUSG00000028580 E023 68.1772664 0.0036878108 0.144167310 0.70906417 4 130479887 130480183 297 + 1.876 1.802 -0.249
ENSMUSG00000028580 E024 61.5251071 0.0004982908 0.992236418 1.00000000 4 130481253 130481489 237 + 1.795 1.796 0.002
ENSMUSG00000028580 E025 85.9841537 0.0003657955 0.185588395 0.76229391 4 130490065 130490332 268 + 1.913 1.962 0.167
ENSMUSG00000028580 E026 29.3188729 0.0021065630 0.240564795 0.80442163 4 130491376 130491505 130 + 1.520 1.442 -0.267
ENSMUSG00000028580 E027 29.4717871 0.0011020745 0.915119853 0.99751275 4 130493232 130493360 129 + 1.487 1.480 -0.024
ENSMUSG00000028580 E028 4.7782466 0.0225000300 0.528963176 0.93574499 4 130493361 130493366 6 + 0.711 0.802 0.365
ENSMUSG00000028580 E029 24.4867255 0.0018816249 0.639209144 0.95668705 4 130496127 130496264 138 + 1.389 1.422 0.115
ENSMUSG00000028580 E030 33.7242446 0.0260922224 0.345164094 0.87285719 4 130499183 130499308 126 + 1.497 1.576 0.273
ENSMUSG00000028580 E031 25.6996095 0.0046173482 0.964188613 1.00000000 4 130499940 130500061 122 + 1.424 1.427 0.011
ENSMUSG00000028580 E032 40.9729623 0.0052841214 0.777747999 0.97903220 4 130501723 130501915 193 + 1.631 1.614 -0.057
ENSMUSG00000028580 E033 517.8462124 0.0002139276 0.635118812 0.95663250 4 130507083 130508875 1793 + 2.711 2.718 0.020

Help

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