ENSMUSG00000028423

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
ENSMUST00000030133 ENSMUSG00000028423 Control shVgll3 Nfx1 protein_coding protein_coding 23.66611 20.86932 26.46289 0.3435 0.5919195 0.3424409 2.2125785 2.805628 1.619529 0.26606329 0.31811070 -0.7890020 0.09773333 0.1345333 0.06093333 -0.073600000 4.917120e-02 4.898355e-08 FALSE  
ENSMUST00000091614 ENSMUSG00000028423 Control shVgll3 Nfx1 protein_coding protein_coding 23.66611 20.86932 26.46289 0.3435 0.5919195 0.3424409 1.5975385 1.760991 1.434086 0.25772929 0.21441277 -0.2943999 0.06923333 0.0843000 0.05416667 -0.030133333 6.460398e-01 4.898355e-08 FALSE  
ENSMUST00000098143 ENSMUSG00000028423 Control shVgll3 Nfx1 protein_coding protein_coding 23.66611 20.86932 26.46289 0.3435 0.5919195 0.3424409 6.3625850 5.271222 7.453948 0.36003498 0.55645073 0.4990670 0.26713333 0.2522667 0.28200000 0.029733333 9.706657e-01 4.898355e-08 FALSE  
ENSMUST00000124595 ENSMUSG00000028423 Control shVgll3 Nfx1 protein_coding protein_coding_CDS_not_defined 23.66611 20.86932 26.46289 0.3435 0.5919195 0.3424409 0.7905428 0.000000 1.581086 0.00000000 0.42177826 7.3138677 0.02978333 0.0000000 0.05956667 0.059566667 4.898355e-08 4.898355e-08 FALSE  
ENSMUST00000131305 ENSMUSG00000028423 Control shVgll3 Nfx1 protein_coding protein_coding_CDS_not_defined 23.66611 20.86932 26.46289 0.3435 0.5919195 0.3424409 2.1039211 1.881862 2.325980 0.09404736 0.14749474 0.3042208 0.08895000 0.0901000 0.08780000 -0.002300000 1.000000e+00 4.898355e-08    
MSTRG.15797.4 ENSMUSG00000028423 Control shVgll3 Nfx1 protein_coding   23.66611 20.86932 26.46289 0.3435 0.5919195 0.3424409 4.6373910 4.027964 5.246818 0.27995515 0.43849939 0.3805618 0.19595000 0.1934667 0.19843333 0.004966667 1.000000e+00 4.898355e-08 TRUE  
MSTRG.15797.5 ENSMUSG00000028423 Control shVgll3 Nfx1 protein_coding   23.66611 20.86932 26.46289 0.3435 0.5919195 0.3424409 5.9062257 5.108872 6.703579 0.12803281 0.03125574 0.3912562 0.24913333 0.2447333 0.25353333 0.008800000 9.796387e-01 4.898355e-08 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
ENSMUSG00000028423 E001 0.8210898 0.0173997969 8.398354e-01 0.986771512 4 40970906 40970983 78 + 0.275 0.239 -0.266
ENSMUSG00000028423 E002 0.9828288 0.0137515828 2.815255e-01 0.827250899 4 40970984 40970991 8 + 0.201 0.393 1.318
ENSMUSG00000028423 E003 40.3517974 0.0037012650 2.375703e-02 0.346089371 4 40970992 40971059 68 + 1.546 1.685 0.471
ENSMUSG00000028423 E004 732.1476331 0.0005535158 7.713161e-01 0.977990679 4 40976353 40977342 990 + 2.860 2.865 0.017
ENSMUSG00000028423 E005 108.5190622 0.0002133793 3.742053e-01 0.878593069 4 40984893 40985051 159 + 2.023 2.053 0.103
ENSMUSG00000028423 E006 67.3040456 0.0003114350 5.680563e-01 0.943543097 4 40986693 40986770 78 + 1.820 1.846 0.085
ENSMUSG00000028423 E007 0.3324796 0.0285535351 8.732111e-01   4 40988617 40988621 5 + 0.112 0.136 0.318
ENSMUSG00000028423 E008 130.5545552 0.0001917520 5.339582e-01 0.936602794 4 40988622 40988727 106 + 2.107 2.127 0.067
ENSMUSG00000028423 E009 74.7357761 0.0002759255 6.555716e-01 0.956687053 4 40990793 40990864 72 + 1.868 1.887 0.064
ENSMUSG00000028423 E010 97.2445915 0.0006969101 2.941087e-02 0.386551279 4 40991744 40991883 140 + 1.951 2.033 0.274
ENSMUSG00000028423 E011 75.8474926 0.0003366301 5.400090e-01 0.936624757 4 40993759 40993858 100 + 1.871 1.897 0.086
ENSMUSG00000028423 E012 126.6258461 0.0002426232 9.185120e-01 0.997686457 4 40993963 40994180 218 + 2.101 2.105 0.013
ENSMUSG00000028423 E013 88.8262050 0.0047167639 3.908039e-01 0.886832884 4 40996815 40996912 98 + 1.931 1.975 0.146
ENSMUSG00000028423 E014 66.5156676 0.0003085161 3.208238e-01 0.856262157 4 40999685 40999715 31 + 1.807 1.850 0.147
ENSMUSG00000028423 E015 182.9457998 0.0003966844 9.098994e-01 0.996401690 4 40999716 41000889 1174 + 2.263 2.260 -0.008
ENSMUSG00000028423 E016 280.1402567 0.0001239421 3.393849e-02 0.416592290 4 41000890 41002509 1620 + 2.465 2.421 -0.147
ENSMUSG00000028423 E017 96.5453110 0.0050311070 4.553858e-01 0.914101865 4 41002510 41003017 508 + 2.002 1.966 -0.122
ENSMUSG00000028423 E018 102.0069405 0.0002180753 4.619989e-01 0.917721667 4 41003018 41003097 80 + 2.021 1.996 -0.084
ENSMUSG00000028423 E019 153.4255749 0.0001735842 8.873965e-01 0.994529627 4 41004328 41004436 109 + 2.187 2.184 -0.011
ENSMUSG00000028423 E020 167.0994872 0.0002114265 6.228674e-01 0.955141978 4 41004826 41004945 120 + 2.216 2.231 0.048
ENSMUSG00000028423 E021 44.6299713 0.0006028154 7.441871e-04 0.038015286 4 41009190 41009206 17 + 1.568 1.746 0.607
ENSMUSG00000028423 E022 70.3397278 0.0003186164 4.539152e-01 0.913957105 4 41009207 41009269 63 + 1.836 1.868 0.109
ENSMUSG00000028423 E023 11.8643848 0.0017524756 1.080428e-01 0.648478721 4 41011527 41011711 185 + 1.030 1.186 0.559
ENSMUSG00000028423 E024 19.1128165 0.0248904336 2.671729e-01 0.816690651 4 41011712 41012057 346 + 1.244 1.363 0.416
ENSMUSG00000028423 E025 287.9289919 0.0001330521 1.837787e-05 0.001919503 4 41012058 41013871 1814 + 2.416 2.505 0.297
ENSMUSG00000028423 E026 74.2223349 0.0002775236 1.886989e-03 0.075861218 4 41015203 41015433 231 + 1.926 1.797 -0.434
ENSMUSG00000028423 E027 105.8136553 0.0002094064 2.202323e-05 0.002240241 4 41015434 41016076 643 + 2.086 1.938 -0.497
ENSMUSG00000028423 E028 48.5030555 0.0005232468 3.316798e-02 0.411143186 4 41016077 41016150 74 + 1.737 1.629 -0.369
ENSMUSG00000028423 E029 50.4760703 0.0007916049 2.767628e-01 0.821839016 4 41017972 41018073 102 + 1.733 1.678 -0.185
ENSMUSG00000028423 E030 29.6475268 0.0006309837 8.611863e-01 0.988842437 4 41018448 41018489 42 + 1.488 1.478 -0.036
ENSMUSG00000028423 E031 2.1403255 0.0155560065 3.238754e-01 0.858634867 4 41021366 41021429 64 + 0.563 0.393 -0.851
ENSMUSG00000028423 E032 58.4277546 0.0003225200 3.251392e-02 0.406268247 4 41021749 41021847 99 + 1.813 1.714 -0.335
ENSMUSG00000028423 E033 55.9311780 0.0003650612 1.460041e-01 0.711404481 4 41022260 41022326 67 + 1.782 1.714 -0.231
ENSMUSG00000028423 E034 18.9206220 0.0010124939 8.213695e-01 0.984110891 4 41023204 41023613 410 + 1.304 1.287 -0.060
ENSMUSG00000028423 E035 98.7705386 0.0002506398 1.064267e-02 0.222781277 4 41023614 41023759 146 + 2.034 1.943 -0.307
ENSMUSG00000028423 E036 64.8771705 0.0003388539 8.018135e-01 0.981651838 4 41024474 41024578 105 + 1.820 1.810 -0.035
ENSMUSG00000028423 E037 297.9259791 0.0003972790 4.831898e-01 0.923728101 4 41024801 41026837 2037 + 2.479 2.465 -0.048

Help

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