ENSMUSG00000040111

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
ENSMUST00000045682 ENSMUSG00000040111 Control shVgll3 Gramd1b protein_coding protein_coding 9.554258 9.890189 9.218327 1.070661 0.8337758 -0.1013869 2.428906 1.3658767 3.491936 0.1088424 0.1412999 1.3478015 0.2651500 0.1434667 0.3868333 0.24336667 0.007299896 0.007299896 FALSE TRUE
ENSMUST00000137454 ENSMUSG00000040111 Control shVgll3 Gramd1b protein_coding protein_coding 9.554258 9.890189 9.218327 1.070661 0.8337758 -0.1013869 1.225424 0.9400677 1.510780 0.1839061 0.3428940 0.6787094 0.1284667 0.0955000 0.1614333 0.06593333 0.716710233 0.007299896 FALSE TRUE
MSTRG.23481.16 ENSMUSG00000040111 Control shVgll3 Gramd1b protein_coding   9.554258 9.890189 9.218327 1.070661 0.8337758 -0.1013869 5.098925 7.0293497 3.168500 1.1097830 1.1198261 -1.1470962 0.5165167 0.7022667 0.3307667 -0.37150000 0.108815479 0.007299896   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
ENSMUSG00000040111 E001 0.0000000       9 40204529 40204531 3 -      
ENSMUSG00000040111 E002 0.0000000       9 40204532 40204534 3 -      
ENSMUSG00000040111 E003 0.0000000       9 40204535 40204540 6 -      
ENSMUSG00000040111 E004 142.4523014 0.0018557779 0.659352682 0.95774869 9 40204541 40205723 1183 - 2.118 2.136 0.059
ENSMUSG00000040111 E005 244.9533911 0.0005667172 0.349794220 0.87517695 9 40205724 40209129 3406 - 2.363 2.346 -0.057
ENSMUSG00000040111 E006 5.9085732 0.0031008561 0.405705499 0.89347807 9 40209130 40209171 42 - 0.844 0.732 -0.445
ENSMUSG00000040111 E007 6.8924116 0.0028498549 0.284178033 0.83132548 9 40209172 40209241 70 - 0.908 0.770 -0.538
ENSMUSG00000040111 E008 6.5423680 0.0516024853 0.665454512 0.95884554 9 40209242 40209281 40 - 0.829 0.894 0.249
ENSMUSG00000040111 E009 14.7614578 0.0192993634 0.859511672 0.98884244 9 40209282 40209375 94 - 1.161 1.181 0.069
ENSMUSG00000040111 E010 19.5893635 0.0081688623 0.649640000 0.95668705 9 40210898 40211015 118 - 1.268 1.312 0.157
ENSMUSG00000040111 E011 13.3336512 0.0183323476 0.373782315 0.87836591 9 40211285 40211325 41 - 1.090 1.194 0.372
ENSMUSG00000040111 E012 11.9922280 0.0024797920 0.215267445 0.78812147 9 40211326 40211392 67 - 1.040 1.167 0.455
ENSMUSG00000040111 E013 1.3194189 0.3755104401 0.473609412 0.92123094 9 40211736 40211747 12 - 0.407 0.172 -1.673
ENSMUSG00000040111 E014 10.3391961 0.0326544548 0.372363998 0.87750082 9 40214794 40214884 91 - 0.984 1.105 0.441
ENSMUSG00000040111 E015 16.3919371 0.0360694461 0.681048855 0.96280154 9 40215619 40215822 204 - 1.223 1.180 -0.152
ENSMUSG00000040111 E016 13.3101244 0.0365968939 0.728674125 0.97107356 9 40216362 40216465 104 - 1.106 1.166 0.216
ENSMUSG00000040111 E017 20.7426523 0.0049525256 0.092646666 0.62720448 9 40217628 40217770 143 - 1.257 1.397 0.488
ENSMUSG00000040111 E018 16.9852325 0.0102316682 0.104523395 0.64156759 9 40218036 40218154 119 - 1.268 1.105 -0.580
ENSMUSG00000040111 E019 1.9750653 0.0089399443 0.251261827 0.80641511 9 40218155 40218291 137 - 0.507 0.296 -1.182
ENSMUSG00000040111 E020 17.6065192 0.0011284122 0.240398407 0.80442163 9 40219152 40219295 144 - 1.267 1.167 -0.357
ENSMUSG00000040111 E021 22.4349928 0.0067510798 0.044034400 0.46701216 9 40219589 40219778 190 - 1.385 1.208 -0.621
ENSMUSG00000040111 E022 17.6138722 0.0055199490 0.372781612 0.87811539 9 40221194 40221350 157 - 1.262 1.181 -0.287
ENSMUSG00000040111 E023 12.6486755 0.0017043635 0.971820332 1.00000000 9 40223054 40223169 116 - 1.105 1.105 -0.003
ENSMUSG00000040111 E024 9.5418277 0.0022015074 0.823338872 0.98411089 9 40226263 40226343 81 - 0.984 1.012 0.102
ENSMUSG00000040111 E025 5.4348689 0.1220208693 0.963632470 1.00000000 9 40226984 40227015 32 - 0.786 0.769 -0.065
ENSMUSG00000040111 E026 10.8777667 0.1196716624 0.101980314 0.63968618 9 40227016 40227079 64 - 0.943 1.209 0.967
ENSMUSG00000040111 E027 0.8221089 0.0226157325 0.577164969 0.94676192 9 40228043 40228160 118 - 0.276 0.173 -0.860
ENSMUSG00000040111 E028 12.0330290 0.0282039625 0.120218421 0.66744902 9 40228161 40228264 104 - 1.013 1.208 0.703
ENSMUSG00000040111 E029 4.2921501 0.0341635021 0.754909042 0.97611650 9 40228805 40228806 2 - 0.678 0.732 0.224
ENSMUSG00000040111 E030 4.2921501 0.0341635021 0.754909042 0.97611650 9 40228807 40228808 2 - 0.678 0.732 0.224
ENSMUSG00000040111 E031 9.2016861 0.0064880258 0.689374271 0.96291900 9 40228809 40228889 81 - 0.964 1.012 0.179
ENSMUSG00000040111 E032 1.9608952 0.0720034114 0.482091426 0.92372810 9 40231840 40232216 377 - 0.406 0.537 0.657
ENSMUSG00000040111 E033 3.9459362 0.0044303178 0.837938324 0.98677151 9 40238714 40238734 21 - 0.658 0.691 0.140
ENSMUSG00000040111 E034 3.1290107 0.0055366561 0.634663289 0.95663250 9 40244741 40244781 41 - 0.613 0.537 -0.345
ENSMUSG00000040111 E035 0.0000000       9 40244782 40244794 13 -      
ENSMUSG00000040111 E036 0.0000000       9 40244795 40244850 56 -      
ENSMUSG00000040111 E037 4.6094561 0.0047137800 0.628435748 0.95595792 9 40244851 40244951 101 - 0.698 0.770 0.292
ENSMUSG00000040111 E038 0.9734320 0.2613323821 0.510373879 0.93083264 9 40257204 40257586 383 - 0.221 0.391 1.138
ENSMUSG00000040111 E039 0.0000000       9 40274319 40274384 66 -      
ENSMUSG00000040111 E040 0.1659033 0.0345625556 0.222230708   9 40287209 40287717 509 - 0.000 0.173 11.169
ENSMUSG00000040111 E041 0.0000000       9 40302976 40303448 473 -      
ENSMUSG00000040111 E042 0.1659033 0.0345625556 0.222230708   9 40303625 40303746 122 - 0.000 0.173 11.169
ENSMUSG00000040111 E043 0.0000000       9 40312857 40313165 309 -      
ENSMUSG00000040111 E044 9.0572285 0.0045985993 0.835604195 0.98626126 9 40324593 40324667 75 - 0.964 0.991 0.100
ENSMUSG00000040111 E045 1.6485702 0.4336359645 0.901845319 0.99563225 9 40324668 40324670 3 - 0.408 0.391 -0.097
ENSMUSG00000040111 E046 3.4590210 0.0057460834 0.001097383 0.05114418 9 40325686 40325784 99 - 0.407 0.894 2.140
ENSMUSG00000040111 E047 17.4334939 0.0324550489 0.014787927 0.27433307 9 40366590 40367060 471 - 1.312 0.991 -1.149
ENSMUSG00000040111 E048 0.0000000       9 40376767 40376860 94 -      
ENSMUSG00000040111 E049 0.0000000       9 40442316 40442679 364 -      

Help

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