ENSMUSG00000030621

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
ENSMUST00000032856 ENSMUSG00000030621 Control shVgll3 Me3 protein_coding protein_coding 1.701118 1.835846 1.566389 0.1287042 0.1369445 -0.2276585 0.4551963 0.4709087 0.4394838 0.02433254 0.0265803 -0.09749394 0.27390000 0.2610333 0.2867667 0.0257333333 0.99918835 0.02815396 FALSE TRUE
ENSMUST00000159167 ENSMUSG00000030621 Control shVgll3 Me3 protein_coding retained_intron 1.701118 1.835846 1.566389 0.1287042 0.1369445 -0.2276585 0.7535726 0.6968319 0.8103134 0.13728985 0.1158112 0.21480807 0.44356667 0.3746667 0.5124667 0.1378000000 0.81261738 0.02815396 FALSE TRUE
ENSMUST00000160995 ENSMUSG00000030621 Control shVgll3 Me3 protein_coding protein_coding_CDS_not_defined 1.701118 1.835846 1.566389 0.1287042 0.1369445 -0.2276585 0.1696949 0.3393898 0.0000000 0.11244049 0.0000000 -5.12676577 0.09331667 0.1866333 0.0000000 -0.1866333333 0.02815396 0.02815396 FALSE TRUE
ENSMUST00000162145 ENSMUSG00000030621 Control shVgll3 Me3 protein_coding protein_coding_CDS_not_defined 1.701118 1.835846 1.566389 0.1287042 0.1369445 -0.2276585 0.2073373 0.2243425 0.1903321 0.05782079 0.0380586 -0.22622508 0.11993333 0.1198667 0.1200000 0.0001333333 1.00000000 0.02815396 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
ENSMUSG00000030621 E001 0.0000000       7 89281600 89281741 142 +      
ENSMUSG00000030621 E002 0.0000000       7 89281742 89281777 36 +      
ENSMUSG00000030621 E003 0.0000000       7 89281911 89282093 183 +      
ENSMUSG00000030621 E004 0.0000000       7 89282094 89282103 10 +      
ENSMUSG00000030621 E005 0.0000000       7 89282104 89282301 198 +      
ENSMUSG00000030621 E006 0.8303830 0.176759765 0.68680120 0.96291900 7 89288399 89288553 155 + 0.295 0.222 -0.543
ENSMUSG00000030621 E007 9.0059133 0.028970589 0.46030911 0.91682762 7 89290235 89292881 2647 + 0.943 1.055 0.411
ENSMUSG00000030621 E008 6.5621257 0.003068321 0.73941390 0.97290014 7 89385836 89385938 103 + 0.855 0.904 0.187
ENSMUSG00000030621 E009 4.5932534 0.026385022 0.98715364 1.00000000 7 89385939 89385969 31 + 0.743 0.754 0.042
ENSMUSG00000030621 E010 7.2327913 0.003931111 0.12512086 0.67699531 7 89389015 89389124 110 + 0.814 1.001 0.710
ENSMUSG00000030621 E011 3.7704073 0.087259283 0.29827009 0.84044841 7 89389125 89389164 40 + 0.556 0.778 0.944
ENSMUSG00000030621 E012 0.0000000       7 89412528 89412601 74 +      
ENSMUSG00000030621 E013 4.6150995 0.004521358 0.02229019 0.33645342 7 89414621 89416938 2318 + 0.874 0.565 -1.279
ENSMUSG00000030621 E014 4.5769216 0.063748267 0.33170044 0.86342496 7 89435634 89435709 76 + 0.659 0.824 0.671
ENSMUSG00000030621 E015 12.9795459 0.001872119 0.43362106 0.90866138 7 89445828 89445989 162 + 1.174 1.115 -0.214
ENSMUSG00000030621 E016 8.8897298 0.002549549 0.98652317 1.00000000 7 89455855 89455958 104 + 0.989 1.001 0.043
ENSMUSG00000030621 E017 3.1232776 0.005719773 0.80938702 0.98325566 7 89455959 89459405 3447 + 0.593 0.637 0.195
ENSMUSG00000030621 E018 1.3059212 0.013376584 0.15200390 0.72005774 7 89467094 89467641 548 + 0.217 0.478 1.627
ENSMUSG00000030621 E019 0.6589100 0.018378543 0.03619861   7 89467829 89468139 311 + 0.000 0.368 10.823
ENSMUSG00000030621 E020 0.0000000       7 89478490 89478548 59 +      
ENSMUSG00000030621 E021 6.0876857 0.003556762 0.62732371 0.95552510 7 89482905 89483014 110 + 0.874 0.825 -0.192
ENSMUSG00000030621 E022 4.4301791 0.004342352 0.18081486 0.76033243 7 89495003 89495100 98 + 0.814 0.637 -0.723
ENSMUSG00000030621 E023 7.2328732 0.002833326 0.00209756 0.08141262 7 89495408 89495521 114 + 1.056 0.700 -1.372
ENSMUSG00000030621 E024 5.9029873 0.012340841 0.76952374 0.97799068 7 89497132 89497237 106 + 0.855 0.825 -0.117
ENSMUSG00000030621 E025 3.9471712 0.102003460 0.34559548 0.87314426 7 89497816 89497958 143 + 0.593 0.779 0.778
ENSMUSG00000030621 E026 0.6503492 0.019446171 0.31094118   7 89497959 89498360 402 + 0.122 0.301 1.628
ENSMUSG00000030621 E027 10.3942771 0.049604884 0.95598314 1.00000000 7 89498802 89498975 174 + 1.057 1.055 -0.007
ENSMUSG00000030621 E028 9.7414143 0.032275273 0.72926436 0.97107356 7 89499541 89499639 99 + 1.004 1.055 0.189
ENSMUSG00000030621 E029 15.9514940 0.026067699 0.99082500 1.00000000 7 89500944 89503567 2624 + 1.227 1.232 0.016

Help

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