ENSMUSG00000034126

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
ENSMUST00000037788 ENSMUSG00000034126 Control shVgll3 Pomt2 protein_coding protein_coding 3.92428 4.127815 3.720746 0.04011937 0.07341408 -0.149405 3.3765896 3.7956690 2.9575102 0.07031292 0.15441955 -0.3588971 0.85736667 0.9193667 0.79536667 -0.12400000 0.2882532 0.0141187 FALSE TRUE
ENSMUST00000221252 ENSMUSG00000034126 Control shVgll3 Pomt2 protein_coding retained_intron 3.92428 4.127815 3.720746 0.04011937 0.07341408 -0.149405 0.2342671 0.2244492 0.2440851 0.05309948 0.11990713 0.1160364 0.05981667 0.0544000 0.06523333 0.01083333 1.0000000 0.0141187   FALSE
ENSMUST00000222634 ENSMUSG00000034126 Control shVgll3 Pomt2 protein_coding nonsense_mediated_decay 3.92428 4.127815 3.720746 0.04011937 0.07341408 -0.149405 0.2914040 0.0898033 0.4930046 0.05564935 0.04116058 2.3334122 0.07721667 0.0219000 0.13253333 0.11063333 0.0141187 0.0141187 TRUE 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
ENSMUSG00000034126 E001 182.329677 0.0001856163 0.253262091 0.80699081 12 87153635 87155577 1943 - 2.249 2.274 0.083
ENSMUSG00000034126 E002 57.752572 0.0005903718 0.240942205 0.80442163 12 87155578 87156067 490 - 1.795 1.743 -0.177
ENSMUSG00000034126 E003 22.550259 0.0009073506 0.282709836 0.82902988 12 87156778 87156892 115 - 1.410 1.334 -0.265
ENSMUSG00000034126 E004 25.197419 0.0047309995 0.865442635 0.98892123 12 87157076 87157216 141 - 1.410 1.423 0.044
ENSMUSG00000034126 E005 16.947746 0.0024524555 0.553864052 0.93867602 12 87158111 87158216 106 - 1.279 1.229 -0.173
ENSMUSG00000034126 E006 2.299964 0.0082069480 0.002547133 0.09196406 12 87158217 87158297 81 - 0.719 0.208 -2.786
ENSMUSG00000034126 E007 11.357840 0.0017568294 0.457700543 0.91634108 12 87158298 87158357 60 - 1.050 1.123 0.263
ENSMUSG00000034126 E008 14.988380 0.0077387502 0.744137184 0.97290014 12 87158653 87158724 72 - 1.218 1.188 -0.107
ENSMUSG00000034126 E009 11.853035 0.0028973901 0.298415017 0.84044841 12 87163305 87163381 77 - 1.159 1.058 -0.362
ENSMUSG00000034126 E010 17.609439 0.0143996497 0.280340969 0.82546576 12 87164159 87164250 92 - 1.209 1.315 0.372
ENSMUSG00000034126 E011 24.169497 0.0012953164 0.375563649 0.87918156 12 87164713 87164864 152 - 1.366 1.428 0.214
ENSMUSG00000034126 E012 4.122735 0.0344116246 0.235489007 0.80428340 12 87165792 87166345 554 - 0.799 0.610 -0.786
ENSMUSG00000034126 E013 13.311867 0.0025483569 0.771136403 0.97799068 12 87166346 87166424 79 - 1.169 1.143 -0.095
ENSMUSG00000034126 E014 14.000364 0.0017201129 0.164753969 0.73847466 12 87169616 87169685 70 - 1.236 1.113 -0.440
ENSMUSG00000034126 E015 13.487934 0.0014651081 0.286369786 0.83307701 12 87171586 87171652 67 - 1.209 1.113 -0.342
ENSMUSG00000034126 E016 1.306555 0.0360836884 0.386423947 0.88546179 12 87171887 87174075 2189 - 0.441 0.283 -0.938
ENSMUSG00000034126 E017 18.260755 0.0010741419 0.523502864 0.93377975 12 87174076 87174185 110 - 1.310 1.260 -0.175
ENSMUSG00000034126 E018 10.521000 0.0018080209 0.422977883 0.90473492 12 87175727 87175809 83 - 1.102 1.022 -0.292
ENSMUSG00000034126 E019 10.203942 0.0061623231 0.082401455 0.60353553 12 87177063 87177169 107 - 1.137 0.953 -0.671
ENSMUSG00000034126 E020 13.334733 0.0014867935 0.030425277 0.39339246 12 87178446 87178605 160 - 1.037 1.237 0.719
ENSMUSG00000034126 E021 14.767290 0.0015943901 0.695601687 0.96462563 12 87180134 87180242 109 - 1.179 1.213 0.121
ENSMUSG00000034126 E022 22.544686 0.0009190323 0.093412016 0.62862654 12 87182269 87182377 109 - 1.302 1.423 0.419
ENSMUSG00000034126 E023 18.890473 0.0042375549 0.530531578 0.93574499 12 87184777 87184881 105 - 1.270 1.321 0.178
ENSMUSG00000034126 E024 8.714602 0.0022142605 0.120342632 0.66782168 12 87186418 87186502 85 - 0.887 1.058 0.638
ENSMUSG00000034126 E025 2.141507 0.0082162108 0.980321194 1.00000000 12 87193945 87194742 798 - 0.494 0.498 0.021

Help

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