ENSMUSG00000025185

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
ENSMUST00000026190 ENSMUSG00000025185 Control shVgll3 Loxl4 protein_coding protein_coding 65.46658 98.7197 32.21346 1.463639 1.936694 -1.615373 25.788492 36.049284 15.527699 1.5312248 1.0848626 -1.214598 0.42345000 0.36530000 0.48160000 0.1163 0.01070287 0.01070287 FALSE TRUE
MSTRG.11943.1 ENSMUSG00000025185 Control shVgll3 Loxl4 protein_coding   65.46658 98.7197 32.21346 1.463639 1.936694 -1.615373 28.763681 44.964506 12.562856 0.7177559 0.6240668 -1.838795 0.42320000 0.45560000 0.39080000 -0.0648 0.22042312 0.01070287 FALSE FALSE
MSTRG.11943.4 ENSMUSG00000025185 Control shVgll3 Loxl4 protein_coding   65.46658 98.7197 32.21346 1.463639 1.936694 -1.615373 3.921742 6.058222 1.785261 0.4633077 0.3023265 -1.757080 0.05801667 0.06126667 0.05476667 -0.0065 0.97066567 0.01070287 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
ENSMUSG00000025185 E001 2175.56434 0.0001570358 5.438239e-28 5.301377e-25 19 42580793 42582420 1628 - 3.200 3.299 0.329
ENSMUSG00000025185 E002 2083.04642 0.0003180779 2.502284e-02 3.539507e-01 19 42582421 42583544 1124 - 3.274 3.251 -0.076
ENSMUSG00000025185 E003 367.45562 0.0001314160 9.254923e-02 6.272045e-01 19 42583545 42583772 228 - 2.532 2.495 -0.121
ENSMUSG00000025185 E004 177.34599 0.0002412642 1.243443e-01 6.749790e-01 19 42583773 42583843 71 - 2.225 2.177 -0.159
ENSMUSG00000025185 E005 204.03725 0.0001462792 5.637066e-01 9.421718e-01 19 42585937 42586048 112 - 2.263 2.246 -0.057
ENSMUSG00000025185 E006 42.56844 0.0044139937 4.842122e-02 4.839731e-01 19 42586049 42586383 335 - 1.673 1.542 -0.445
ENSMUSG00000025185 E007 219.78440 0.0003866246 8.318233e-01 9.854840e-01 19 42586384 42586520 137 - 2.288 2.281 -0.023
ENSMUSG00000025185 E008 43.74743 0.0004272022 1.874075e-02 3.083393e-01 19 42586521 42587139 619 - 1.688 1.552 -0.465
ENSMUSG00000025185 E009 216.99507 0.0001867037 4.272869e-02 4.623120e-01 19 42587140 42587255 116 - 2.318 2.262 -0.188
ENSMUSG00000025185 E010 106.97145 0.0036529220 3.321917e-03 1.097734e-01 19 42587256 42588315 1060 - 2.071 1.933 -0.463
ENSMUSG00000025185 E011 390.07948 0.0017205811 3.111426e-02 3.977864e-01 19 42588316 42588559 244 - 2.575 2.515 -0.200
ENSMUSG00000025185 E012 13.49752 0.0014268913 7.217447e-01 9.706108e-01 19 42588560 42588724 165 - 1.131 1.094 -0.133
ENSMUSG00000025185 E013 22.02980 0.0008529268 1.225241e-01 6.713287e-01 19 42589992 42590368 377 - 1.199 1.333 0.474
ENSMUSG00000025185 E014 179.96272 0.0015228494 2.089823e-01 7.828663e-01 19 42590612 42590774 163 - 2.229 2.184 -0.149
ENSMUSG00000025185 E015 173.64439 0.0001615559 7.243405e-01 9.710736e-01 19 42591626 42591793 168 - 2.189 2.178 -0.039
ENSMUSG00000025185 E016 190.47218 0.0010030512 8.006560e-01 9.816518e-01 19 42592294 42592448 155 - 2.228 2.218 -0.030
ENSMUSG00000025185 E017 230.36565 0.0015000785 3.011987e-01 8.425210e-01 19 42592571 42592754 184 - 2.328 2.294 -0.113
ENSMUSG00000025185 E018 10.05038 0.0108241548 7.186891e-01 9.692695e-01 19 42592755 42592757 3 - 0.953 0.998 0.167
ENSMUSG00000025185 E019 248.24991 0.0035166125 5.031027e-01 9.278351e-01 19 42593246 42593465 220 - 2.355 2.328 -0.088
ENSMUSG00000025185 E020 71.02236 0.0004330473 1.439818e-01 7.090642e-01 19 42593685 42593723 39 - 1.848 1.778 -0.235
ENSMUSG00000025185 E021 223.44320 0.0003592773 1.903290e-01 7.658913e-01 19 42595009 42595214 206 - 2.317 2.280 -0.124
ENSMUSG00000025185 E022 80.54774 0.0002563176 6.076806e-01 9.533477e-01 19 42595993 42596047 55 - 1.833 1.856 0.076
ENSMUSG00000025185 E023 93.24188 0.0002362990 3.545719e-01 8.751770e-01 19 42596048 42596171 124 - 1.942 1.903 -0.132
ENSMUSG00000025185 E024 232.31136 0.0014050100 9.797994e-02 6.331714e-01 19 42596691 42596986 296 - 2.345 2.292 -0.175
ENSMUSG00000025185 E025 24.84837 0.0057443763 6.159964e-01 9.542188e-01 19 42599073 42599167 95 - 1.320 1.363 0.149
ENSMUSG00000025185 E026 62.19558 0.0105764622 1.024531e-03 4.932085e-02 19 42601157 42601473 317 - 1.897 1.671 -0.765

Help

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