ENSMUSG00000029701

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
ENSMUST00000007993 ENSMUSG00000029701 Control shVgll3 Rbm28 protein_coding protein_coding 34.20829 25.00458 43.412 0.4196557 1.254841 0.7956569 2.096536 2.392988 1.800083 0.18969079 0.1507544 -0.4087741 0.06876667 0.0960000 0.04153333 -0.05446667 0.001509991 0.001509991 FALSE  
ENSMUST00000169214 ENSMUSG00000029701 Control shVgll3 Rbm28 protein_coding retained_intron 34.20829 25.00458 43.412 0.4196557 1.254841 0.7956569 13.565111 9.767284 17.362938 1.09400314 0.2488608 0.8293361 0.39500000 0.3895667 0.40043333 0.01086667 1.000000000 0.001509991 FALSE  
ENSMUST00000170473 ENSMUSG00000029701 Control shVgll3 Rbm28 protein_coding retained_intron 34.20829 25.00458 43.412 0.4196557 1.254841 0.7956569 4.688263 2.763776 6.612750 0.40381317 0.7245601 1.2555793 0.13101667 0.1104000 0.15163333 0.04123333 0.784376157 0.001509991 FALSE  
ENSMUST00000170750 ENSMUSG00000029701 Control shVgll3 Rbm28 protein_coding retained_intron 34.20829 25.00458 43.412 0.4196557 1.254841 0.7956569 3.717953 2.873928 4.561977 0.01931265 0.5099623 0.6647831 0.10978333 0.1149667 0.10460000 -0.01036667 0.970665669 0.001509991 FALSE  
MSTRG.18898.1 ENSMUSG00000029701 Control shVgll3 Rbm28 protein_coding   34.20829 25.00458 43.412 0.4196557 1.254841 0.7956569 9.407637 6.101162 12.714111 0.08503892 0.2846731 1.0580462 0.26881667 0.2441667 0.29346667 0.04930000 0.615909900 0.001509991 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
ENSMUSG00000029701 E001 0.0000000       6 29123575 29123638 64 -      
ENSMUSG00000029701 E002 278.9064646 0.0025628185 6.744781e-04 3.570156e-02 6 29123639 29125140 1502 - 2.385 2.496 0.368
ENSMUSG00000029701 E003 20.4207783 0.0034418156 4.005182e-01 8.905649e-01 6 29125141 29125179 39 - 1.285 1.358 0.254
ENSMUSG00000029701 E004 147.8576804 0.0001752108 1.904322e-01 7.658913e-01 6 29125180 29125523 344 - 2.137 2.181 0.147
ENSMUSG00000029701 E005 107.9073424 0.0062951602 5.065437e-01 9.302983e-01 6 29127797 29127899 103 - 2.004 2.041 0.123
ENSMUSG00000029701 E006 310.2850604 0.0001118960 4.924689e-01 9.267463e-01 6 29128428 29128684 257 - 2.467 2.486 0.063
ENSMUSG00000029701 E007 128.1742364 0.0035876748 9.275261e-01 9.993033e-01 6 29131266 29131338 73 - 2.091 2.093 0.006
ENSMUSG00000029701 E008 45.4705598 0.0004225232 3.548486e-01 8.751770e-01 6 29131339 29131340 2 - 1.663 1.618 -0.155
ENSMUSG00000029701 E009 188.5747167 0.0016835828 9.426145e-01 9.998994e-01 6 29131626 29131775 150 - 2.258 2.260 0.008
ENSMUSG00000029701 E010 145.1609343 0.0001661417 3.777543e-01 8.796539e-01 6 29135407 29135565 159 - 2.134 2.166 0.105
ENSMUSG00000029701 E011 84.2398247 0.0002544828 8.215092e-01 9.841109e-01 6 29137578 29137642 65 - 1.907 1.920 0.047
ENSMUSG00000029701 E012 112.6495635 0.0003577091 7.029102e-01 9.657358e-01 6 29138502 29138637 136 - 2.039 2.030 -0.028
ENSMUSG00000029701 E013 72.3433642 0.0042557603 5.386507e-01 9.366248e-01 6 29139552 29139625 74 - 1.833 1.869 0.122
ENSMUSG00000029701 E014 121.5408784 0.0004918963 7.036551e-01 9.659286e-01 6 29143553 29143662 110 - 2.072 2.063 -0.027
ENSMUSG00000029701 E015 79.3216570 0.0002641702 4.738333e-02 4.810500e-01 6 29152281 29152353 73 - 1.854 1.939 0.286
ENSMUSG00000029701 E016 56.2252199 0.0054249315 2.139186e-01 7.869245e-01 6 29152354 29152904 551 - 1.709 1.786 0.258
ENSMUSG00000029701 E017 121.4923075 0.0042074856 6.322647e-01 9.563245e-01 6 29154753 29154892 140 - 2.060 2.086 0.089
ENSMUSG00000029701 E018 11.6827362 0.0016569282 5.153975e-01 9.314929e-01 6 29154893 29155025 133 - 1.060 1.129 0.249
ENSMUSG00000029701 E019 130.8053118 0.0001900684 5.275018e-01 9.357450e-01 6 29155026 29155188 163 - 2.092 2.117 0.084
ENSMUSG00000029701 E020 335.7463097 0.0001322409 1.474766e-07 2.924036e-05 6 29155189 29156293 1105 - 2.541 2.440 -0.337
ENSMUSG00000029701 E021 142.9130522 0.0003637126 8.775345e-03 2.032752e-01 6 29156294 29156678 385 - 2.165 2.086 -0.263
ENSMUSG00000029701 E022 139.4329254 0.0001752757 5.906823e-03 1.599491e-01 6 29156679 29157066 388 - 2.155 2.073 -0.275
ENSMUSG00000029701 E023 30.0946035 0.0006555328 3.071002e-01 8.470590e-01 6 29157067 29157088 22 - 1.448 1.519 0.244
ENSMUSG00000029701 E024 32.4042810 0.0006052136 7.959990e-01 9.810080e-01 6 29157089 29157138 50 - 1.498 1.519 0.072
ENSMUSG00000029701 E025 61.8830706 0.0003320268 9.191680e-01 9.976865e-01 6 29158169 29158261 93 - 1.776 1.785 0.032
ENSMUSG00000029701 E026 57.1905969 0.0006223128 8.004593e-01 9.816518e-01 6 29158846 29158921 76 - 1.739 1.756 0.058
ENSMUSG00000029701 E027 99.4303790 0.0002291305 9.773180e-01 1.000000e+00 6 29159655 29159749 95 - 1.981 1.985 0.013
ENSMUSG00000029701 E028 0.4941893 0.0214406074 2.186129e-01   6 29159750 29159930 181 - 0.238 0.000 -9.600
ENSMUSG00000029701 E029 121.1255645 0.0002140631 2.678501e-01 8.170214e-01 6 29160036 29160194 159 - 2.079 2.046 -0.108
ENSMUSG00000029701 E030 86.2658063 0.0002323842 2.072207e-01 7.820062e-01 6 29164490 29165005 516 - 1.937 1.892 -0.152

Help

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