ENSMUSG00000021902

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
ENSMUST00000022459 ENSMUSG00000021902 Control shVgll3 Phf7 protein_coding protein_coding 2.701532 2.420492 2.982572 0.1729604 0.2339905 0.3001377 0.4603966 0.7427753 0.1780179 0.25634571 0.11371167 -2.00134887 0.18390000 0.30783333 0.05996667 -0.24786667 0.529809728 0.004376737 FALSE TRUE
ENSMUST00000226565 ENSMUSG00000021902 Control shVgll3 Phf7 protein_coding protein_coding 2.701532 2.420492 2.982572 0.1729604 0.2339905 0.3001377 1.4679958 1.2225076 1.7134841 0.23461761 0.23351051 0.48373152 0.53881667 0.50473333 0.57290000 0.06816667 0.970665669 0.004376737 FALSE TRUE
ENSMUST00000227668 ENSMUSG00000021902 Control shVgll3 Phf7 protein_coding retained_intron 2.701532 2.420492 2.982572 0.1729604 0.2339905 0.3001377 0.5647934 0.1805858 0.9490009 0.09117572 0.07250933 2.33109137 0.19495000 0.06966667 0.32023333 0.25056667 0.004376737 0.004376737   FALSE
ENSMUST00000228140 ENSMUSG00000021902 Control shVgll3 Phf7 protein_coding retained_intron 2.701532 2.420492 2.982572 0.1729604 0.2339905 0.3001377 0.1387652 0.1354612 0.1420693 0.01078715 0.02643512 0.06409401 0.05191667 0.05693333 0.04690000 -0.01003333 1.000000000 0.004376737   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
ENSMUSG00000021902 E001 0.000000       14 30959646 30959651 6 -      
ENSMUSG00000021902 E002 0.000000       14 30959652 30959652 1 -      
ENSMUSG00000021902 E003 4.433279 0.0048002268 0.731069581 0.97159982 14 30959653 30959767 115 - 0.709 0.758 0.198
ENSMUSG00000021902 E004 3.602060 0.0384087386 0.561294946 0.94136606 14 30959768 30959768 1 - 0.612 0.707 0.406
ENSMUSG00000021902 E005 21.366355 0.0009436631 0.252447269 0.80673156 14 30959769 30960110 342 - 1.306 1.386 0.278
ENSMUSG00000021902 E006 7.570098 0.0025345957 0.992061545 1.00000000 14 30960294 30960394 101 - 0.932 0.933 0.002
ENSMUSG00000021902 E007 4.767758 0.0040703071 0.241733391 0.80442163 14 30960395 30960439 45 - 0.835 0.680 -0.627
ENSMUSG00000021902 E008 2.790021 0.0089872685 0.001677156 0.07122958 14 30961077 30961193 117 - 0.227 0.758 2.782
ENSMUSG00000021902 E009 8.736098 0.0024181569 0.452328295 0.91349987 14 30961588 30961694 107 - 1.026 0.948 -0.288
ENSMUSG00000021902 E010 2.477642 0.0081350860 0.345247812 0.87285719 14 30961695 30961951 257 - 0.612 0.461 -0.709
ENSMUSG00000021902 E011 12.536031 0.0019416585 0.380779138 0.88103212 14 30962231 30962390 160 - 1.169 1.092 -0.276
ENSMUSG00000021902 E012 11.717879 0.0227181637 0.653074636 0.95668705 14 30962816 30962940 125 - 1.126 1.081 -0.165
ENSMUSG00000021902 E013 0.000000       14 30962941 30962966 26 -      
ENSMUSG00000021902 E014 9.213850 0.0022210091 0.308036391 0.84753465 14 30963683 30963784 102 - 0.949 1.057 0.397
ENSMUSG00000021902 E015 6.906311 0.0027357176 0.740925215 0.97290014 14 30967089 30969999 2911 - 0.877 0.916 0.152
ENSMUSG00000021902 E016 4.774576 0.0318498006 0.099864670 0.63635866 14 30970000 30970091 92 - 0.612 0.864 1.029
ENSMUSG00000021902 E017 3.133540 0.0074178734 0.624705548 0.95514198 14 30970952 30971004 53 - 0.574 0.650 0.335
ENSMUSG00000021902 E018 6.760474 0.0029218224 0.893401341 0.99549749 14 30971565 30971674 110 - 0.896 0.882 -0.054
ENSMUSG00000021902 E019 28.397944 0.0016874656 0.063122818 0.54605852 14 30972662 30973274 613 - 1.522 1.413 -0.375

Help

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