ENSMUSG00000022594

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
ENSMUST00000023259 ENSMUSG00000022594 Control shVgll3 Lynx1 protein_coding protein_coding 6.861258 5.654833 8.067683 0.1180987 0.2820258 0.5119081 5.340322 5.509094 5.171550 0.01269335 0.29192095 -0.09104786 0.8075000 0.9749667 0.6400333 -0.3349333 5.088993e-06 2.360805e-23 FALSE FALSE
ENSMUST00000189128 ENSMUSG00000022594 Control shVgll3 Lynx1 protein_coding protein_coding 6.861258 5.654833 8.067683 0.1180987 0.2820258 0.5119081 1.376153 0.000000 2.752306 0.00000000 0.05776452 8.10972940 0.1711833 0.0000000 0.3423667 0.3423667 2.360805e-23 2.360805e-23 FALSE 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
ENSMUSG00000022594 E001 483.9031846 0.0002016726 0.0003396606 0.02136210 15 74619701 74623276 3576 - 2.672 2.699 0.093
ENSMUSG00000022594 E002 32.0646655 0.0006375872 0.2436389999 0.80442163 15 74623392 74623443 52 - 1.553 1.484 -0.235
ENSMUSG00000022594 E003 29.6194180 0.0006815218 0.4063970759 0.89390915 15 74623444 74623493 50 - 1.511 1.460 -0.173
ENSMUSG00000022594 E004 48.2651027 0.0005656050 0.0025040572 0.09068873 15 74623704 74623886 183 - 1.760 1.612 -0.500
ENSMUSG00000022594 E005 0.1613534 0.0343190169 0.4812199412   15 74623982 74624054 73 - 0.124 0.000 -9.025
ENSMUSG00000022594 E006 1.9782297 0.1459828923 0.9153829233 0.99751275 15 74624168 74624733 566 - 0.474 0.473 -0.008
ENSMUSG00000022594 E007 15.9368010 0.0014727824 0.2455425981 0.80442163 15 74624734 74624895 162 - 1.275 1.179 -0.342

Help

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