ENSMUSG00000025491

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
ENSMUST00000026564 ENSMUSG00000025491 Control shVgll3 Ifitm1 protein_coding protein_coding 191.9131 135.4701 248.3561 4.089037 11.52159 0.874388 39.69776 26.06819 53.327341 2.1303505 2.953777 1.032302 0.20435 0.1936667 0.21503333 0.02136667 9.706657e-01 3.284965e-32 FALSE FALSE
ENSMUST00000106040 ENSMUSG00000025491 Control shVgll3 Ifitm1 protein_coding protein_coding 191.9131 135.4701 248.3561 4.089037 11.52159 0.874388 136.89908 88.03332 185.764846 5.8979495 9.181181 1.077270 0.69815 0.6484000 0.74790000 0.09950000 1.043613e-01 3.284965e-32 FALSE TRUE
ENSMUST00000106042 ENSMUSG00000025491 Control shVgll3 Ifitm1 protein_coding protein_coding 191.9131 135.4701 248.3561 4.089037 11.52159 0.874388 15.31625 21.36855 9.263943 0.6858924 1.111932 -1.204909 0.09750 0.1579333 0.03706667 -0.12086667 3.284965e-32 3.284965e-32 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
ENSMUSG00000025491 E001 97.635521 0.0002297998 4.250753e-55 7.103616e-52 7 140547134 140547479 346 + 1.680 2.235 1.866
ENSMUSG00000025491 E002 2.470016 0.0271343799 3.610637e-01 8.753500e-01 7 140547941 140547952 12 + 0.591 0.423 -0.815
ENSMUSG00000025491 E003 2.138026 0.0505784418 2.751066e-01 8.203408e-01 7 140547953 140547964 12 + 0.560 0.349 -1.094
ENSMUSG00000025491 E004 36.529615 0.0005658747 7.797679e-02 5.907853e-01 7 140547965 140548152 188 + 1.604 1.492 -0.384
ENSMUSG00000025491 E005 518.117999 0.0003137630 3.318306e-02 4.111432e-01 7 140548153 140548351 199 + 2.718 2.680 -0.128
ENSMUSG00000025491 E006 968.239742 0.0005019697 2.705802e-05 2.659872e-03 7 140549402 140549738 337 + 2.992 2.948 -0.145

Help

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