ENSG00000139921

1 Isoform Switch

Summary Plot

Only the isoforms with fraction > 5% are shown below.

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
ENST00000457354 ENSG00000139921 HEK293_OSMI2_2hA HEK293_TMG_2hB TMX1 protein_coding protein_coding 27.66386 8.220926 48.08269 2.84866 0.2698178 2.546691 23.117787 7.8202041 40.073502 2.6585094 0.9247618 2.355887 0.8640458 0.95666667 0.8333333 -0.1233333 0.0003824206 0.0003824206 FALSE TRUE
ENST00000555574 ENSG00000139921 HEK293_OSMI2_2hA HEK293_TMG_2hB TMX1 protein_coding retained_intron 27.66386 8.220926 48.08269 2.84866 0.2698178 2.546691 4.400465 0.4007221 7.915046 0.2019898 0.8134219 4.270185 0.1323750 0.04333333 0.1647000 0.1213667 0.0006002588 0.0003824206   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.

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 HEK293_TMG_2hB HEK293_OSMI2_2hA log2fold_HEK293_OSMI2_2hA_HEK293_TMG_2hB
ENSG00000139921 E001 28.978598 0.0019967057 2.195065e-02 5.557316e-02 14 51240162 51240246 85 + 1.366 1.242 -0.434
ENSG00000139921 E002 29.492366 0.0035450291 1.815871e-02 4.747276e-02 14 51240247 51240249 3 + 1.376 1.242 -0.469
ENSG00000139921 E003 379.058200 0.0024541779 6.341774e-13 1.607479e-11 14 51240250 51240444 195 + 2.469 2.292 -0.593
ENSG00000139921 E004 387.812305 0.0004476998 9.077023e-15 3.004744e-13 14 51243856 51243971 116 + 2.473 2.353 -0.399
ENSG00000139921 E005 1.656061 0.3870861633 3.342889e-01 4.780167e-01 14 51243972 51243976 5 + 0.385 0.001 -9.714
ENSG00000139921 E006 256.258133 0.0002374228 5.612898e-06 3.949878e-05 14 51245313 51245358 46 + 2.285 2.238 -0.156
ENSG00000139921 E007 3.409559 0.0045280592 7.754007e-02 1.555125e-01 14 51245359 51245454 96 + 0.583 0.261 -1.780
ENSG00000139921 E008 10.293080 0.0016415201 2.635038e-02 6.464705e-02 14 51245455 51245851 397 + 0.965 0.709 -0.999
ENSG00000139921 E009 366.684996 0.0005279742 1.279180e-07 1.273045e-06 14 51247092 51247220 129 + 2.441 2.389 -0.173
ENSG00000139921 E010 238.652243 0.0001909010 3.693014e-06 2.710380e-05 14 51249326 51249371 46 + 2.256 2.204 -0.176
ENSG00000139921 E011 366.567860 0.0001651040 6.964813e-09 8.839438e-08 14 51249468 51249569 102 + 2.442 2.388 -0.178
ENSG00000139921 E012 275.686453 0.0001873809 5.536424e-06 3.902005e-05 14 51249693 51249765 73 + 2.317 2.278 -0.131
ENSG00000139921 E013 1537.466248 0.0017898731 7.756285e-43 3.187429e-40 14 51254341 51257655 3315 + 2.996 3.277 0.936