ENSG00000065978

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
ENST00000321358 ENSG00000065978 HEK293_OSMI2_2hA HEK293_TMG_2hB YBX1 protein_coding protein_coding 970.9615 1074.885 983.88 97.8353 12.61246 -0.1276264 435.4301 565.4341 403.9761 53.07974 9.52178 -0.48507884 0.4466750 0.5257 0.4104667 -0.11523333 4.263891e-14 4.263891e-14 FALSE TRUE
ENST00000467957 ENSG00000065978 HEK293_OSMI2_2hA HEK293_TMG_2hB YBX1 protein_coding processed_transcript 970.9615 1074.885 983.88 97.8353 12.61246 -0.1276264 500.6326 494.8773 525.3193 45.30445 12.82371 0.08612201 0.5170125 0.4606 0.5338667 0.07326667 1.589531e-03 4.263891e-14   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
ENSG00000065978 E001 134.14825 7.833327e-04 2.059106e-17 9.655727e-16 1 42682418 42682439 22 + 2.268 2.001 -0.894
ENSG00000065978 E002 4035.07945 5.496902e-03 1.743640e-04 8.542211e-04 1 42682440 42682731 292 + 3.670 3.538 -0.439
ENSG00000065978 E003 36.28720 7.536550e-03 9.861850e-07 8.192134e-06 1 42682987 42683155 169 + 1.738 1.398 -1.160
ENSG00000065978 E004 91.69451 2.805865e-03 5.880917e-09 7.582673e-08 1 42683156 42683365 210 + 2.095 1.844 -0.841
ENSG00000065978 E005 48.03612 8.598049e-03 1.877346e-02 4.883929e-02 1 42683366 42683402 37 + 1.767 1.611 -0.528
ENSG00000065978 E006 4822.17389 1.025263e-03 8.789302e-08 9.018126e-07 1 42683403 42683466 64 + 3.719 3.638 -0.270
ENSG00000065978 E007 6084.99738 3.483901e-04 1.823588e-13 5.001060e-12 1 42693490 42693523 34 + 3.812 3.746 -0.219
ENSG00000065978 E008 10209.62144 1.651972e-05 6.402306e-25 6.966672e-23 1 42696199 42696288 90 + 4.016 3.990 -0.088
ENSG00000065978 E009 18385.86644 7.839033e-05 1.060445e-13 3.002065e-12 1 42696642 42696944 303 + 4.267 4.244 -0.077
ENSG00000065978 E010 10479.47601 2.097941e-04 6.239849e-01 7.404498e-01 1 42697180 42697262 83 + 4.005 4.009 0.013
ENSG00000065978 E011 18911.57557 3.122796e-04 8.676525e-09 1.081836e-07 1 42700781 42701046 266 + 4.232 4.281 0.162
ENSG00000065978 E012 14134.16463 1.745583e-04 4.971323e-92 1.162719e-88 1 42701981 42703805 1825 + 4.048 4.184 0.451