ENSG00000125484

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
ENST00000372146 ENSG00000125484 HEK293_OSMI2_2hA HEK293_TMG_2hB GTF3C4 protein_coding protein_coding 16.21853 8.131092 27.38642 0.8938987 0.4461676 1.750693 13.7245132 6.597420 23.25631211 0.81826508 0.51532863 1.816084 0.83675000 0.8085333 0.8490333 0.0405000 3.228441e-01 1.054254e-29 FALSE TRUE
ENST00000483873 ENSG00000125484 HEK293_OSMI2_2hA HEK293_TMG_2hB GTF3C4 protein_coding protein_coding 16.21853 8.131092 27.38642 0.8938987 0.4461676 1.750693 1.7662155 0.000000 4.09628299 0.00000000 0.11003935 8.681689 0.07706667 0.0000000 0.1497667 0.1497667 1.406778e-24 1.054254e-29 FALSE TRUE
MSTRG.33559.1 ENSG00000125484 HEK293_OSMI2_2hA HEK293_TMG_2hB GTF3C4 protein_coding   16.21853 8.131092 27.38642 0.8938987 0.4461676 1.750693 0.7278023 1.533672 0.03382472 0.07783489 0.03382472 -5.138478 0.08618333 0.1914667 0.0012000 -0.1902667 1.054254e-29 1.054254e-29 FALSE 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
ENSG00000125484 E001 56.10888 0.0004721540 4.811498e-03 1.540673e-02 9 132670035 132670463 429 + 1.736 1.652 -0.287
ENSG00000125484 E002 126.22544 0.0070557892 2.800292e-05 1.677068e-04 9 132670464 132670955 492 + 2.106 1.938 -0.563
ENSG00000125484 E003 90.20904 0.0042260649 1.820319e-08 2.138496e-07 9 132677977 132678039 63 + 1.978 1.734 -0.822
ENSG00000125484 E004 462.31437 0.0033326525 7.760888e-13 1.940191e-11 9 132678040 132678877 838 + 2.667 2.498 -0.563
ENSG00000125484 E005 291.06023 0.0002109255 1.280047e-11 2.618520e-10 9 132678878 132679310 433 + 2.450 2.357 -0.311
ENSG00000125484 E006 345.45040 0.0004843083 5.860761e-02 1.242423e-01 9 132679311 132679803 493 + 2.493 2.517 0.081
ENSG00000125484 E007 155.33181 0.0003133714 3.359138e-02 7.895027e-02 9 132683563 132683693 131 + 2.113 2.245 0.441
ENSG00000125484 E008 140.82150 0.0002460227 1.156363e-02 3.249808e-02 9 132687239 132687327 89 + 2.063 2.210 0.491
ENSG00000125484 E009 2336.77426 0.0036488162 3.223510e-09 4.349200e-08 9 132688881 132694953 6073 + 3.283 3.419 0.455