ENSG00000139970

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
ENST00000267484 ENSG00000139970 HEK293_OSMI2_2hA HEK293_TMG_2hB RTN1 protein_coding protein_coding 4.213981 5.711771 3.459872 0.09585825 0.1882543 -0.7215791 2.9389852 2.9777622 3.1119402 0.3209056 0.08540774 0.06337758 0.71919583 0.52010000 0.90553333 0.38543333 5.051069e-03 5.342781e-12 FALSE TRUE
ENST00000342503 ENSG00000139970 HEK293_OSMI2_2hA HEK293_TMG_2hB RTN1 protein_coding protein_coding 4.213981 5.711771 3.459872 0.09585825 0.1882543 -0.7215791 0.4790100 0.6149226 0.2949448 0.1136519 0.25941086 -1.03512948 0.11666250 0.10826667 0.07886667 -0.02940000 6.122561e-01 5.342781e-12 FALSE TRUE
ENST00000432103 ENSG00000139970 HEK293_OSMI2_2hA HEK293_TMG_2hB RTN1 protein_coding retained_intron 4.213981 5.711771 3.459872 0.09585825 0.1882543 -0.7215791 0.1700636 0.4189827 0.0000000 0.4189827 0.00000000 -5.42284764 0.02939583 0.07583333 0.00000000 -0.07583333 8.851661e-01 5.342781e-12 FALSE TRUE
ENST00000474911 ENSG00000139970 HEK293_OSMI2_2hA HEK293_TMG_2hB RTN1 protein_coding retained_intron 4.213981 5.711771 3.459872 0.09585825 0.1882543 -0.7215791 0.5585537 1.6434834 0.0000000 0.2938836 0.00000000 -7.36936473 0.11821250 0.28616667 0.00000000 -0.28616667 5.342781e-12 5.342781e-12   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.

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
ENSG00000139970 E001 0.0000000       14 59595976 59595976 1 -      
ENSG00000139970 E002 0.1482932 0.0413999959 6.989860e-01   14 59595977 59595982 6 - 0.000 0.102 10.044
ENSG00000139970 E003 0.1482932 0.0413999959 6.989860e-01   14 59595983 59596004 22 - 0.000 0.102 10.044
ENSG00000139970 E004 0.1482932 0.0413999959 6.989860e-01   14 59596005 59596013 9 - 0.000 0.102 10.044
ENSG00000139970 E005 103.5372874 0.0043825662 2.304774e-04 1.093659e-03 14 59596014 59596756 743 - 1.891 2.051 0.534
ENSG00000139970 E006 34.3592822 0.0007144416 8.827486e-02 1.724898e-01 14 59596757 59596787 31 - 1.461 1.567 0.363
ENSG00000139970 E007 41.9656756 0.0016997967 7.799503e-01 8.585312e-01 14 59603065 59603123 59 - 1.607 1.625 0.061
ENSG00000139970 E008 33.8477755 0.0006817970 2.901806e-01 4.309714e-01 14 59603212 59603258 47 - 1.484 1.551 0.228
ENSG00000139970 E009 0.0000000       14 59603761 59603851 91 -      
ENSG00000139970 E010 39.5240846 0.0006363068 5.370805e-01 6.687236e-01 14 59603852 59603921 70 - 1.571 1.608 0.127
ENSG00000139970 E011 0.3666179 0.0303052917 7.667879e-01 8.491841e-01 14 59603922 59605367 1446 - 0.146 0.103 -0.580
ENSG00000139970 E012 48.7242448 0.0004961745 4.802691e-01 6.185684e-01 14 59605368 59605506 139 - 1.655 1.693 0.129
ENSG00000139970 E013 0.0000000       14 59605507 59606102 596 -      
ENSG00000139970 E014 51.7733997 0.0026712751 3.449512e-01 4.890367e-01 14 59607285 59607492 208 - 1.667 1.719 0.178
ENSG00000139970 E015 0.1817044 0.0398799143 6.971466e-01   14 59607493 59607607 115 - 0.000 0.102 10.049
ENSG00000139970 E016 0.6664265 0.0178945034 6.847596e-01 7.876768e-01 14 59610122 59610232 111 - 0.255 0.185 -0.584
ENSG00000139970 E017 4.4209723 0.0683037347 5.810221e-01 7.056459e-01 14 59630446 59630814 369 - 0.661 0.743 0.340
ENSG00000139970 E018 82.0385094 0.0004217491 8.843277e-02 1.727236e-01 14 59726919 59727668 750 - 1.938 1.878 -0.203
ENSG00000139970 E019 0.1817044 0.0398799143 6.971466e-01   14 59727669 59727713 45 - 0.000 0.102 10.049
ENSG00000139970 E020 89.9039826 0.0026360925 8.421808e-05 4.480067e-04 14 59745708 59746481 774 - 2.034 1.882 -0.510
ENSG00000139970 E021 18.5786821 0.0071528881 4.680926e-06 3.353707e-05 14 59870390 59870776 387 - 1.484 1.094 -1.368