ENSG00000164109

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
ENST00000296509 ENSG00000164109 HEK293_OSMI2_2hA HEK293_TMG_2hB MAD2L1 protein_coding protein_coding 85.12575 36.09931 150.0056 10.29382 6.313596 2.05467 11.321483 4.227257 20.58365 1.230586 0.5978855 2.280997 0.12529583 0.1167667 0.13743333 0.02066667 2.531786e-01 4.879161e-10 FALSE TRUE
ENST00000333047 ENSG00000164109 HEK293_OSMI2_2hA HEK293_TMG_2hB MAD2L1 protein_coding nonsense_mediated_decay 85.12575 36.09931 150.0056 10.29382 6.313596 2.05467 63.829165 31.001999 113.23648 8.812054 2.7603810 1.868568 0.77081667 0.8591333 0.75606667 -0.10306667 1.632320e-05 4.879161e-10 TRUE FALSE
ENST00000512484 ENSG00000164109 HEK293_OSMI2_2hA HEK293_TMG_2hB MAD2L1 protein_coding retained_intron 85.12575 36.09931 150.0056 10.29382 6.313596 2.05467 7.444663 0.000000 11.79342 0.000000 3.6035235 10.204989 0.07070417 0.0000000 0.07683333 0.07683333 4.879161e-10 4.879161e-10   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
ENSG00000164109 E001 439.615351 1.405057e-02 5.369169e-03 1.693284e-02 4 120055623 120059436 3814 - 2.622 2.479 -0.475
ENSG00000164109 E002 948.096281 1.147368e-03 3.522943e-23 3.187254e-21 4 120059437 120059827 391 - 2.872 3.051 0.598
ENSG00000164109 E003 1797.106355 5.181422e-04 1.712272e-02 4.521231e-02 4 120059828 120060290 463 - 3.196 3.219 0.077
ENSG00000164109 E004 866.767044 8.912084e-05 1.460767e-01 2.563439e-01 4 120060874 120060977 104 - 2.892 2.873 -0.063
ENSG00000164109 E005 2.526779 8.857268e-03 9.397546e-01 9.661620e-01 4 120060978 120061036 59 - 0.515 0.533 0.085
ENSG00000164109 E006 743.682472 9.960505e-04 5.074640e-01 6.429787e-01 4 120061975 120062095 121 - 2.825 2.801 -0.078
ENSG00000164109 E007 6.257776 1.073702e-02 2.303289e-01 3.628579e-01 4 120065451 120065671 221 - 0.853 0.665 -0.757
ENSG00000164109 E008 874.235270 1.799106e-03 7.364654e-06 5.043602e-05 4 120065672 120065818 147 - 2.916 2.794 -0.406
ENSG00000164109 E009 577.486860 2.793347e-03 1.425010e-05 9.133054e-05 4 120066662 120066858 197 - 2.741 2.592 -0.498