ENSG00000128534

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
ENST00000249299 ENSG00000128534 HEK293_OSMI2_2hA HEK293_TMG_2hB LSM8 protein_coding protein_coding 24.30578 21.79359 26.67978 1.948497 0.8383311 0.2917215 1.958031 1.571644 2.724616 0.2464564 0.1496528 0.7899135 0.0801375 0.0715000 0.1026667 0.03116667 0.2113869384 7.604273e-05 FALSE  
ENST00000411938 ENSG00000128534 HEK293_OSMI2_2hA HEK293_TMG_2hB LSM8 protein_coding protein_coding 24.30578 21.79359 26.67978 1.948497 0.8383311 0.2917215 20.637559 19.327079 21.539931 1.7014679 0.9197351 0.1563134 0.8504917 0.8871333 0.8067667 -0.08036667 0.0003570888 7.604273e-05    
  • 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
ENSG00000128534 E001 55.35549 0.0084950076 1.029755e-02 2.949964e-02 7 118184073 118184143 71 + 1.680 1.813 0.451
ENSG00000128534 E002 70.87992 0.0066145691 9.840905e-04 3.904969e-03 7 118184144 118184155 12 + 1.774 1.931 0.527
ENSG00000128534 E003 80.00302 0.0100588311 8.646784e-04 3.489790e-03 7 118184156 118184163 8 + 1.816 1.988 0.579
ENSG00000128534 E004 81.22119 0.0102187990 4.020754e-03 1.319978e-02 7 118184164 118184166 3 + 1.839 1.983 0.483
ENSG00000128534 E005 390.97798 0.0019703255 7.038874e-03 2.132566e-02 7 118184167 118184254 88 + 2.572 2.615 0.143
ENSG00000128534 E006 36.36263 0.0073343617 1.171463e-05 7.662537e-05 7 118184255 118184280 26 + 1.408 1.691 0.965
ENSG00000128534 E007 93.07304 0.0071825678 3.398706e-06 2.513859e-05 7 118184281 118185646 1366 + 2.089 1.802 -0.963
ENSG00000128534 E008 29.24794 0.0017252445 1.516046e-02 4.085032e-02 7 118185647 118185653 7 + 1.408 1.544 0.467
ENSG00000128534 E009 433.01297 0.0004743385 2.540015e-04 1.191881e-03 7 118185654 118185694 41 + 2.618 2.661 0.144
ENSG00000128534 E010 670.74261 0.0010031657 5.096705e-06 3.620788e-05 7 118188278 118188405 128 + 2.801 2.857 0.185
ENSG00000128534 E011 89.31785 0.0068545203 3.952059e-17 1.783057e-15 7 118188406 118191911 3506 + 2.138 1.627 -1.723
ENSG00000128534 E012 853.92433 0.0024414355 1.395627e-11 2.838404e-10 7 118191912 118204035 12124 + 3.005 2.842 -0.542