ENSG00000004142

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
ENST00000540200 ENSG00000004142 HEK293_OSMI2_2hA HEK293_TMG_2hB POLDIP2 protein_coding protein_coding 121.9374 213.7283 75.26903 5.987261 1.089232 -1.505525 39.32360 66.47320 23.67050 1.325621 0.2796378 -1.489290 0.3372375 0.3112333 0.3146667 0.003433333 0.954526148 0.003580232 FALSE  
ENST00000618887 ENSG00000004142 HEK293_OSMI2_2hA HEK293_TMG_2hB POLDIP2 protein_coding protein_coding 121.9374 213.7283 75.26903 5.987261 1.089232 -1.505525 41.95748 71.86368 28.96262 3.689848 1.2148913 -1.310773 0.3445833 0.3358000 0.3844667 0.048666667 0.126324686 0.003580232 FALSE  
MSTRG.13945.2 ENSG00000004142 HEK293_OSMI2_2hA HEK293_TMG_2hB POLDIP2 protein_coding   121.9374 213.7283 75.26903 5.987261 1.089232 -1.505525 40.65636 75.39140 22.63591 1.316114 0.2076203 -1.735341 0.3181708 0.3529667 0.3008333 -0.052133333 0.003580232 0.003580232 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
ENSG00000004142 E001 221.9029 3.051876e-03 3.341069e-01 4.778551e-01 17 28346633 28347175 543 - 2.287 2.253 -0.115
ENSG00000004142 E002 2006.0665 7.841318e-04 1.677735e-10 2.850600e-09 17 28347176 28347660 485 - 3.129 3.233 0.343
ENSG00000004142 E003 3108.8173 2.609274e-04 4.845569e-22 3.884801e-20 17 28347661 28348231 571 - 3.324 3.422 0.326
ENSG00000004142 E004 1078.3918 9.878836e-05 3.178750e-06 2.364459e-05 17 28349083 28349162 80 - 2.891 2.956 0.217
ENSG00000004142 E005 1524.6793 1.004000e-04 9.277325e-01 9.585400e-01 17 28350438 28350563 126 - 3.092 3.092 0.002
ENSG00000004142 E006 913.0258 8.600539e-05 4.773635e-02 1.051497e-01 17 28350766 28350792 27 - 2.890 2.864 -0.087
ENSG00000004142 E007 1591.7726 1.037493e-04 6.467398e-02 1.345001e-01 17 28351664 28351800 137 - 3.126 3.108 -0.061
ENSG00000004142 E008 1460.7862 8.793830e-05 7.957206e-03 2.366770e-02 17 28352912 28353019 108 - 3.096 3.068 -0.094
ENSG00000004142 E009 1306.3498 1.323870e-04 5.116516e-05 2.876116e-04 17 28353241 28353316 76 - 3.064 3.016 -0.158
ENSG00000004142 E010 1227.0988 5.311875e-04 3.997988e-03 1.313711e-02 17 28353695 28353791 97 - 3.033 2.990 -0.142
ENSG00000004142 E011 827.2222 6.589285e-04 1.789045e-03 6.564578e-03 17 28354488 28354531 44 - 2.871 2.815 -0.185
ENSG00000004142 E012 735.1983 2.974250e-04 5.858581e-04 2.481423e-03 17 28354532 28354585 54 - 2.820 2.764 -0.188
ENSG00000004142 E013 845.5168 7.904421e-04 3.735649e-08 4.129464e-07 17 28355795 28355876 82 - 2.915 2.813 -0.340
ENSG00000004142 E014 624.9874 9.303798e-03 1.097718e-03 4.295971e-03 17 28357288 28357563 276 - 2.822 2.670 -0.507