ENSG00000139438

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
ENST00000358906 ENSG00000139438 HEK293_OSMI2_2hA HEK293_TMG_2hB FAM222A protein_coding protein_coding 8.383712 15.93613 4.891634 1.19407 0.1934487 -1.701871 2.923599 7.718221 0.2172283 0.3962469 0.2172283 -5.0879215 0.3048250 0.4910667 0.04816667 -0.4429000 0.0219584903 0.0001977127 FALSE TRUE
ENST00000538780 ENSG00000139438 HEK293_OSMI2_2hA HEK293_TMG_2hB FAM222A protein_coding protein_coding 8.383712 15.93613 4.891634 1.19407 0.1934487 -1.701871 2.703803 3.368413 2.3664045 0.5726839 0.3205288 -0.5075652 0.3457583 0.2084000 0.48003333 0.2716333 0.0001977127 0.0001977127 FALSE TRUE
MSTRG.7984.1 ENSG00000139438 HEK293_OSMI2_2hA HEK293_TMG_2hB FAM222A protein_coding   8.383712 15.93613 4.891634 1.19407 0.1934487 -1.701871 2.756311 4.849493 2.3080008 0.7602869 0.1231597 -1.0679247 0.3494167 0.3005333 0.47180000 0.1712667 0.0093217318 0.0001977127 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
ENSG00000139438 E001 0.2955422 0.0300696460 4.000532e-01   12 109713691 109713731 41 + 0.187 0.078 -1.463
ENSG00000139438 E002 37.3851501 0.0009175291 6.701452e-06 4.635158e-05 12 109713825 109714323 499 + 1.661 1.446 -0.735
ENSG00000139438 E003 62.6399127 0.0085089744 8.852545e-03 2.591338e-02 12 109714324 109714734 411 + 1.803 1.700 -0.350
ENSG00000139438 E004 71.6182763 0.0004101374 3.404852e-04 1.542273e-03 12 109714735 109714897 163 + 1.859 1.757 -0.343
ENSG00000139438 E005 0.0000000       12 109722532 109722825 294 +      
ENSG00000139438 E006 0.4428904 0.4507692296 1.000000e+00 1.000000e+00 12 109734767 109734900 134 + 0.000 0.150 8.971
ENSG00000139438 E007 38.3165650 0.0006151314 1.315217e-01 2.362571e-01 12 109744101 109744114 14 + 1.544 1.508 -0.123
ENSG00000139438 E008 72.5808913 0.0003873441 3.245474e-02 7.672428e-02 12 109744115 109744228 114 + 1.818 1.780 -0.128
ENSG00000139438 E009 816.6677054 0.0044991806 5.103958e-07 4.507830e-06 12 109768012 109770495 2484 + 2.734 2.865 0.433