ENSG00000128408

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
ENST00000466226 ENSG00000128408 HEK293_OSMI2_2hA HEK293_TMG_2hB RIBC2 protein_coding processed_transcript 3.11793 4.657366 1.744044 0.326332 0.2340235 -1.411924 0.1917525 0.2196787 0.0000000 0.007014425 0.00000000 -4.5215454 0.0522750 0.04743333 0.0000000 -0.04743333 0.0050591971 1.75493e-05 FALSE FALSE
ENST00000614167 ENSG00000128408 HEK293_OSMI2_2hA HEK293_TMG_2hB RIBC2 protein_coding protein_coding 3.11793 4.657366 1.744044 0.326332 0.2340235 -1.411924 1.0037592 1.0735445 0.8223425 0.216833839 0.02837516 -0.3805092 0.3436750 0.22633333 0.4868333 0.26050000 0.0078493853 1.75493e-05 FALSE TRUE
ENST00000621287 ENSG00000128408 HEK293_OSMI2_2hA HEK293_TMG_2hB RIBC2 protein_coding retained_intron 3.11793 4.657366 1.744044 0.326332 0.2340235 -1.411924 1.5790456 2.6167873 0.9217011 0.228239341 0.20787493 -1.4953602 0.4889542 0.56093333 0.5131667 -0.04776667 0.8194674199 1.75493e-05 FALSE TRUE
MSTRG.22319.2 ENSG00000128408 HEK293_OSMI2_2hA HEK293_TMG_2hB RIBC2 protein_coding   3.11793 4.657366 1.744044 0.326332 0.2340235 -1.411924 0.3433731 0.7473557 0.0000000 0.131546235 0.00000000 -6.2428991 0.1150792 0.16526667 0.0000000 -0.16526667 0.0000175493 1.75493e-05 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
ENSG00000128408 E001 2.098367 0.0076910829 0.2277728889 0.359761641 22 45413693 45413712 20 + 0.577 0.369 -1.050
ENSG00000128408 E002 19.479553 0.0012031437 0.6759552890 0.781063486 22 45413713 45414015 303 + 1.260 1.227 -0.117
ENSG00000128408 E003 6.156043 0.0036288102 0.2498289120 0.385708859 22 45414322 45414322 1 + 0.884 0.732 -0.597
ENSG00000128408 E004 13.872086 0.0015167634 0.0620315517 0.130039741 22 45414323 45414403 81 + 1.218 1.047 -0.616
ENSG00000128408 E005 34.602496 0.0008725777 0.9899132620 0.997803115 22 45417602 45417946 345 + 1.466 1.467 0.001
ENSG00000128408 E006 2.431370 0.0066822061 0.3050640837 0.447103367 22 45418007 45418244 238 + 0.324 0.517 1.047
ENSG00000128408 E007 22.390402 0.0010037631 0.0571836139 0.121778943 22 45422290 45422408 119 + 1.156 1.316 0.565
ENSG00000128408 E008 14.153989 0.0016451992 0.0003014297 0.001385404 22 45422409 45422506 98 + 0.735 1.169 1.633
ENSG00000128408 E009 13.775197 0.0014625779 0.8315453051 0.894422630 22 45425948 45426175 228 + 1.102 1.082 -0.071
ENSG00000128408 E010 8.981229 0.0021469323 0.0753081115 0.152014830 22 45430900 45431066 167 + 1.062 0.864 -0.740
ENSG00000128408 E011 4.763756 0.0040635441 0.4335000436 0.575909585 22 45432284 45432509 226 + 0.777 0.666 -0.459
ENSG00000128408 E012 0.000000       22 45440783 45440836 54 +