ENSG00000029993

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
ENST00000325307 ENSG00000029993 HEK293_DMSO_6hA HEK293_OSMI2_6hA HMGB3 protein_coding protein_coding 202.3321 127.5116 198.0361 12.53293 36.32358 0.6350948 41.75724 28.74830 33.68148 3.158228 5.725936 0.2284050 0.2152500 0.2250 0.1722333 -0.05276667 0.147172490 0.004548632 FALSE TRUE
ENST00000430118 ENSG00000029993 HEK293_DMSO_6hA HEK293_OSMI2_6hA HMGB3 protein_coding protein_coding 202.3321 127.5116 198.0361 12.53293 36.32358 0.6350948 138.53475 81.01635 145.19527 8.284414 27.857041 0.8416308 0.6722667 0.6354 0.7309333 0.09553333 0.004548632 0.004548632 FALSE FALSE
MSTRG.35040.2 ENSG00000029993 HEK293_DMSO_6hA HEK293_OSMI2_6hA HMGB3 protein_coding   202.3321 127.5116 198.0361 12.53293 36.32358 0.6350948 17.91059 13.37056 15.57194 1.374045 3.520582 0.2197363 0.0913000 0.1052 0.0770000 -0.02820000 0.235864720 0.004548632 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_OSMI2_6hA HEK293_DMSO_6hA log2fold_HEK293_DMSO_6hA_HEK293_OSMI2_6hA
ENSG00000029993 E001 0.000000       X 150980509 150980644 136 +      
ENSG00000029993 E002 151.103563 0.0052903607 2.111106e-01 0.6154956348 X 150983236 150983334 99 + 2.191 2.176 -0.050
ENSG00000029993 E003 341.450798 0.0052205074 1.212564e-02 0.1902051601 X 150983335 150983376 42 + 2.560 2.503 -0.188
ENSG00000029993 E004 0.000000       X 150983385 150983405 21 +      
ENSG00000029993 E005 1.273391 0.0126085945 6.429780e-01   X 150983406 150983436 31 + 0.376 0.322 -0.324
ENSG00000029993 E006 31.375023 0.0008545081 1.421639e-01 0.5283692667 X 150983437 150983591 155 + 1.442 1.579 0.470
ENSG00000029993 E007 6.156740 0.0040763017 7.463951e-02 0.4059485090 X 150984454 150984625 172 + 0.710 0.974 1.028
ENSG00000029993 E008 29.890004 0.1414985450 2.880962e-01 0.6899566536 X 150985031 150985144 114 + 1.360 1.598 0.818
ENSG00000029993 E009 24.422022 0.0796115665 1.978885e-01 0.6010019445 X 150985531 150985594 64 + 1.280 1.513 0.807
ENSG00000029993 E010 335.022784 0.0033684540 2.273888e-02 0.2489003649 X 150985595 150985598 4 + 2.541 2.509 -0.107
ENSG00000029993 E011 1167.711463 0.0012817841 9.128649e-05 0.0128194859 X 150985599 150985749 151 + 3.078 3.054 -0.078
ENSG00000029993 E012 1546.195847 0.0009744248 1.580623e-06 0.0008059185 X 150986051 150986190 140 + 3.200 3.175 -0.084
ENSG00000029993 E013 1693.853951 0.0002347495 3.280156e-07 0.0002526677 X 150987128 150987302 175 + 3.230 3.228 -0.005
ENSG00000029993 E014 4038.666617 0.0039854580 7.735631e-06 0.0025740234 X 150987777 150990771 2995 + 3.537 3.673 0.453