ENSG00000122958

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
ENST00000263559 ENSG00000122958 HEK293_OSMI2_6hA HEK293_TMG_6hB VPS26A protein_coding protein_coding 37.53054 11.52525 63.80342 3.924604 2.33739 2.46781 17.08411 7.2698310 24.30177 2.4291451 1.046323 1.739678 0.5701833 0.62473333 0.3810333 -0.2437000 0.006906722 0.006906722 FALSE TRUE
ENST00000489656 ENSG00000122958 HEK293_OSMI2_6hA HEK293_TMG_6hB VPS26A protein_coding nonsense_mediated_decay 37.53054 11.52525 63.80342 3.924604 2.33739 2.46781 11.68075 3.4570883 21.21201 2.1139691 3.112920 2.613765 0.2621458 0.22066667 0.3298667 0.1092000 0.841647177 0.006906722 FALSE FALSE
ENST00000497564 ENSG00000122958 HEK293_OSMI2_6hA HEK293_TMG_6hB VPS26A protein_coding processed_transcript 37.53054 11.52525 63.80342 3.924604 2.33739 2.46781 7.36747 0.3943374 14.19823 0.3943374 2.926194 5.135023 0.1252875 0.08583333 0.2254000 0.1395667 0.295447861 0.006906722 FALSE 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_6hB HEK293_OSMI2_6hA log2fold_HEK293_OSMI2_6hA_HEK293_TMG_6hB
ENSG00000122958 E001 0.5233527 0.0230354163 6.910218e-01   10 69123512 69123546 35 + 0.129 0.204 0.793
ENSG00000122958 E002 2.9630756 0.0081439350 4.681376e-01 0.6788079456 10 69123660 69124151 492 + 0.557 0.447 -0.531
ENSG00000122958 E003 0.3088520 0.0251302936 3.843243e-01   10 69124152 69124155 4 + 0.070 0.204 1.787
ENSG00000122958 E004 1.4343360 0.0126477162 3.516680e-01 0.5887701813 10 69124156 69124177 22 + 0.378 0.204 -1.211
ENSG00000122958 E005 3.3438639 0.0077696853 6.083457e-01 0.7758161619 10 69124178 69124185 8 + 0.596 0.532 -0.296
ENSG00000122958 E006 19.6827027 0.0219404332 8.659614e-01 0.9337070902 10 69124186 69124211 26 + 1.243 1.287 0.154
ENSG00000122958 E007 50.7374434 0.0033056137 2.145214e-01 0.4469612196 10 69124212 69124245 34 + 1.657 1.607 -0.171
ENSG00000122958 E008 95.4798621 0.0046410145 6.081368e-01 0.7756569736 10 69124246 69124280 35 + 1.915 1.916 0.002
ENSG00000122958 E009 265.0926996 0.0026952483 8.411181e-03 0.0512067381 10 69132898 69133047 150 + 2.367 2.301 -0.223
ENSG00000122958 E010 237.4707991 0.0002039491 2.281375e-05 0.0004274854 10 69155812 69155887 76 + 2.324 2.241 -0.277
ENSG00000122958 E011 321.9725208 0.0032755921 1.956718e-03 0.0167775241 10 69157007 69157163 157 + 2.452 2.381 -0.238
ENSG00000122958 E012 282.8366518 0.0058275201 4.914388e-01 0.6949300006 10 69158047 69158211 165 + 2.379 2.388 0.030
ENSG00000122958 E013 221.3203109 0.0004029666 4.111657e-01 0.6369187360 10 69162406 69162512 107 + 2.275 2.286 0.036
ENSG00000122958 E014 233.9876920 0.0013599109 2.456028e-01 0.4831013042 10 69166042 69166110 69 + 2.302 2.297 -0.014
ENSG00000122958 E015 322.1449867 0.0001696934 7.569964e-01 0.8708546338 10 69168489 69168631 143 + 2.429 2.469 0.135
ENSG00000122958 E016 6.0122316 0.1596735819 7.321258e-01 0.8555018441 10 69170034 69170369 336 + 0.769 0.812 0.172
ENSG00000122958 E017 1103.9418086 0.0037529340 8.032715e-06 0.0001735768 10 69171156 69174412 3257 + 2.941 3.051 0.368