ENSG00000056558

1 Isoform Switch

Summary Plot

Only the isoforms with fraction > 5% are shown below.

  • Note:

    • About the Coding Potential: Please check the spreadsheet in the “Results” tag to confirm the coding potential. The above figure only show the predicted coding potential. The “gene_biotype” in the result spreadsheet is from the database record. Therefore, if you find conflicts between “gene_biotype” and “codingPotential”, please trust the “gene_biotype”.

    • 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
ENST00000373887 ENSG00000056558 No_inf pgKDN_inf TRAF1 protein_coding protein_coding 25.03413 12.82806 29.52326 0.9009903 0.7738219 1.201913 4.567209 10.5556447 1.306048 0.5748396 0.2675896 -3.005097 0.3130750 0.839175 0.04380 -0.795375 2.767520e-08 2.76752e-08 FALSE TRUE
ENST00000540010 ENSG00000056558 No_inf pgKDN_inf TRAF1 protein_coding protein_coding 25.03413 12.82806 29.52326 0.9009903 0.7738219 1.201913 10.059747 1.6593246 13.487061 1.1480803 0.7431126 3.015309 0.3440083 0.115800 0.45875 0.342950 9.400964e-02 2.76752e-08 FALSE TRUE
ENST00000546084 ENSG00000056558 No_inf pgKDN_inf TRAF1 protein_coding protein_coding 25.03413 12.82806 29.52326 0.9009903 0.7738219 1.201913 10.325112 0.3669186 14.730153 0.3669186 1.1152303 5.289355 0.3373833 0.028400 0.49745 0.469050 1.199716e-04 2.76752e-08 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.

Help

Please Click HERE to learn more details about the results of IsoformSwitchAnalyzeR.

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 pgKDN.inf No.inf log2fold_No.inf_pgKDN.inf
ENSG00000056558 E001 298.6783605 0.0000876079 7.136889e-48 1.012950e-44 9 120902393 120905238 2846 - 2.528 2.380 -0.496
ENSG00000056558 E002 32.2565116 0.0004988640 4.257653e-02 2.010756e-01 9 120909230 120909378 149 - 1.546 1.473 -0.251
ENSG00000056558 E003 0.3629044 0.0166570727 7.894620e-01   9 120909434 120909470 37 - 0.148 0.113 -0.450
ENSG00000056558 E004 29.0755338 0.0005316987 1.657464e-02 1.121148e-01 9 120911336 120911513 178 - 1.513 1.413 -0.343
ENSG00000056558 E005 51.0901912 0.0003365996 1.441891e-06 6.370377e-05 9 120913328 120913738 411 - 1.776 1.606 -0.574
ENSG00000056558 E006 16.8659997 0.0061605309 3.297761e-01 6.222186e-01 9 120914235 120914300 66 - 1.265 1.223 -0.148
ENSG00000056558 E007 0.2346346 0.0156796496 3.653695e-01   9 120914508 120914572 65 - 0.148 0.000 -11.510
ENSG00000056558 E008 16.4599005 0.0021415269 6.511163e-01 8.530243e-01 9 120923705 120923792 88 - 1.209 1.273 0.228
ENSG00000056558 E009 27.6931181 0.0005280349 1.117931e-05 3.763702e-04 9 120925936 120926301 366 - 1.314 1.590 0.950
ENSG00000056558 E010 5.5504840 0.0025192319 1.593045e-11 1.751252e-09 9 120926550 120926688 139 - 0.257 1.109 3.872
ENSG00000056558 E011 73.5909413 0.0026729518 5.413447e-110 4.866148e-106 9 120926689 120928906 2218 - 1.132 2.192 3.624
ENSG00000056558 E012 0.1272623 0.0123377213 3.946797e-01   9 120929114 120929173 60 - 0.000 0.113 10.410

Help

Please Click HERE to learn more details about the results from DEXseq.