ENSG00000006007

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
ENST00000353258 ENSG00000006007 HEK293_OSMI2_2hA HEK293_TMG_2hB GDE1 protein_coding protein_coding 49.98329 38.09055 58.35055 6.655409 0.8554866 0.6151817 30.389498 24.575203 34.795751 3.8923933 0.9722343 0.50153542 0.6126083 0.6488667 0.5968333 -0.05203333 0.39640548 0.03439595 FALSE TRUE
ENST00000563645 ENSG00000006007 HEK293_OSMI2_2hA HEK293_TMG_2hB GDE1 protein_coding retained_intron 49.98329 38.09055 58.35055 6.655409 0.8554866 0.6151817 9.813570 8.700357 8.818701 2.9074919 1.3409291 0.01946925 0.2045292 0.2176333 0.1507333 -0.06690000 0.39285429 0.03439595 FALSE TRUE
ENST00000564172 ENSG00000006007 HEK293_OSMI2_2hA HEK293_TMG_2hB GDE1 protein_coding nonsense_mediated_decay 49.98329 38.09055 58.35055 6.655409 0.8554866 0.6151817 9.638804 4.717217 14.642943 0.7135686 0.4169606 1.63212755 0.1801667 0.1310667 0.2508333 0.11976667 0.03439595 0.03439595 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
ENSG00000006007 E001 498.6409710 0.0030254530 7.111019e-06 4.888458e-05 16 19501693 19502382 690 - 2.634 2.769 0.449
ENSG00000006007 E002 771.2137676 0.0001478800 1.473654e-06 1.180512e-05 16 19502383 19503100 718 - 2.861 2.927 0.220
ENSG00000006007 E003 907.1479897 0.0002219821 1.062597e-02 3.027564e-02 16 19503101 19503617 517 - 2.946 2.983 0.120
ENSG00000006007 E004 3.8040076 0.0057921489 4.745746e-01 6.133921e-01 16 19503861 19504880 1020 - 0.637 0.746 0.457
ENSG00000006007 E005 531.9678018 0.0001601913 7.703431e-01 8.516756e-01 16 19504881 19505092 212 - 2.731 2.732 0.006
ENSG00000006007 E006 0.6717251 0.0191552500 4.813982e-01 6.196247e-01 16 19505093 19505132 40 - 0.263 0.141 -1.125
ENSG00000006007 E007 0.5921286 0.1610566069 2.832413e-01 4.233302e-01 16 19507655 19507684 30 - 0.106 0.326 2.008
ENSG00000006007 E008 0.5921286 0.1610566069 2.832413e-01 4.233302e-01 16 19507685 19507686 2 - 0.106 0.326 2.008
ENSG00000006007 E009 355.7983129 0.0008343098 3.967729e-02 9.042699e-02 16 19507687 19507779 93 - 2.576 2.532 -0.145
ENSG00000006007 E010 360.6390304 0.0002112511 1.010400e-04 5.267107e-04 16 19510839 19510944 106 - 2.593 2.525 -0.226
ENSG00000006007 E011 422.3694669 0.0005978258 1.810626e-10 3.056653e-09 16 19517014 19517185 172 - 2.684 2.561 -0.409
ENSG00000006007 E012 128.6212388 0.0033930685 7.289436e-05 3.940989e-04 16 19517186 19517189 4 - 2.186 2.018 -0.562
ENSG00000006007 E013 0.4772466 0.0220398829 4.070918e-01 5.507006e-01 16 19521223 19521703 481 - 0.106 0.246 1.457
ENSG00000006007 E014 392.2241067 0.0026934763 3.959212e-02 9.027741e-02 16 19521704 19522123 420 - 2.625 2.562 -0.210