ENSG00000129038

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
ENST00000261921 ENSG00000129038 HEK293_OSMI2_2hA HEK293_TMG_2hB LOXL1 protein_coding protein_coding 9.087249 18.45995 4.638366 0.7523845 0.5317937 -1.990385 3.619609 5.617989 2.6407154 0.6849510 0.06721381 -1.086238 0.4476083 0.3035333 0.5887333 0.2852 0.03480728 0.03480728 FALSE TRUE
ENST00000566530 ENSG00000129038 HEK293_OSMI2_2hA HEK293_TMG_2hB LOXL1 protein_coding retained_intron 9.087249 18.45995 4.638366 0.7523845 0.5317937 -1.990385 1.749665 3.931831 0.6583989 0.7304120 0.65839886 -2.560085 0.1777667 0.2110667 0.1220667 -0.0890 0.26546115 0.03480728 FALSE FALSE
MSTRG.11193.3 ENSG00000129038 HEK293_OSMI2_2hA HEK293_TMG_2hB LOXL1 protein_coding   9.087249 18.45995 4.638366 0.7523845 0.5317937 -1.990385 3.435530 8.754609 1.2856626 0.3599609 0.41641268 -2.758000 0.3411417 0.4768333 0.2787333 -0.1981 0.18799248 0.03480728 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
ENSG00000129038 E001 0.1515154 0.0421816444 1.245108e-01   15 73925989 73926461 473 + 0.213 0.000 -12.046
ENSG00000129038 E002 138.5214543 0.0111252671 4.089464e-05 0.0002352035 15 73926462 73927841 1380 + 2.209 1.976 -0.780
ENSG00000129038 E003 24.7945815 0.0008835798 9.188437e-03 0.0267555563 15 73927842 73927885 44 + 1.479 1.257 -0.769
ENSG00000129038 E004 1.9164593 0.0076347945 2.640119e-01 0.4019565476 15 73941875 73942058 184 + 0.213 0.427 1.404
ENSG00000129038 E005 56.6717632 0.0007334859 7.398600e-01 0.8294577292 15 73942854 73942962 109 + 1.650 1.645 -0.015
ENSG00000129038 E006 0.3697384 0.0274424043 9.337996e-01 0.9622693834 15 73946368 73946416 49 + 0.000 0.125 8.939
ENSG00000129038 E007 72.6979365 0.0005833447 9.644140e-01 0.9815888598 15 73946417 73946554 138 + 1.768 1.746 -0.072
ENSG00000129038 E008 110.3187877 0.0003165603 1.785291e-01 0.2993079693 15 73947067 73947215 149 + 1.903 1.934 0.103
ENSG00000129038 E009 52.7253784 0.0008124588 7.079837e-01 0.8057275396 15 73947216 73947223 8 + 1.611 1.610 -0.004
ENSG00000129038 E010 1.7735534 0.0103016641 2.035870e-01 0.3307033535 15 73947224 73947806 583 + 0.548 0.302 -1.330
ENSG00000129038 E011 55.1919758 0.0004743719 7.472195e-01 0.8347741671 15 73947807 73947827 21 + 1.637 1.632 -0.017
ENSG00000129038 E012 93.7872324 0.0003752218 9.502664e-02 0.1829151693 15 73947828 73947902 75 + 1.821 1.871 0.171
ENSG00000129038 E013 90.2762443 0.0040276053 8.280339e-02 0.1639365383 15 73949459 73949537 79 + 1.790 1.861 0.237
ENSG00000129038 E014 73.9516258 0.0003901434 1.323987e-01 0.2374205887 15 73949538 73949574 37 + 1.718 1.770 0.177
ENSG00000129038 E015 0.6265839 0.0619443101 3.743323e-01 0.5187567835 15 73949575 73949575 1 + 0.000 0.221 9.925
ENSG00000129038 E016 108.7689787 0.0003673941 9.953992e-03 0.0286471184 15 73951831 73952137 307 + 1.856 1.941 0.283