ENSMUSG00000047539

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
ENSMUST00000051431 ENSMUSG00000047539 Control shVgll3 Fbxo28 protein_coding protein_coding 9.897523 9.717928 10.07712 0.4717749 0.07585684 0.05230949 3.6690320 4.6292906 2.7087734 0.2498444 0.09389456 -0.7709483 0.37356667 0.47840000 0.2687333 -0.20966667 0.001846508 0.001846508 FALSE TRUE
ENSMUST00000192544 ENSMUSG00000047539 Control shVgll3 Fbxo28 protein_coding nonsense_mediated_decay 9.897523 9.717928 10.07712 0.4717749 0.07585684 0.05230949 3.3220237 2.8608420 3.7832054 0.1821144 0.19629798 0.4019435 0.33541667 0.29506667 0.3757667 0.08070000 0.638667544 0.001846508 FALSE TRUE
ENSMUST00000193700 ENSMUSG00000047539 Control shVgll3 Fbxo28 protein_coding retained_intron 9.897523 9.717928 10.07712 0.4717749 0.07585684 0.05230949 1.5362515 1.2773055 1.7951975 0.2829058 0.23621748 0.4878022 0.15603333 0.13423333 0.1778333 0.04360000 0.970665669 0.001846508 FALSE FALSE
ENSMUST00000194213 ENSMUSG00000047539 Control shVgll3 Fbxo28 protein_coding nonsense_mediated_decay 9.897523 9.717928 10.07712 0.4717749 0.07585684 0.05230949 0.8208066 0.2455559 1.3960573 0.2455559 0.38581077 2.4599446 0.08255000 0.02606667 0.1390333 0.11296667 0.597387777 0.001846508 TRUE TRUE
ENSMUST00000195061 ENSMUSG00000047539 Control shVgll3 Fbxo28 protein_coding nonsense_mediated_decay 9.897523 9.717928 10.07712 0.4717749 0.07585684 0.05230949 0.5494088 0.7049340 0.3938837 0.7049340 0.39388366 -0.8238702 0.05246667 0.06623333 0.0387000 -0.02753333 1.000000000 0.001846508 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 shVgll3 Control log2fold_Control_shVgll3
ENSMUSG00000047539 E001 176.106657 0.0018721059 3.637637e-09 9.456241e-07 1 182140667 182142752 2086 - 2.138 2.320 0.607
ENSMUSG00000047539 E002 200.516695 0.0001950400 2.249960e-01 7.984698e-01 1 182142753 182144027 1275 - 2.284 2.318 0.112
ENSMUSG00000047539 E003 119.826220 0.0007729671 6.930753e-02 5.662654e-01 1 182144028 182144555 528 - 2.107 2.056 -0.171
ENSMUSG00000047539 E004 97.264444 0.0002634960 5.952687e-04 3.269227e-02 1 182144556 182144808 253 - 2.047 1.937 -0.369
ENSMUSG00000047539 E005 28.987387 0.0146357710 3.163937e-01 8.526612e-01 1 182144809 182144850 42 - 1.515 1.438 -0.265
ENSMUSG00000047539 E006 43.899650 0.0005027773 4.019620e-01 8.921147e-01 1 182145375 182145501 127 - 1.671 1.634 -0.126
ENSMUSG00000047539 E007 14.813143 0.0013078996 6.031262e-01 9.530216e-01 1 182145502 182145523 22 - 1.218 1.179 -0.138
ENSMUSG00000047539 E008 20.865803 0.0032206924 9.777771e-02 6.331714e-01 1 182145524 182145570 47 - 1.401 1.279 -0.425
ENSMUSG00000047539 E009 4.102106 0.0044701594 7.685243e-01 9.779907e-01 1 182145571 182145952 382 - 0.727 0.690 -0.151
ENSMUSG00000047539 E010 32.688784 0.0010078158 6.316712e-03 1.671785e-01 1 182153819 182153957 139 - 1.606 1.447 -0.543
ENSMUSG00000047539 E011 32.409499 0.0048180023 4.276774e-01 9.061620e-01 1 182157439 182157548 110 - 1.548 1.500 -0.164
ENSMUSG00000047539 E012 47.382435 0.0091041369 6.719251e-01 9.611150e-01 1 182168888 182169194 307 - 1.693 1.674 -0.065

Help

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