ENSMUSG00000034387

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
ENSMUST00000060847 ENSMUSG00000034387 Control shVgll3 Ssu2 protein_coding protein_coding 2.188269 2.447325 1.929214 0.2371088 0.2141792 -0.3416166 0.1080243 0.04690634 0.1691422 0.02809348 0.04143932 1.6544444 0.05713333 0.01996667 0.09430000 0.07433333 0.602581397 0.006442427 FALSE TRUE
ENSMUST00000123254 ENSMUSG00000034387 Control shVgll3 Ssu2 protein_coding retained_intron 2.188269 2.447325 1.929214 0.2371088 0.2141792 -0.3416166 0.6285305 0.58343652 0.6736244 0.29777142 0.07865893 0.2041103 0.31130000 0.26423333 0.35836667 0.09413333 0.970665669 0.006442427 FALSE FALSE
ENSMUST00000143134 ENSMUSG00000034387 Control shVgll3 Ssu2 protein_coding protein_coding_CDS_not_defined 2.188269 2.447325 1.929214 0.2371088 0.2141792 -0.3416166 0.4978689 0.82801407 0.1677238 0.04164644 0.03315773 -2.2373378 0.21583333 0.34393333 0.08773333 -0.25620000 0.006442427 0.006442427 FALSE FALSE
MSTRG.19635.2 ENSMUSG00000034387 Control shVgll3 Ssu2 protein_coding   2.188269 2.447325 1.929214 0.2371088 0.2141792 -0.3416166 0.9538456 0.98896781 0.9187234 0.49990536 0.25020180 -0.1051891 0.41573333 0.37186667 0.45960000 0.08773333 0.970665669 0.006442427 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.

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
ENSMUSG00000034387 E001 0.6653156 0.021822096 0.1390157129   6 112336285 112336313 29 - 0.357 0.099 -2.321
ENSMUSG00000034387 E002 5.4056595 0.004908826 0.0001557053 0.01103903 6 112336314 112336597 284 - 1.032 0.550 -1.937
ENSMUSG00000034387 E003 1.6420952 0.009736287 0.5833927014 0.94855494 6 112337681 112337779 99 - 0.357 0.445 0.487
ENSMUSG00000034387 E004 6.5919658 0.023034854 0.0859928210 0.61178330 6 112345701 112346235 535 - 0.720 0.937 0.851
ENSMUSG00000034387 E005 6.7196145 0.003234112 0.1041043348 0.64156759 6 112346236 112346620 385 - 0.754 0.937 0.712
ENSMUSG00000034387 E006 8.7207943 0.004321007 0.8303415200 0.98548395 6 112346621 112346803 183 - 0.996 0.962 -0.128
ENSMUSG00000034387 E007 10.6870592 0.002102212 0.9759931754 1.00000000 6 112351740 112351847 108 - 1.065 1.049 -0.057
ENSMUSG00000034387 E008 8.7027702 0.002503144 0.1851344850 0.76205979 6 112352514 112352619 106 - 0.892 1.019 0.474
ENSMUSG00000034387 E009 2.1401716 0.008394923 0.9884238884 1.00000000 6 112352620 112352681 62 - 0.495 0.483 -0.057
ENSMUSG00000034387 E010 0.4995853 0.025930447 0.0321677785   6 112353353 112353445 93 - 0.357 0.000 -11.450
ENSMUSG00000034387 E011 0.1667494 0.035657044 0.3068728696   6 112354546 112354631 86 - 0.154 0.000 -9.865
ENSMUSG00000034387 E012 0.0000000       6 112354632 112354688 57 -      
ENSMUSG00000034387 E013 0.0000000       6 112356193 112356255 63 -      
ENSMUSG00000034387 E014 0.0000000       6 112357511 112357635 125 -      
ENSMUSG00000034387 E015 0.0000000       6 112357939 112357999 61 -      
ENSMUSG00000034387 E016 0.0000000       6 112359277 112359406 130 -      
ENSMUSG00000034387 E017 0.0000000       6 112359407 112359409 3 -      
ENSMUSG00000034387 E018 0.0000000       6 112360847 112360928 82 -      
ENSMUSG00000034387 E019 0.0000000       6 112361328 112361426 99 -      
ENSMUSG00000034387 E020 0.0000000       6 112364933 112364984 52 -      

Help

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