ENSMUSG00000030199

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
ENSMUST00000081028 ENSMUSG00000030199 Control shVgll3 Etv6 protein_coding protein_coding 3.559538 3.109036 4.01004 0.4150729 0.07672611 0.3661097 1.1059253 1.4093691 0.8024815 0.2317975 0.2472823 -0.8048430 0.3412167 0.4807667 0.2016667 -0.2791000 6.276107e-01 3.404299e-15 FALSE TRUE
ENSMUST00000111963 ENSMUSG00000030199 Control shVgll3 Etv6 protein_coding protein_coding 3.559538 3.109036 4.01004 0.4150729 0.07672611 0.3661097 1.1944178 0.9895689 1.3992668 0.1774572 0.1319048 0.4955668 0.3325833 0.3164333 0.3487333 0.0323000 9.719459e-01 3.404299e-15 FALSE TRUE
ENSMUST00000145869 ENSMUSG00000030199 Control shVgll3 Etv6 protein_coding protein_coding_CDS_not_defined 3.559538 3.109036 4.01004 0.4150729 0.07672611 0.3661097 0.3550488 0.7100975 0.0000000 0.3999496 0.0000000 -6.1701204 0.1013833 0.2027667 0.0000000 -0.2027667 5.874649e-01 3.404299e-15 FALSE FALSE
ENSMUST00000164648 ENSMUSG00000030199 Control shVgll3 Etv6 protein_coding protein_coding 3.559538 3.109036 4.01004 0.4150729 0.07672611 0.3661097 0.9041457 0.0000000 1.8082913 0.0000000 0.1941798 7.5064396 0.2247833 0.0000000 0.4495667 0.4495667 3.404299e-15 3.404299e-15 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
ENSMUSG00000030199 E001 4.9543630 0.0341527927 0.3269482157 0.86140546 6 134012663 134012931 269 + 0.693 0.843 0.601
ENSMUSG00000030199 E002 10.0181996 0.0034577266 0.6749444462 0.96164256 6 134012932 134013101 170 + 1.021 1.064 0.158
ENSMUSG00000030199 E003 6.9031374 0.0027628920 0.2339814271 0.80378281 6 134043270 134043428 159 + 0.963 0.821 -0.540
ENSMUSG00000030199 E004 3.2854872 0.0056938498 0.3898360564 0.88618387 6 134114248 134114250 3 + 0.693 0.562 -0.569
ENSMUSG00000030199 E005 12.0017889 0.0017213522 0.0037418442 0.11862356 6 134114251 134114380 130 + 1.231 0.951 -1.014
ENSMUSG00000030199 E006 10.6666209 0.0253861944 0.1954528065 0.77082536 6 134199828 134199992 165 + 1.138 0.982 -0.569
ENSMUSG00000030199 E007 0.0000000       6 134210482 134210562 81 +      
ENSMUSG00000030199 E008 0.0000000       6 134210563 134210616 54 +      
ENSMUSG00000030199 E009 0.0000000       6 134224528 134224616 89 +      
ENSMUSG00000030199 E010 52.5043420 0.0003812155 0.0485789933 0.48397308 6 134225237 134225767 531 + 1.770 1.681 -0.302
ENSMUSG00000030199 E011 14.2882174 0.0135583385 0.4237106852 0.90545038 6 134238653 134238795 143 + 1.223 1.143 -0.284
ENSMUSG00000030199 E012 0.1667494 0.0344536256 0.4920305214   6 134238796 134238982 187 + 0.123 0.000 -8.627
ENSMUSG00000030199 E013 12.9765428 0.0060537114 0.8813900953 0.99206209 6 134239982 134240082 101 + 1.139 1.153 0.053
ENSMUSG00000030199 E014 240.0081614 0.0002810633 0.0004646132 0.02704003 6 134243221 134247121 3901 + 2.358 2.405 0.159

Help

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