ENSMUSG00000020359

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
ENSMUST00000020625 ENSMUSG00000020359 Control shVgll3 Phykpl protein_coding protein_coding 11.00259 11.82924 10.17594 0.4227768 0.3484574 -0.2169982 2.7807229 2.1920423 3.3694035 0.2358036 0.27106055 0.6179264 0.25855000 0.18656667 0.33053333 0.143966667 0.06662390 0.01636287 FALSE TRUE
ENSMUST00000101250 ENSMUSG00000020359 Control shVgll3 Phykpl protein_coding nonsense_mediated_decay 11.00259 11.82924 10.17594 0.4227768 0.3484574 -0.2169982 1.1943001 0.7316135 1.6569867 0.4530448 0.35465480 1.1685032 0.11281667 0.06480000 0.16083333 0.096033333 0.94890808 0.01636287 TRUE TRUE
ENSMUST00000109105 ENSMUSG00000020359 Control shVgll3 Phykpl protein_coding retained_intron 11.00259 11.82924 10.17594 0.4227768 0.3484574 -0.2169982 0.7600864 0.7872626 0.7329103 0.1869314 0.11957358 -0.1018670 0.06908333 0.06620000 0.07196667 0.005766667 0.99215139 0.01636287 FALSE TRUE
ENSMUST00000156128 ENSMUSG00000020359 Control shVgll3 Phykpl protein_coding retained_intron 11.00259 11.82924 10.17594 0.4227768 0.3484574 -0.2169982 0.7664040 0.5174448 1.0153632 0.3543583 0.27560489 0.9590431 0.07241667 0.04603333 0.09880000 0.052766667 0.97066567 0.01636287 TRUE TRUE
ENSMUST00000167797 ENSMUSG00000020359 Control shVgll3 Phykpl protein_coding protein_coding 11.00259 11.82924 10.17594 0.4227768 0.3484574 -0.2169982 1.3625309 2.0401733 0.6848884 0.5577324 0.34654419 -1.5608925 0.11940000 0.16953333 0.06926667 -0.100266667 0.97066567 0.01636287 FALSE TRUE
ENSMUST00000169995 ENSMUSG00000020359 Control shVgll3 Phykpl protein_coding retained_intron 11.00259 11.82924 10.17594 0.4227768 0.3484574 -0.2169982 2.9475346 3.8761897 2.0188794 0.2673902 0.04889606 -0.9376732 0.26318333 0.32723333 0.19913333 -0.128100000 0.01636287 0.01636287   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
ENSMUSG00000020359 E001 0.4941990 0.0218026347 0.571093251   11 51475584 51475615 32 + 0.124 0.219 0.996
ENSMUSG00000020359 E002 0.8212826 0.0158116485 0.661776100 0.95817326 11 51475616 51475629 14 + 0.220 0.298 0.582
ENSMUSG00000020359 E003 0.9826360 0.0139514685 0.995286923 1.00000000 11 51475630 51475633 4 + 0.298 0.298 -0.003
ENSMUSG00000020359 E004 1.1493854 0.0132038456 0.704636069 0.96592857 11 51475634 51475637 4 + 0.365 0.298 -0.418
ENSMUSG00000020359 E005 13.9819235 0.0014172524 0.246922245 0.80442163 11 51475638 51475706 69 + 1.120 1.225 0.373
ENSMUSG00000020359 E006 30.6273606 0.0006538582 0.583420483 0.94855494 11 51476341 51476459 119 + 1.482 1.517 0.121
ENSMUSG00000020359 E007 11.2018045 0.0118333054 0.798186056 0.98120854 11 51476460 51477387 928 + 1.098 1.074 -0.088
ENSMUSG00000020359 E008 43.6373099 0.0108589115 0.669677373 0.95991740 11 51477388 51477547 160 + 1.635 1.663 0.094
ENSMUSG00000020359 E009 6.0875861 0.0038104523 0.427633444 0.90616200 11 51477548 51478144 597 + 0.797 0.898 0.389
ENSMUSG00000020359 E010 21.2446201 0.0009536636 0.633371652 0.95643679 11 51482226 51482273 48 + 1.363 1.330 -0.115
ENSMUSG00000020359 E011 14.4784505 0.0013652475 0.083685307 0.60429057 11 51482274 51482300 27 + 1.258 1.108 -0.533
ENSMUSG00000020359 E012 26.1338474 0.0014883312 0.852994024 0.98810194 11 51482833 51482920 88 + 1.426 1.441 0.051
ENSMUSG00000020359 E013 6.7531837 0.0523518867 0.553230609 0.93833430 11 51482921 51482946 26 + 0.841 0.932 0.347
ENSMUSG00000020359 E014 9.2219090 0.0037003383 0.584461712 0.94928229 11 51482947 51482995 49 + 1.037 0.980 -0.210
ENSMUSG00000020359 E015 24.8362862 0.0007351496 0.111350681 0.65453028 11 51482996 51483112 117 + 1.462 1.356 -0.368
ENSMUSG00000020359 E016 12.8385693 0.0030255070 0.975686086 1.00000000 11 51483113 51483739 627 + 1.141 1.140 -0.003
ENSMUSG00000020359 E017 1.8118166 0.0107039828 0.375632537 0.87918156 11 51483740 51483854 115 + 0.365 0.519 0.805
ENSMUSG00000020359 E018 3.1201229 0.0056019005 0.487611812 0.92579672 11 51483855 51484133 279 + 0.665 0.560 -0.462
ENSMUSG00000020359 E019 17.7815523 0.0010995865 0.676303539 0.96164256 11 51484431 51484513 83 + 1.289 1.258 -0.110
ENSMUSG00000020359 E020 19.5901254 0.0010088581 0.955517950 1.00000000 11 51484514 51484742 229 + 1.310 1.316 0.021
ENSMUSG00000020359 E021 43.5676582 0.0015933363 0.485973074 0.92538469 11 51484743 51484968 226 + 1.667 1.631 -0.123
ENSMUSG00000020359 E022 89.3894047 0.0003657361 0.726771133 0.97107356 11 51484969 51487869 2901 + 1.962 1.951 -0.035
ENSMUSG00000020359 E023 36.2085260 0.0005536442 0.067862505 0.56261912 11 51489103 51489257 155 + 1.618 1.517 -0.346
ENSMUSG00000020359 E024 23.6625666 0.0008653065 0.709307621 0.96617147 11 51489478 51489567 90 + 1.404 1.380 -0.083
ENSMUSG00000020359 E025 23.5025837 0.0008009819 0.002094289 0.08141262 11 51490094 51490292 199 + 1.266 1.486 0.761
ENSMUSG00000020359 E026 37.5170557 0.0005129383 0.959500862 1.00000000 11 51490293 51490423 131 + 1.586 1.585 -0.003
ENSMUSG00000020359 E027 0.0000000       11 51491396 51491449 54 +      
ENSMUSG00000020359 E028 0.0000000       11 51491450 51491894 445 +      
ENSMUSG00000020359 E029 0.0000000       11 51491936 51492155 220 +      
ENSMUSG00000020359 E030 91.5381676 0.0025090772 0.284623332 0.83154939 11 51493622 51495316 1695 + 1.944 1.988 0.148

Help

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