ENSMUSG00000028614

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
ENSMUST00000030357 ENSMUSG00000028614 Control shVgll3 Ndc1 protein_coding nonsense_mediated_decay 9.35377 6.494358 12.21318 0.1571718 0.4481723 0.9101412 0.4389361 0.8778722 0.000000 0.4645313 0.0000000 -6.4722801 0.06918333 0.1383667 0.00000000 -0.13836667 5.868898e-01 4.739386e-09 FALSE TRUE
ENSMUST00000125342 ENSMUSG00000028614 Control shVgll3 Ndc1 protein_coding nonsense_mediated_decay 9.35377 6.494358 12.21318 0.1571718 0.4481723 0.9101412 0.9837937 0.0000000 1.967587 0.0000000 0.2897564 7.6275977 0.08118333 0.0000000 0.16236667 0.16236667 4.739386e-09 4.739386e-09 FALSE FALSE
ENSMUST00000132950 ENSMUSG00000028614 Control shVgll3 Ndc1 protein_coding retained_intron 9.35377 6.494358 12.21318 0.1571718 0.4481723 0.9101412 2.2534920 1.3073112 3.199673 0.2855115 0.8414390 1.2848300 0.22871667 0.1995000 0.25793333 0.05843333 9.706657e-01 4.739386e-09 FALSE FALSE
ENSMUST00000139560 ENSMUSG00000028614 Control shVgll3 Ndc1 protein_coding protein_coding 9.35377 6.494358 12.21318 0.1571718 0.4481723 0.9101412 4.4138509 2.9498272 5.877875 0.6595699 0.6594358 0.9922340 0.46953333 0.4563333 0.48273333 0.02640000 1.000000e+00 4.739386e-09 FALSE TRUE
ENSMUST00000149366 ENSMUSG00000028614 Control shVgll3 Ndc1 protein_coding nonsense_mediated_decay 9.35377 6.494358 12.21318 0.1571718 0.4481723 0.9101412 1.2636971 1.3593476 1.168047 0.6908586 0.5940137 -0.2170922 0.15138333 0.2058000 0.09696667 -0.10883333 9.803959e-01 4.739386e-09 TRUE 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
ENSMUSG00000028614 E001 0.3272567 0.0283837654 0.7583150511   4 107224981 107225076 96 + 0.102 0.149 0.625
ENSMUSG00000028614 E002 0.3272567 0.0283837654 0.7583150511   4 107225077 107225111 35 + 0.102 0.149 0.625
ENSMUSG00000028614 E003 3.9546995 0.0045398617 0.3111374128 0.84979533 4 107225112 107225248 137 + 0.621 0.771 0.625
ENSMUSG00000028614 E004 15.9427428 0.0012020796 0.7697802056 0.97799068 4 107225249 107225345 97 + 1.228 1.207 -0.072
ENSMUSG00000028614 E005 28.6235216 0.0006625384 0.5431249777 0.93688185 4 107225954 107226074 121 + 1.475 1.440 -0.121
ENSMUSG00000028614 E006 27.3216002 0.0007832212 0.7798896422 0.97903220 4 107228459 107228560 102 + 1.448 1.434 -0.047
ENSMUSG00000028614 E007 42.1476918 0.0004370656 0.0615671686 0.53908139 4 107231344 107231518 175 + 1.661 1.563 -0.333
ENSMUSG00000028614 E008 35.0529356 0.0005795013 0.6365234125 0.95668705 4 107232275 107232413 139 + 1.556 1.533 -0.079
ENSMUSG00000028614 E009 25.0021079 0.0011097644 0.1739150434 0.75582537 4 107237795 107237903 109 + 1.439 1.347 -0.318
ENSMUSG00000028614 E010 0.0000000       4 107238282 107238407 126 +      
ENSMUSG00000028614 E011 0.3276328 0.0279425846 0.7594032593   4 107238659 107238872 214 + 0.102 0.149 0.625
ENSMUSG00000028614 E012 16.9530163 0.0016211029 0.5753410713 0.94604067 4 107238873 107238924 52 + 1.261 1.218 -0.149
ENSMUSG00000028614 E013 35.5691576 0.0005729754 0.4367367828 0.91079676 4 107240782 107240917 136 + 1.569 1.528 -0.140
ENSMUSG00000028614 E014 36.2581723 0.0083239525 0.7122492759 0.96812431 4 107241983 107242075 93 + 1.569 1.548 -0.070
ENSMUSG00000028614 E015 31.6345777 0.0008607043 0.4565429373 0.91464965 4 107243793 107243874 82 + 1.519 1.477 -0.144
ENSMUSG00000028614 E016 53.7790925 0.0032812828 0.2861148680 0.83288058 4 107246648 107246803 156 + 1.749 1.696 -0.180
ENSMUSG00000028614 E017 86.1008820 0.0006421302 0.6455745948 0.95668705 4 107247419 107247658 240 + 1.935 1.922 -0.043
ENSMUSG00000028614 E018 18.4177278 0.0083286972 0.3386905084 0.86809850 4 107247746 107247802 57 + 1.241 1.331 0.314
ENSMUSG00000028614 E019 18.5554917 0.0071877650 0.6259622282 0.95514198 4 107247803 107247861 59 + 1.297 1.259 -0.133
ENSMUSG00000028614 E020 19.3693672 0.0358624876 0.4031614001 0.89211465 4 107250340 107250390 51 + 1.335 1.239 -0.339
ENSMUSG00000028614 E021 28.4068941 0.0133881718 0.7881535396 0.98020403 4 107252195 107252258 64 + 1.467 1.447 -0.071
ENSMUSG00000028614 E022 47.6834498 0.0019569062 0.1748231171 0.75671639 4 107252929 107253029 101 + 1.704 1.634 -0.235
ENSMUSG00000028614 E023 58.1025682 0.0004003886 0.7262798051 0.97107356 4 107268263 107268423 161 + 1.753 1.774 0.071
ENSMUSG00000028614 E024 319.8801295 0.0011638334 0.0003001618 0.01918739 4 107271223 107273543 2321 + 2.465 2.540 0.253

Help

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