ENSMUSG00000040195

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
ENSMUST00000048099 ENSMUSG00000040195 Control shVgll3 Nemp1 protein_coding protein_coding 5.850839 5.854977 5.8467 0.3583567 0.1450988 -0.002037352 2.0887141 1.9174428 2.2599854 0.29228439 0.51887843 0.23599499 0.35863333 0.33450000 0.38276667 0.0482666667 0.97774312 0.01001426 FALSE TRUE
ENSMUST00000118612 ENSMUSG00000040195 Control shVgll3 Nemp1 protein_coding protein_coding 5.850839 5.854977 5.8467 0.3583567 0.1450988 -0.002037352 0.6354921 0.6300772 0.6409069 0.05986271 0.15915067 0.02420537 0.10843333 0.10816667 0.10870000 0.0005333333 1.00000000 0.01001426 FALSE TRUE
ENSMUST00000124388 ENSMUSG00000040195 Control shVgll3 Nemp1 protein_coding protein_coding_CDS_not_defined 5.850839 5.854977 5.8467 0.3583567 0.1450988 -0.002037352 1.1528930 1.5930552 0.7127307 0.18362274 0.05554227 -1.14929404 0.19593333 0.27023333 0.12163333 -0.1486000000 0.01001426 0.01001426   FALSE
ENSMUST00000133505 ENSMUSG00000040195 Control shVgll3 Nemp1 protein_coding protein_coding_CDS_not_defined 5.850839 5.854977 5.8467 0.3583567 0.1450988 -0.002037352 0.6748786 0.4601490 0.8896082 0.06949156 0.28888880 0.93617872 0.11568333 0.07956667 0.15180000 0.0722333333 0.86970110 0.01001426   FALSE
MSTRG.2952.5 ENSMUSG00000040195 Control shVgll3 Nemp1 protein_coding   5.850839 5.854977 5.8467 0.3583567 0.1450988 -0.002037352 0.6716379 0.7863619 0.5569138 0.15224362 0.17451329 -0.49029494 0.11428333 0.13243333 0.09613333 -0.0363000000 0.97066567 0.01001426   FALSE
MSTRG.2952.6 ENSMUSG00000040195 Control shVgll3 Nemp1 protein_coding   5.850839 5.854977 5.8467 0.3583567 0.1450988 -0.002037352 0.4273477 0.3953888 0.4593066 0.39538884 0.45930660 0.21122437 0.07193333 0.06166667 0.08220000 0.0205333333 1.00000000 0.01001426 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
ENSMUSG00000040195 E001 5.7579954 0.0032471025 0.63381361 0.95646045 10 127502770 127502987 218 + 0.853 0.792 -0.237
ENSMUSG00000040195 E002 0.8210898 0.0169014139 0.85844300 0.98884244 10 127502992 127503012 21 + 0.273 0.241 -0.236
ENSMUSG00000040195 E003 0.6597364 0.0181561198 0.81207370   10 127503013 127503034 22 + 0.200 0.241 0.348
ENSMUSG00000040195 E004 6.5718425 0.0028498830 0.00104298 0.04971953 10 127503035 127503252 218 + 0.653 1.057 1.571
ENSMUSG00000040195 E005 4.2693154 0.0042520728 0.57199374 0.94460955 10 127503549 127503733 185 + 0.753 0.673 -0.330
ENSMUSG00000040195 E006 0.0000000       10 127504287 127504294 8 +      
ENSMUSG00000040195 E007 6.0945646 0.0035269323 0.37884108 0.88000058 10 127504295 127504720 426 + 0.796 0.906 0.426
ENSMUSG00000040195 E008 1.1536288 0.0133984214 0.95153903 1.00000000 10 127512509 127512669 161 + 0.336 0.325 -0.067
ENSMUSG00000040195 E009 0.4938330 0.0218213081 0.71382280   10 127512670 127512697 28 + 0.200 0.137 -0.652
ENSMUSG00000040195 E010 0.0000000       10 127512933 127512934 2 +      
ENSMUSG00000040195 E011 5.2407680 0.0481293934 0.25959411 0.81353043 10 127512935 127513096 162 + 0.706 0.885 0.711
ENSMUSG00000040195 E012 0.3328359 0.0261942790 0.27184522   10 127514803 127515004 202 + 0.200 0.000 -9.532
ENSMUSG00000040195 E013 10.2037628 0.0170009127 0.29229503 0.83781095 10 127524102 127524217 116 + 0.989 1.110 0.441
ENSMUSG00000040195 E014 24.1637301 0.0008200376 0.64912448 0.95668705 10 127525094 127525313 220 + 1.411 1.381 -0.107
ENSMUSG00000040195 E015 10.0476728 0.0018799922 0.63465833 0.95663250 10 127526730 127526802 73 + 1.061 1.012 -0.178
ENSMUSG00000040195 E016 10.3579412 0.0020051371 0.49163643 0.92674629 10 127528837 127528930 94 + 1.082 1.012 -0.256
ENSMUSG00000040195 E017 11.8353801 0.0068209245 0.29544140 0.83838005 10 127529353 127529467 115 + 1.150 1.042 -0.389
ENSMUSG00000040195 E018 23.3394759 0.0010052034 0.26709511 0.81669065 10 127530298 127530523 226 + 1.416 1.338 -0.271
ENSMUSG00000040195 E019 7.3979727 0.0025936476 0.12491940 0.67653109 10 127530524 127531037 514 + 0.835 1.012 0.670
ENSMUSG00000040195 E020 13.8262564 0.0047723322 0.39544468 0.88763883 10 127531238 127531411 174 + 1.201 1.122 -0.280
ENSMUSG00000040195 E021 355.7032072 0.0002580890 0.97942722 1.00000000 10 127532097 127536918 4822 + 2.549 2.549 0.001

Help

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