ENSMUSG00000028412

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
ENSMUST00000102911 ENSMUSG00000028412 Control shVgll3 Slc44a1 protein_coding protein_coding 46.23193 44.83298 47.63089 0.5312804 0.318167 0.08731824 16.92273 14.60621 19.23926 0.03331438 0.5078744 0.39723371 0.3649000 0.3259000 0.4039000 0.0780 0.02346993 0.02346993 FALSE  
ENSMUST00000107651 ENSMUSG00000028412 Control shVgll3 Slc44a1 protein_coding protein_coding 46.23193 44.83298 47.63089 0.5312804 0.318167 0.08731824 26.96230 27.12658 26.79801 0.49536197 1.1161572 -0.01757453 0.5839167 0.6054667 0.5623667 -0.0431 0.97066567 0.02346993 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
ENSMUSG00000028412 E001 149.3842596 0.0015444811 5.308261e-01 9.357450e-01 4 53440413 53440670 258 + 2.179 2.173 -0.022
ENSMUSG00000028412 E002 70.5507811 0.0037899731 2.102221e-01 7.828663e-01 4 53440671 53440683 13 + 1.876 1.827 -0.165
ENSMUSG00000028412 E003 98.8217510 0.0111151077 4.351191e-01 9.092574e-01 4 53440684 53440716 33 + 2.012 1.982 -0.102
ENSMUSG00000028412 E004 131.1976542 0.0056310237 9.842280e-01 1.000000e+00 4 53481464 53481553 90 + 2.114 2.127 0.044
ENSMUSG00000028412 E005 183.5923604 0.0001603820 3.597657e-01 8.751770e-01 4 53491388 53491530 143 + 2.269 2.260 -0.032
ENSMUSG00000028412 E006 142.2447742 0.0001797806 2.729048e-01 8.189943e-01 4 53517545 53517681 137 + 2.163 2.145 -0.061
ENSMUSG00000028412 E007 129.8332196 0.0001916475 9.517909e-02 6.302892e-01 4 53528655 53528748 94 + 2.133 2.095 -0.126
ENSMUSG00000028412 E008 0.4938330 0.0225717846 6.276865e-01   4 53535612 53536322 711 + 0.208 0.131 -0.806
ENSMUSG00000028412 E009 161.1748290 0.0002289447 4.784470e-01 9.232691e-01 4 53536323 53536492 170 + 2.212 2.206 -0.019
ENSMUSG00000028412 E010 98.7240216 0.0002263977 9.428560e-01 9.998994e-01 4 53538390 53538479 90 + 1.992 2.004 0.040
ENSMUSG00000028412 E011 144.9732996 0.0001634833 3.729359e-01 8.781154e-01 4 53541301 53541440 140 + 2.169 2.157 -0.039
ENSMUSG00000028412 E012 142.1702416 0.0001744695 7.479012e-01 9.742705e-01 4 53542365 53542551 187 + 2.143 2.167 0.080
ENSMUSG00000028412 E013 235.4348022 0.0001265904 4.221310e-02 4.609233e-01 4 53543542 53543707 166 + 2.388 2.355 -0.108
ENSMUSG00000028412 E014 348.8197051 0.0001127678 1.153864e-01 6.614480e-01 4 53544541 53544697 157 + 2.550 2.535 -0.050
ENSMUSG00000028412 E015 206.5269177 0.0001362939 5.048591e-01 9.290615e-01 4 53545685 53545768 84 + 2.317 2.315 -0.006
ENSMUSG00000028412 E016 0.8266690 0.0161724968 2.071333e-01 7.820062e-01 4 53549989 53550200 212 + 0.348 0.131 -1.806
ENSMUSG00000028412 E017 155.1011254 0.0001696006 8.327600e-01 9.854840e-01 4 53553486 53553623 138 + 2.188 2.197 0.028
ENSMUSG00000028412 E018 210.7307823 0.0001413296 5.701721e-01 9.438727e-01 4 53560915 53561151 237 + 2.325 2.325 0.002
ENSMUSG00000028412 E019 0.0000000       4 53563141 53563221 81 +      
ENSMUSG00000028412 E020 0.0000000       4 53563222 53563450 229 +      
ENSMUSG00000028412 E021 1884.1731120 0.0007791136 1.228898e-06 1.711386e-04 4 53565397 53567818 2422 + 3.242 3.308 0.219
ENSMUSG00000028412 E022 0.1615462 0.0342486173 4.436690e-01   4 53596105 53596373 269 + 0.000 0.131 8.969
ENSMUSG00000028412 E023 359.6770085 0.0001290796 3.563746e-07 6.130692e-05 4 53621595 53622478 884 + 2.592 2.511 -0.269

Help

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