ENSG00000122140

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
ENST00000241600 ENSG00000122140 No_inf pgKDN_inf MRPS2 protein_coding protein_coding 27.25551 22.7968 28.45497 0.4822049 0.7411963 0.3197235 22.9359258 16.731367 26.306478 1.9791143 0.7743363 0.6525491 0.83435000 0.734025 0.926450 0.192425 0.17549974 0.02944595 FALSE  
ENST00000453385 ENSG00000122140 No_inf pgKDN_inf MRPS2 protein_coding retained_intron 27.25551 22.7968 28.45497 0.4822049 0.7411963 0.3197235 0.6664010 1.999203 0.000000 0.6784668 0.0000000 -7.6504795 0.02885000 0.086550 0.000000 -0.086550 0.02944595 0.02944595 FALSE  
ENST00000485333 ENSG00000122140 No_inf pgKDN_inf MRPS2 protein_coding nonsense_mediated_decay 27.25551 22.7968 28.45497 0.4822049 0.7411963 0.3197235 0.8425185 1.812947 0.198681 0.9484353 0.1986810 -3.1269016 0.03483333 0.081125 0.006825 -0.074300 0.44719384 0.02944595 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 pgKDN.inf No.inf log2fold_No.inf_pgKDN.inf
ENSG00000122140 E001 0.0000000       9 135499984 135500051 68 +      
ENSG00000122140 E002 0.0000000       9 135500570 135500630 61 +      
ENSG00000122140 E003 0.3627784 0.0167312609 6.400334e-01   9 135500631 135500681 51 + 0.164 0.101 -0.816
ENSG00000122140 E004 6.8972595 0.0022748712 5.093911e-02 0.223325459 9 135500682 135500753 72 + 0.978 0.794 -0.704
ENSG00000122140 E005 0.5085150 0.0158658557 3.636430e-02 0.183262207 9 135500913 135500997 85 + 0.000 0.310 13.109
ENSG00000122140 E006 18.5242079 0.0010937792 4.332177e-01 0.710705866 9 135500998 135501123 126 + 1.307 1.273 -0.121
ENSG00000122140 E007 0.6351783 0.0219862186 1.621795e-02 0.110665367 9 135501124 135501326 203 + 0.000 0.363 13.370
ENSG00000122140 E008 0.2441403 0.0163273698 9.444047e-01   9 135501699 135501843 145 + 0.090 0.101 0.184
ENSG00000122140 E009 14.0243062 0.0010556928 4.445433e-01 0.719103729 9 135501844 135501973 130 + 1.196 1.155 -0.144
ENSG00000122140 E010 1.3509746 0.0110529932 6.555620e-01 0.855585790 9 135502069 135502266 198 + 0.332 0.409 0.447
ENSG00000122140 E011 0.9984270 0.0115958564 1.191320e-01 0.364781841 9 135502574 135502637 64 + 0.164 0.409 1.769
ENSG00000122140 E012 1.5230883 0.0136494677 6.780727e-05 0.001710532 9 135503136 135503278 143 + 0.000 0.616 14.452
ENSG00000122140 E013 91.3554519 0.0004127505 7.809610e-01 0.915659751 9 135503542 135504673 1132 + 1.955 1.976 0.072

Help

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