ENSG00000114904

1 Isoform Switch

Summary Plot

Only the isoforms with fraction > 5% are shown below.

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
ENST00000233027 ENSG00000114904 HEK293_OSMI2_6hA HEK293_TMG_6hB NEK4 protein_coding protein_coding 23.15215 8.587109 41.46431 0.6929759 1.709946 2.270295 4.2386890 3.0625435 4.687399 0.70837091 0.7100594 0.6124288 0.29080833 0.3479333 0.1141333 -0.23380000 1.094551e-02 8.187325e-08 FALSE TRUE
ENST00000493199 ENSG00000114904 HEK293_OSMI2_6hA HEK293_TMG_6hB NEK4 protein_coding retained_intron 23.15215 8.587109 41.46431 0.6929759 1.709946 2.270295 2.8797545 0.7578037 5.940911 0.27197291 1.4797103 2.9543011 0.12762500 0.0932000 0.1416333 0.04843333 7.818211e-01 8.187325e-08 FALSE FALSE
ENST00000535191 ENSG00000114904 HEK293_OSMI2_6hA HEK293_TMG_6hB NEK4 protein_coding protein_coding 23.15215 8.587109 41.46431 0.6929759 1.709946 2.270295 4.1800440 0.7759095 8.309510 0.56060677 0.3714639 3.4040633 0.12749583 0.0896000 0.2003667 0.11076667 6.270422e-01 8.187325e-08 FALSE TRUE
MSTRG.23066.2 ENSG00000114904 HEK293_OSMI2_6hA HEK293_TMG_6hB NEK4 protein_coding   23.15215 8.587109 41.46431 0.6929759 1.709946 2.270295 1.0084478 0.0000000 2.425145 0.00000000 0.2604903 7.9278641 0.02965833 0.0000000 0.0592000 0.05920000 8.187325e-08 8.187325e-08 TRUE TRUE
MSTRG.23066.3 ENSG00000114904 HEK293_OSMI2_6hA HEK293_TMG_6hB NEK4 protein_coding   23.15215 8.587109 41.46431 0.6929759 1.709946 2.270295 0.6291442 0.1653112 0.000000 0.08423365 0.0000000 -4.1318465 0.06005000 0.0178000 0.0000000 -0.01780000 5.969425e-02 8.187325e-08 FALSE TRUE
MSTRG.23066.4 ENSG00000114904 HEK293_OSMI2_6hA HEK293_TMG_6hB NEK4 protein_coding   23.15215 8.587109 41.46431 0.6929759 1.709946 2.270295 8.2104637 3.1040951 16.526951 0.17773841 0.9386975 2.4088084 0.27473333 0.3630333 0.3986333 0.03560000 8.004039e-01 8.187325e-08 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.

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 HEK293_TMG_6hB HEK293_OSMI2_6hA log2fold_HEK293_OSMI2_6hA_HEK293_TMG_6hB
ENSG00000114904 E001 269.791881 0.0322897709 4.250873e-07 0.000013437 3 52708444 52711634 3191 - 2.196 2.667 1.571
ENSG00000114904 E002 89.779235 0.0004457390 2.235915e-01 0.457724261 3 52711635 52711713 79 - 1.885 1.873 -0.042
ENSG00000114904 E003 51.279234 0.0009420325 7.074573e-01 0.840222078 3 52711714 52711744 31 - 1.641 1.660 0.065
ENSG00000114904 E004 62.130830 0.0007590344 4.034858e-01 0.631112823 3 52711745 52711776 32 - 1.727 1.724 -0.012
ENSG00000114904 E005 114.128725 0.0006045660 1.797412e-01 0.403614898 3 52711777 52711869 93 - 1.985 1.973 -0.041
ENSG00000114904 E006 0.648799 0.1761646197 2.960540e-01   3 52732462 52732519 58 - 0.128 0.346 1.829
ENSG00000114904 E007 1.475394 0.0154165023 4.517491e-02 0.168051918 3 52737498 52737585 88 - 0.228 0.605 2.134
ENSG00000114904 E008 169.262534 0.0002686991 2.813633e-01 0.521659872 3 52737586 52737719 134 - 2.153 2.160 0.024
ENSG00000114904 E009 218.558987 0.0011264381 8.303320e-01 0.913970626 3 52739429 52739585 157 - 2.253 2.301 0.160
ENSG00000114904 E010 141.389810 0.0007141072 6.928133e-01 0.830930737 3 52739586 52739634 49 - 2.069 2.096 0.091
ENSG00000114904 E011 152.646927 0.0003871624 8.035654e-01 0.898356156 3 52741411 52741499 89 - 2.097 2.146 0.165
ENSG00000114904 E012 14.224695 0.0659032450 2.862787e-01 0.526953312 3 52743228 52743351 124 - 1.136 0.979 -0.569
ENSG00000114904 E013 150.346375 0.0003218113 6.545969e-01 0.806459485 3 52743352 52743461 110 - 2.097 2.123 0.088
ENSG00000114904 E014 133.639749 0.0006567609 2.656843e-01 0.505091069 3 52744239 52744305 67 - 2.051 2.052 0.001
ENSG00000114904 E015 163.026587 0.0003643023 3.356154e-03 0.025512627 3 52746061 52746149 89 - 2.151 2.094 -0.190
ENSG00000114904 E016 117.496564 0.0004065826 3.217758e-03 0.024711681 3 52746150 52746210 61 - 2.012 1.935 -0.256
ENSG00000114904 E017 164.535999 0.0003125563 7.218693e-02 0.229191606 3 52746734 52746904 171 - 2.146 2.129 -0.058
ENSG00000114904 E018 2.831587 0.0099480426 5.426309e-01 0.730993663 3 52747330 52747451 122 - 0.533 0.449 -0.413
ENSG00000114904 E019 88.993881 0.0005256192 6.576456e-01 0.808432641 3 52749692 52749829 138 - 1.875 1.897 0.072
ENSG00000114904 E020 269.512528 0.0004396441 1.762156e-04 0.002405777 3 52751932 52752336 405 - 2.369 2.311 -0.196
ENSG00000114904 E021 122.824970 0.0003325379 1.334690e-01 0.337242994 3 52760795 52760936 142 - 2.021 2.005 -0.052
ENSG00000114904 E022 128.920543 0.0003506747 9.869630e-01 0.995314733 3 52763470 52763624 155 - 2.027 2.068 0.136
ENSG00000114904 E023 118.064304 0.0004849218 4.734258e-01 0.682413818 3 52765887 52765994 108 - 1.995 2.008 0.045
ENSG00000114904 E024 160.702162 0.0003042992 4.575696e-03 0.032345087 3 52766178 52766315 138 - 2.142 2.088 -0.182
ENSG00000114904 E025 112.537205 0.0024521821 2.365437e-02 0.108017314 3 52766316 52766375 60 - 1.991 1.926 -0.219
ENSG00000114904 E026 180.371612 0.0004610694 3.688923e-02 0.146651066 3 52768338 52768566 229 - 2.187 2.161 -0.088
ENSG00000114904 E027 60.297516 0.0055291466 8.797215e-01 0.941099518 3 52768567 52768604 38 - 1.702 1.748 0.157
ENSG00000114904 E028 98.088953 0.0122132344 5.875854e-01 0.762047242 3 52770654 52770946 293 - 1.903 1.978 0.251