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CpG interval report generated on 20/05/20 with pycoMeth 0.4.6
Interval details
| pvalue rank | chromosome | start | end | length | number of samples | number of CpGs | pvalue | adjusted pvalue |
|---|---|---|---|---|---|---|---|---|
| #108 | X | 3346387 | 3347488 | 1101 | 3 | 39 | 3.11702e-17 | 2.87026e-15 |
Methylation log-likelihood ratio by CpG position
Distribution of CpG methylation log-likelihood ratio by sample
Closest transcripts TSS
| distance to tss | transcript id | gene id | transcript name | chromosome | start | end | strand | feature type | transcript biotype |
|---|---|---|---|---|---|---|---|---|---|
| 0 | enst00000217939 | sg00000101825 | mxra5-201 | X | 3308565 | 3346652 | - | mRNA | protein_coding |
| 19661 | enst00000439462 | sg00000213487 | ass1p4-201 | X | 3367149 | 3368382 | + | pseudogenic_transcript | processed_pseudogene |
| -74768 | enst00000656741 | sg00000228459 | linc01546-202 | X | 3271619 | 3279067 | + | lnc_RNA | lncrna |
| -74803 | enst00000668035 | sg00000228459 | linc01546-204 | X | 3271584 | 3279065 | + | lnc_RNA | lncrna |
| -74803 | enst00000668004 | sg00000228459 | linc01546-203 | X | 3271584 | 3278953 | + | lnc_RNA | lncrna |
| -74843 | enst00000457435 | sg00000228459 | linc01546-201 | X | 3271544 | 3286138 | + | lnc_RNA | lncrna |
| 184763 | enst00000390912 | sg00000212214 | snora48b-201 | X | 3532117 | 3532251 | - | snoRNA | snorna |
| 225369 | enst00000384704 | sg00000207435 | rnu6-114p-201 | X | 3572857 | 3572961 | + | snRNA | snrna |
| -232791 | enst00000443851 | sg00000230249 | ac112653.1-201 | X | 3112900 | 3113596 | - | pseudogenic_transcript | processed_pseudogene |
| 259877 | enst00000384602 | sg00000207332 | rnu6-146p-201 | X | 3607258 | 3607365 | - | snRNA | snrna |
| 264767 | enst00000496648 | sg00000183943 | prkx-204 | X | 3610951 | 3612255 | - | lnc_RNA | processed_transcript |
| 264793 | enst00000462736 | sg00000183943 | prkx-203 | X | 3608625 | 3612281 | - | lnc_RNA | processed_transcript |
| -279554 | enst00000359361 | sg00000062096 | arsf-201 | X | 3066833 | 3112706 | + | mRNA | protein_coding |
| -287885 | enst00000477781 | sg00000239228 | rn7sl578p-201 | X | 3058220 | 3058502 | - | ncRNA | misc_rna |
| 294067 | enst00000384590 | sg00000207320 | ac007685.2-201 | X | 3641443 | 3641555 | - | ncRNA | misc_rna |
| -304916 | enst00000381127 | sg00000062096 | arsf-202 | X | 3041471 | 3112727 | + | mRNA | protein_coding |
| 311999 | enst00000414074 | sg00000236188 | prkx-as1-201 | X | 3659487 | 3668192 | + | lnc_RNA | lncrna |
| 322727 | enst00000425240 | sg00000183943 | prkx-202 | X | 3612310 | 3670215 | - | lnc_RNA | processed_transcript |
| -339774 | enst00000381130 | sg00000205667 | arsh-201 | X | 3006613 | 3033571 | + | mRNA | protein_coding |
| 366161 | enst00000262848 | sg00000183943 | prkx-201 | X | 3604340 | 3713649 | - | mRNA | protein_coding |
| 369661 | enst00000329806 | sg00000182888 | ac007685.1-201 | X | 3717149 | 3717600 | + | pseudogenic_transcript | processed_pseudogene |
| -377912 | enst00000672097 | sg00000157399 | arsl-207 | X | 2934640 | 2968475 | - | mRNA | protein_coding |
| -378077 | enst00000540563 | sg00000157399 | arsl-204 | X | 2934632 | 2968310 | - | mRNA | protein_coding |
| -378111 | enst00000673032 | sg00000157399 | arsl-210 | X | 2934521 | 2968276 | - | mRNA | protein_coding |
| -378129 | enst00000672606 | sg00000157399 | arsl-208 | X | 2943147 | 2968258 | - | mRNA | protein_coding |
| -378142 | enst00000672027 | sg00000157399 | arsl-206 | X | 2934832 | 2968245 | - | mRNA | protein_coding |
| -378142 | enst00000672761 | sg00000157399 | arsl-209 | X | 2934658 | 2968245 | - | mRNA | protein_coding |
| -382046 | enst00000381134 | sg00000157399 | arsl-201 | X | 2934521 | 2964341 | - | mRNA | protein_coding |
| -382103 | enst00000545496 | sg00000157399 | arsl-205 | X | 2934811 | 2964284 | - | mRNA | protein_coding |
| -382123 | enst00000438544 | sg00000157399 | arsl-202 | X | 2949623 | 2964264 | - | mRNA | protein_coding |
| -393159 | enst00000483425 | sg00000157399 | arsl-203 | X | 2952831 | 2953228 | - | lnc_RNA | processed_transcript |
| -417038 | enst00000495294 | sg00000006756 | arsd-206 | X | 2906156 | 2929349 | - | lnc_RNA | processed_transcript |
| -417048 | enst00000381154 | sg00000006756 | arsd-202 | X | 2903972 | 2929339 | - | mRNA | protein_coding |
| -417048 | enst00000559324 | sg00000006756 | arsd-207 | X | 2920676 | 2929339 | - | mRNA | nonsense_mediated_decay |
| -417108 | enst00000494870 | sg00000006756 | arsd-205 | X | 2920381 | 2929279 | - | lnc_RNA | retained_intron |
| -417112 | enst00000217890 | sg00000006756 | arsd-201 | X | 2913614 | 2929275 | - | lnc_RNA | processed_transcript |
| -428509 | enst00000481340 | sg00000006756 | arsd-204 | X | 2914497 | 2917878 | - | lnc_RNA | processed_transcript |
| -436467 | enst00000458014 | sg00000006756 | arsd-203 | X | 2904918 | 2909920 | - | mRNA | protein_coding |
| -441483 | enst00000414053 | sg00000229851 | arsd-as1-201 | X | 2904904 | 2906081 | + | lnc_RNA | lncrna |
| 472436 | enst00000660920 | sg00000286431 | bx842570.1-201 | X | 3819924 | 3823898 | + | lnc_RNA | lncrna |
| 475053 | enst00000657193 | sg00000285756 | bx890604.2-223 | X | 3817534 | 3822541 | - | lnc_RNA | lncrna |
| 475134 | enst00000461011 | sg00000285756 | bx890604.2-222 | X | 3817528 | 3822622 | - | lnc_RNA | lncrna |
| 477110 | enst00000471090 | sg00000285756 | bx890604.2-207 | X | 3817535 | 3824598 | - | lnc_RNA | lncrna |
| 477715 | enst00000469903 | sg00000285756 | bx890604.2-202 | X | 3817528 | 3825203 | - | lnc_RNA | lncrna |
| 479143 | enst00000653447 | sg00000285756 | bx890604.2-201 | X | 3817528 | 3826631 | - | lnc_RNA | lncrna |
| 479143 | enst00000669937 | sg00000285756 | bx890604.2-224 | X | 3817528 | 3826631 | - | lnc_RNA | lncrna |
| 481109 | enst00000486571 | sg00000285756 | bx890604.2-208 | X | 3821681 | 3828597 | - | lnc_RNA | lncrna |
| 481491 | enst00000671495 | sg00000285756 | bx890604.2-227 | X | 3817727 | 3828979 | - | lnc_RNA | lncrna |
| 481906 | enst00000483854 | sg00000285756 | bx890604.2-203 | X | 3817528 | 3829394 | - | lnc_RNA | lncrna |
| -491266 | enst00000381157 | sg00000056998 | gyg2-202 | X | 2855121 | 2881091 | + | mRNA | protein_coding |
| -492327 | enst00000453106 | sg00000056998 | gyg2-206 | X | 2854060 | 2877443 | + | lnc_RNA | processed_transcript |
| -492627 | enst00000445107 | sg00000235483 | gyg2-as1-201 | X | 2852740 | 2853760 | - | lnc_RNA | lncrna |
| 495927 | enst00000475317 | sg00000285756 | bx890604.2-225 | X | 3817528 | 3843415 | - | lnc_RNA | lncrna |
| 496020 | enst00000490920 | sg00000285756 | bx890604.2-204 | X | 3817528 | 3843508 | - | lnc_RNA | lncrna |
| 496078 | enst00000662024 | sg00000285756 | bx890604.2-209 | X | 3817528 | 3843566 | - | lnc_RNA | lncrna |
| 496283 | enst00000671583 | sg00000285756 | bx890604.2-228 | X | 3827151 | 3843771 | - | lnc_RNA | lncrna |
| 496369 | enst00000425492 | sg00000285756 | bx890604.2-205 | X | 3817528 | 3843857 | - | lnc_RNA | lncrna |
Source file: /hps/research1/birney/users/adrien/analyses/cancer_DNA_promethion/run_1_2_3_4/DNA_pipeline_2/results/methylation/pycometh_meth_comp_CGI_3/out.tsv.gz
MD5 hash: 9aa0e3f69cb4e12345c3758eb68a5efc