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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 |
|---|---|---|---|---|---|---|---|---|
| #152 | 14 | 56797809 | 56798963 | 1154 | 3 | 39 | 1.8991e-15 | 1.24254e-13 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 6685 | enst00000554845 | sg00000165588 | otx2-205 | 14 | 56801913 | 56805648 | - | mRNA | protein_coding |
| 6685 | enst00000554788 | sg00000165588 | otx2-204 | 14 | 56801810 | 56805648 | - | mRNA | protein_coding |
| 6704 | enst00000408990 | sg00000165588 | otx2-202 | 14 | 56800707 | 56805667 | - | mRNA | protein_coding |
| 11423 | enst00000672125 | sg00000165588 | otx2-208 | 14 | 56800739 | 56810386 | - | mRNA | protein_coding |
| 11426 | enst00000673481 | sg00000165588 | otx2-211 | 14 | 56800739 | 56810389 | - | mRNA | protein_coding |
| 11485 | enst00000555006 | sg00000165588 | otx2-206 | 14 | 56801735 | 56810448 | - | mRNA | protein_coding |
| 11485 | enst00000339475 | sg00000165588 | otx2-201 | 14 | 56799905 | 56810448 | - | mRNA | protein_coding |
| 11516 | enst00000555804 | sg00000165588 | otx2-207 | 14 | 56802115 | 56810479 | - | mRNA | protein_coding |
| 11516 | enst00000554559 | sg00000165588 | otx2-203 | 14 | 56802025 | 56810479 | - | mRNA | protein_coding |
| 11516 | enst00000672264 | sg00000165588 | otx2-209 | 14 | 56800707 | 56810479 | - | mRNA | protein_coding |
| 14220 | enst00000534909 | sg00000248550 | otx2-as1-201 | 14 | 56813183 | 56930833 | + | lnc_RNA | lncrna |
| 14270 | enst00000554428 | sg00000248550 | otx2-as1-203 | 14 | 56813233 | 56919792 | + | lnc_RNA | lncrna |
| 14308 | enst00000554725 | sg00000248550 | otx2-as1-204 | 14 | 56813271 | 57152177 | + | lnc_RNA | lncrna |
| 14316 | enst00000653425 | sg00000248550 | otx2-as1-205 | 14 | 56813279 | 56931220 | + | lnc_RNA | lncrna |
| 14328 | enst00000554358 | sg00000248550 | otx2-as1-202 | 14 | 56813291 | 56929039 | + | lnc_RNA | lncrna |
| 17730 | enst00000673035 | sg00000165588 | otx2-210 | 14 | 56800741 | 56816693 | - | mRNA | protein_coding |
| 25693 | enst00000484915 | sg00000243801 | rn7sl461p-201 | 14 | 56824375 | 56824656 | - | ncRNA | misc_rna |
| 26023 | enst00000363948 | sg00000200818 | rnu6-1204p-201 | 14 | 56824986 | 56825092 | + | snRNA | snrna |
| -38430 | enst00000555316 | sg00000258703 | al161757.3-201 | 14 | 56759379 | 56765757 | + | lnc_RNA | lncrna |
| -67274 | enst00000556696 | sg00000259133 | al161757.5-202 | 14 | 56723137 | 56730535 | - | lnc_RNA | lncrna |
| -67303 | enst00000554597 | sg00000259133 | al161757.5-201 | 14 | 56648965 | 56730506 | - | lnc_RNA | lncrna |
| 94196 | enst00000555946 | sg00000258776 | al161757.4-203 | 14 | 56880818 | 56893159 | - | lnc_RNA | lncrna |
| 94286 | enst00000557136 | sg00000258776 | al161757.4-204 | 14 | 56885671 | 56893249 | - | lnc_RNA | lncrna |
| 94385 | enst00000554149 | sg00000258776 | al161757.4-201 | 14 | 56817570 | 56893348 | - | lnc_RNA | lncrna |
| 94747 | enst00000557467 | sg00000258776 | al161757.4-202 | 14 | 56817754 | 56893710 | - | lnc_RNA | lncrna |
| -114068 | enst00000471982 | sg00000242995 | al161757.1-201 | 14 | 56683421 | 56683741 | - | pseudogenic_transcript | processed_pseudogene |
| -149151 | enst00000555924 | sg00000258428 | al161757.2-202 | 14 | 56633249 | 56648658 | - | lnc_RNA | lncrna |
| -150037 | enst00000553800 | sg00000258428 | al161757.2-201 | 14 | 56633244 | 56647772 | - | lnc_RNA | lncrna |
| -161293 | enst00000555046 | sg00000070269 | tmem260-206 | 14 | 56636516 | 56650606 | + | mRNA | protein_coding |
| 164524 | enst00000669124 | sg00000286257 | al137100.3-207 | 14 | 56953826 | 56963487 | - | lnc_RNA | lncrna |
| 179446 | enst00000467870 | sg00000243388 | rpl3p3-201 | 14 | 56978409 | 56979621 | + | pseudogenic_transcript | processed_pseudogene |
| -182358 | enst00000556648 | sg00000070269 | tmem260-211 | 14 | 56615451 | 56647922 | + | lnc_RNA | retained_intron |
| -188564 | enst00000553335 | sg00000070269 | tmem260-204 | 14 | 56609245 | 56619466 | + | lnc_RNA | processed_transcript |
| -188668 | enst00000555905 | sg00000070269 | tmem260-208 | 14 | 56609141 | 56633171 | + | mRNA | nonsense_mediated_decay |
| 193489 | enst00000669623 | sg00000286257 | al137100.3-208 | 14 | 56951008 | 56992452 | - | lnc_RNA | lncrna |
| 193533 | enst00000669773 | sg00000286257 | al137100.3-203 | 14 | 56951008 | 56992496 | - | lnc_RNA | lncrna |
| 193540 | enst00000666046 | sg00000286257 | al137100.3-204 | 14 | 56953828 | 56992503 | - | lnc_RNA | lncrna |
| 193540 | enst00000661639 | sg00000286257 | al137100.3-209 | 14 | 56963366 | 56992503 | - | lnc_RNA | lncrna |
| 193545 | enst00000651959 | sg00000286257 | al137100.3-201 | 14 | 56951008 | 56992508 | - | lnc_RNA | lncrna |
| -211954 | enst00000556929 | sg00000070269 | tmem260-213 | 14 | 56585855 | 56618663 | + | mRNA | nonsense_mediated_decay |
| -212115 | enst00000554981 | sg00000070269 | tmem260-205 | 14 | 56585694 | 56603941 | + | lnc_RNA | retained_intron |
| -212116 | enst00000556079 | sg00000070269 | tmem260-209 | 14 | 56585693 | 56609189 | + | lnc_RNA | retained_intron |
| -217925 | enst00000538838 | sg00000070269 | tmem260-202 | 14 | 56579884 | 56634953 | + | mRNA | protein_coding |
| -217968 | enst00000539559 | sg00000070269 | tmem260-203 | 14 | 56579841 | 56648094 | + | mRNA | nonsense_mediated_decay |
| -217978 | enst00000557626 | sg00000070269 | tmem260-215 | 14 | 56579831 | 56616264 | + | lnc_RNA | retained_intron |
| -217983 | enst00000555497 | sg00000070269 | tmem260-207 | 14 | 56579826 | 56647852 | + | mRNA | nonsense_mediated_decay |
| -217983 | enst00000556975 | sg00000070269 | tmem260-214 | 14 | 56579826 | 56593224 | + | lnc_RNA | processed_transcript |
| -217984 | enst00000557657 | sg00000070269 | tmem260-216 | 14 | 56579825 | 56613910 | + | lnc_RNA | retained_intron |
| -218011 | enst00000261556 | sg00000070269 | tmem260-201 | 14 | 56579798 | 56649515 | + | mRNA | protein_coding |
| -218189 | enst00000556422 | sg00000070269 | tmem260-210 | 14 | 56579620 | 56649515 | + | mRNA | nonsense_mediated_decay |
| 241922 | enst00000556703 | sg00000258758 | al137100.1-201 | 14 | 57040885 | 57042504 | + | pseudogenic_transcript | processed_pseudogene |
| 245997 | enst00000555786 | sg00000259136 | al137100.2-201 | 14 | 57044646 | 57044960 | - | pseudogenic_transcript | processed_pseudogene |
| 257088 | enst00000655065 | sg00000286257 | al137100.3-206 | 14 | 57033460 | 57056051 | - | lnc_RNA | lncrna |
| 257088 | enst00000653538 | sg00000286257 | al137100.3-202 | 14 | 56953829 | 57056051 | - | lnc_RNA | lncrna |
| 261752 | enst00000670848 | sg00000286257 | al137100.3-205 | 14 | 56954167 | 57060715 | - | lnc_RNA | lncrna |
| 269579 | enst00000554160 | sg00000258592 | al391152.1-201 | 14 | 57066260 | 57068542 | - | lnc_RNA | lncrna |
| -283478 | enst00000557246 | sg00000258803 | al355103.1-201 | 14 | 56514331 | 56551309 | + | lnc_RNA | lncrna |
| -309455 | enst00000556810 | sg00000070269 | tmem260-212 | 14 | 56488354 | 56585902 | + | mRNA | protein_coding |
| 313697 | enst00000551408 | sg00000258592 | al391152.1-202 | 14 | 57067008 | 57112660 | - | lnc_RNA | lncrna |
| 433409 | enst00000554011 | sg00000070367 | exoc5-203 | 14 | 57206794 | 57232372 | - | lnc_RNA | retained_intron |
| 434260 | enst00000554934 | sg00000070367 | exoc5-205 | 14 | 57232140 | 57233223 | - | lnc_RNA | processed_transcript |
| 438543 | enst00000556629 | sg00000070367 | exoc5-209 | 14 | 57231571 | 57237506 | - | lnc_RNA | retained_intron |
| 448680 | enst00000556911 | sg00000070367 | exoc5-210 | 14 | 57243248 | 57247643 | - | lnc_RNA | processed_transcript |
| 469477 | enst00000556318 | sg00000070367 | exoc5-208 | 14 | 57244279 | 57268440 | - | mRNA | protein_coding |
| 469762 | enst00000555749 | sg00000070367 | exoc5-207 | 14 | 57244113 | 57268725 | - | lnc_RNA | retained_intron |
| 469860 | enst00000554598 | sg00000070367 | exoc5-204 | 14 | 57239528 | 57268823 | - | lnc_RNA | retained_intron |
| 469874 | enst00000555148 | sg00000070367 | exoc5-206 | 14 | 57208545 | 57268837 | - | mRNA | nonsense_mediated_decay |
| 469936 | enst00000413566 | sg00000070367 | exoc5-202 | 14 | 57202483 | 57268899 | - | mRNA | protein_coding |
| 469936 | enst00000340918 | sg00000070367 | exoc5-201 | 14 | 57208160 | 57268899 | - | mRNA | protein_coding |
| 469942 | enst00000621441 | sg00000070367 | exoc5-211 | 14 | 57200507 | 57268905 | - | mRNA | protein_coding |
| 469961 | enst00000554931 | sg00000053770 | ap5m1-205 | 14 | 57268924 | 57275469 | + | lnc_RNA | retained_intron |
| 469977 | enst00000556995 | sg00000053770 | ap5m1-209 | 14 | 57268940 | 57274723 | + | mRNA | protein_coding |
| 470008 | enst00000261558 | sg00000053770 | ap5m1-201 | 14 | 57268971 | 57298742 | + | mRNA | protein_coding |
| 470063 | enst00000555448 | sg00000053770 | ap5m1-206 | 14 | 57269026 | 57283019 | + | mRNA | nonsense_mediated_decay |
| 470093 | enst00000431972 | sg00000053770 | ap5m1-202 | 14 | 57269056 | 57288925 | + | mRNA | protein_coding |
| 470131 | enst00000554213 | sg00000053770 | ap5m1-203 | 14 | 57269094 | 57271365 | + | lnc_RNA | processed_transcript |
| 479459 | enst00000556723 | sg00000053770 | ap5m1-208 | 14 | 57278422 | 57283243 | + | lnc_RNA | processed_transcript |
| 484022 | enst00000554863 | sg00000053770 | ap5m1-204 | 14 | 57282985 | 57286564 | + | mRNA | protein_coding |
| -486820 | enst00000664536 | sg00000259719 | linc02284-205 | 14 | 56310989 | 56333710 | + | lnc_RNA | lncrna |
| -486865 | enst00000664388 | sg00000259719 | linc02284-204 | 14 | 56310944 | 56427032 | + | lnc_RNA | lncrna |
| -486868 | enst00000666463 | sg00000259719 | linc02284-206 | 14 | 56310941 | 56312374 | + | lnc_RNA | lncrna |
| -486873 | enst00000560924 | sg00000259719 | linc02284-202 | 14 | 56310936 | 56393311 | + | lnc_RNA | lncrna |
| -486929 | enst00000663878 | sg00000259719 | linc02284-203 | 14 | 56310880 | 56333710 | + | lnc_RNA | lncrna |
| -486929 | enst00000558120 | sg00000259719 | linc02284-201 | 14 | 56310880 | 56326208 | + | lnc_RNA | lncrna |
| -487048 | enst00000560296 | sg00000259483 | al355073.1-201 | 14 | 56303490 | 56310761 | - | lnc_RNA | lncrna |
| 487260 | enst00000556377 | sg00000053770 | ap5m1-207 | 14 | 57286223 | 57290074 | + | mRNA | nonsense_mediated_decay |
| -491971 | enst00000612106 | sg00000275569 | al355073.2-201 | 14 | 56305838 | 56306394 | + | 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