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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 |
|---|---|---|---|---|---|---|---|---|
| #65 | 7 | 27141823 | 27143630 | 1807 | 3 | 53 | 3.62251e-20 | 5.53144e-18 |
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 | enst00000520854 | sg00000106004 | hoxa5-202 | 7 | 27141807 | 27142775 | - | lnc_RNA | processed_transcript |
| 51 | enst00000222726 | sg00000106004 | hoxa5-201 | 7 | 27141052 | 27143681 | - | mRNA | protein_coding |
| -1459 | enst00000521197 | sg00000254369 | hoxa-as3-203 | 7 | 27140364 | 27152697 | + | lnc_RNA | lncrna |
| -1598 | enst00000521401 | sg00000105997 | hoxa3-204 | 7 | 27110691 | 27140225 | - | lnc_RNA | processed_transcript |
| -1604 | enst00000317201 | sg00000105997 | hoxa3-201 | 7 | 27107012 | 27140219 | - | mRNA | protein_coding |
| -1617 | enst00000522788 | sg00000105997 | hoxa3-206 | 7 | 27110388 | 27140206 | - | mRNA | protein_coding |
| 3533 | enst00000518947 | sg00000254369 | hoxa-as3-202 | 7 | 27147163 | 27155928 | + | lnc_RNA | lncrna |
| 3853 | enst00000521231 | sg00000254369 | hoxa-as3-204 | 7 | 27147483 | 27152703 | + | lnc_RNA | lncrna |
| 4144 | enst00000222728 | sg00000106006 | hoxa6-201 | 7 | 27145396 | 27147774 | - | mRNA | protein_coding |
| 6422 | enst00000524304 | sg00000254369 | hoxa-as3-205 | 7 | 27150052 | 27152726 | + | lnc_RNA | lncrna |
| 6973 | enst00000521478 | sg00000106006 | hoxa6-202 | 7 | 27145662 | 27150603 | - | lnc_RNA | processed_transcript |
| 8931 | enst00000467897 | sg00000273433 | ac004080.6-201 | 7 | 27128969 | 27152561 | - | lnc_RNA | lncrna |
| 8951 | enst00000518451 | sg00000105997 | hoxa3-203 | 7 | 27126928 | 27152581 | - | lnc_RNA | processed_transcript |
| 8968 | enst00000498652 | sg00000272801 | ac004080.5-201 | 7 | 27147366 | 27152598 | - | lnc_RNA | lncrna |
| -11043 | enst00000610970 | sg00000197576 | hoxa4-204 | 7 | 27128507 | 27130780 | - | mRNA | protein_coding |
| -11066 | enst00000360046 | sg00000197576 | hoxa4-201 | 7 | 27128525 | 27130757 | - | mRNA | protein_coding |
| -11090 | enst00000428284 | sg00000197576 | hoxa4-202 | 7 | 27128533 | 27130733 | - | mRNA | protein_coding |
| -11632 | enst00000511914 | sg00000197576 | hoxa4-203 | 7 | 27128664 | 27130191 | - | mRNA | protein_coding |
| -11846 | enst00000518848 | sg00000254369 | hoxa-as3-201 | 7 | 27129977 | 27152576 | + | lnc_RNA | lncrna |
| 12368 | enst00000523796 | sg00000122592 | hoxa7-203 | 7 | 27154783 | 27155998 | - | lnc_RNA | processed_transcript |
| 13045 | enst00000242159 | sg00000122592 | hoxa7-201 | 7 | 27153716 | 27156675 | - | mRNA | protein_coding |
| 14306 | enst00000519842 | sg00000122592 | hoxa7-202 | 7 | 27156454 | 27157936 | - | mRNA | protein_coding |
| 14714 | enst00000602610 | sg00000270182 | ac004080.4-201 | 7 | 27158344 | 27158976 | + | lnc_RNA | lncrna |
| -14803 | enst00000612286 | sg00000105997 | hoxa3-207 | 7 | 27106190 | 27127020 | - | mRNA | protein_coding |
| -18655 | enst00000524048 | sg00000253552 | hoxa-as2-210 | 7 | 27123168 | 27124267 | + | lnc_RNA | lncrna |
| -19247 | enst00000521687 | sg00000253552 | hoxa-as2-207 | 7 | 27122576 | 27128693 | + | lnc_RNA | lncrna |
| -19275 | enst00000521159 | sg00000253552 | hoxa-as2-206 | 7 | 27122548 | 27134302 | + | lnc_RNA | lncrna |
| -19380 | enst00000517641 | sg00000253552 | hoxa-as2-203 | 7 | 27122443 | 27123818 | + | lnc_RNA | lncrna |
| -19906 | enst00000517550 | sg00000253552 | hoxa-as2-201 | 7 | 27121917 | 27128760 | + | lnc_RNA | lncrna |
| -20886 | enst00000523364 | sg00000253552 | hoxa-as2-209 | 7 | 27120937 | 27122650 | + | lnc_RNA | lncrna |
| 21827 | enst00000673917 | sg00000078399 | hoxa9-208 | 7 | 27163603 | 27165457 | - | mRNA | protein_coding |
| 21827 | enst00000673744 | sg00000078399 | hoxa9-207 | 7 | 27163603 | 27165457 | - | mRNA | protein_coding |
| 21896 | enst00000396345 | sg00000078399 | hoxa9-202 | 7 | 27163521 | 27165526 | - | mRNA | protein_coding |
| 21907 | enst00000343483 | sg00000078399 | hoxa9-201 | 7 | 27162438 | 27165537 | - | mRNA | protein_coding |
| -22228 | enst00000396352 | sg00000105997 | hoxa3-202 | 7 | 27106184 | 27119595 | - | mRNA | protein_coding |
| 24989 | enst00000519694 | sg00000253187 | hoxa10-as-201 | 7 | 27168619 | 27171373 | + | lnc_RNA | lncrna |
| 25269 | enst00000519935 | sg00000253187 | hoxa10-as-202 | 7 | 27168899 | 27171915 | + | lnc_RNA | lncrna |
| 25464 | enst00000523790 | sg00000253187 | hoxa10-as-203 | 7 | 27169094 | 27171765 | + | lnc_RNA | lncrna |
| -25787 | enst00000593438 | sg00000253552 | hoxa-as2-211 | 7 | 27116036 | 27116664 | + | lnc_RNA | lncrna |
| 25814 | enst00000497089 | sg00000078399 | hoxa9-206 | 7 | 27162600 | 27169444 | - | lnc_RNA | processed_transcript |
| 25933 | enst00000384852 | sg00000283745 | mir196b-201 | 7 | 27169480 | 27169563 | - | miRNA | mirna |
| 26107 | enst00000489695 | sg00000078399 | hoxa9-205 | 7 | 27163682 | 27169737 | - | lnc_RNA | processed_transcript |
| -26418 | enst00000518046 | sg00000253552 | hoxa-as2-204 | 7 | 27115405 | 27122173 | + | lnc_RNA | lncrna |
| -26475 | enst00000517635 | sg00000253552 | hoxa-as2-202 | 7 | 27115348 | 27123377 | + | lnc_RNA | lncrna |
| 26868 | enst00000487384 | sg00000078399 | hoxa9-204 | 7 | 27163307 | 27170498 | - | lnc_RNA | processed_transcript |
| -27887 | enst00000522193 | sg00000253552 | hoxa-as2-208 | 7 | 27113936 | 27122199 | + | lnc_RNA | lncrna |
| -27978 | enst00000522456 | sg00000105997 | hoxa3-205 | 7 | 27110479 | 27113845 | - | mRNA | protein_coding |
| 29259 | enst00000521421 | sg00000253293 | hoxa10-204 | 7 | 27171463 | 27172889 | - | lnc_RNA | processed_transcript |
| 29259 | enst00000519593 | sg00000253293 | hoxa10-203 | 7 | 27171777 | 27172889 | - | lnc_RNA | processed_transcript |
| 29333 | enst00000524368 | sg00000253293 | hoxa10-205 | 7 | 27171378 | 27172963 | - | lnc_RNA | processed_transcript |
| 30625 | enst00000613671 | sg00000253293 | hoxa10-206 | 7 | 27170592 | 27174255 | - | mRNA | protein_coding |
| 30690 | enst00000283921 | sg00000253293 | hoxa10-201 | 7 | 27170605 | 27174320 | - | mRNA | protein_coding |
| 31550 | enst00000465941 | sg00000078399 | hoxa9-203 | 7 | 27163664 | 27175180 | - | lnc_RNA | processed_transcript |
| -33818 | enst00000669815 | sg00000253552 | hoxa-as2-213 | 7 | 27108005 | 27122887 | + | lnc_RNA | lncrna |
| -33818 | enst00000658768 | sg00000253552 | hoxa-as2-212 | 7 | 27108005 | 27122879 | + | lnc_RNA | lncrna |
| -34046 | enst00000518088 | sg00000253552 | hoxa-as2-205 | 7 | 27107777 | 27122173 | + | lnc_RNA | lncrna |
| 36383 | enst00000470747 | sg00000257184 | ac004080.3-201 | 7 | 27163535 | 27180013 | - | mRNA | protein_coding |
| 36631 | enst00000396344 | sg00000253293 | hoxa10-202 | 7 | 27171220 | 27180261 | - | mRNA | protein_coding |
| -39137 | enst00000612779 | sg00000105996 | hoxa2-202 | 7 | 27100694 | 27102686 | - | lnc_RNA | retained_intron |
| -39140 | enst00000222718 | sg00000105996 | hoxa2-201 | 7 | 27100354 | 27102683 | - | mRNA | protein_coding |
| 40877 | enst00000520360 | sg00000240990 | hoxa11-as-202 | 7 | 27184507 | 27189298 | + | lnc_RNA | lncrna |
| 40942 | enst00000647851 | sg00000240990 | hoxa11-as-207 | 7 | 27184572 | 27188797 | + | lnc_RNA | lncrna |
| 41041 | enst00000522863 | sg00000240990 | hoxa11-as-205 | 7 | 27184671 | 27189169 | + | lnc_RNA | lncrna |
| 41593 | enst00000517402 | sg00000005073 | hoxa11-202 | 7 | 27181510 | 27185223 | - | mRNA | protein_coding |
| 41602 | enst00000006015 | sg00000005073 | hoxa11-201 | 7 | 27181157 | 27185232 | - | mRNA | protein_coding |
| 41605 | enst00000647680 | sg00000240990 | hoxa11-as-206 | 7 | 27185235 | 27186229 | + | lnc_RNA | lncrna |
| 41778 | enst00000522674 | sg00000240990 | hoxa11-as-204 | 7 | 27185408 | 27189293 | + | lnc_RNA | lncrna |
| 41793 | enst00000648491 | sg00000240990 | hoxa11-as-208 | 7 | 27185423 | 27189298 | + | lnc_RNA | lncrna |
| 41802 | enst00000648499 | sg00000240990 | hoxa11-as-209 | 7 | 27185432 | 27188897 | + | lnc_RNA | lncrna |
| 41803 | enst00000613939 | sg00000273961 | ac004080.7-201 | 7 | 27185433 | 27185530 | + | ncRNA | misc_rna |
| -41856 | enst00000619311 | sg00000277694 | ac004079.5-201 | 7 | 27099967 | 27100111 | + | ncRNA | misc_rna |
| 41904 | enst00000520395 | sg00000240990 | hoxa11-as-203 | 7 | 27185534 | 27187153 | + | lnc_RNA | lncrna |
| -41967 | enst00000617934 | sg00000274396 | ac004079.1-201 | 7 | 27099856 | 27099957 | + | ncRNA | misc_rna |
| -42045 | enst00000619974 | sg00000274864 | ac004079.2-201 | 7 | 27099778 | 27099836 | + | ncRNA | misc_rna |
| 42202 | enst00000615604 | sg00000278334 | ac004080.14-201 | 7 | 27185832 | 27186018 | + | ncRNA | misc_rna |
| -42204 | enst00000593300 | sg00000233429 | hotairm1-206 | 7 | 27099619 | 27100265 | + | lnc_RNA | lncrna |
| 42504 | enst00000650141 | sg00000240990 | hoxa11-as-210 | 7 | 27186134 | 27189083 | + | lnc_RNA | lncrna |
| 42536 | enst00000613383 | sg00000276496 | ac004080.8-201 | 7 | 27186166 | 27186263 | + | ncRNA | misc_rna |
| -42923 | enst00000616712 | sg00000276771 | ac004079.4-201 | 7 | 27098900 | 27099114 | + | ncRNA | misc_rna |
| -42984 | enst00000428939 | sg00000233429 | hotairm1-202 | 7 | 27098839 | 27100139 | + | lnc_RNA | lncrna |
| 43262 | enst00000620901 | sg00000277966 | ac004080.12-201 | 7 | 27186892 | 27187124 | + | ncRNA | misc_rna |
| 44189 | enst00000620211 | sg00000278592 | ac004080.15-201 | 7 | 27187819 | 27188021 | + | ncRNA | misc_rna |
| 44189 | enst00000479766 | sg00000240990 | hoxa11-as-201 | 7 | 27187819 | 27189222 | + | lnc_RNA | lncrna |
| 45186 | enst00000620092 | sg00000278020 | ac004080.13-201 | 7 | 27188816 | 27188994 | + | ncRNA | misc_rna |
| -45590 | enst00000425358 | sg00000233429 | hotairm1-201 | 7 | 27096233 | 27099966 | + | lnc_RNA | lncrna |
| -45699 | enst00000622675 | sg00000276528 | ac004079.3-201 | 7 | 27096124 | 27096248 | + | ncRNA | misc_rna |
| -45699 | enst00000429611 | sg00000233429 | hotairm1-203 | 7 | 27096124 | 27099966 | + | lnc_RNA | lncrna |
| -45729 | enst00000434063 | sg00000233429 | hotairm1-204 | 7 | 27096094 | 27100154 | + | lnc_RNA | lncrna |
| -45827 | enst00000355633 | sg00000105991 | hoxa1-201 | 7 | 27093313 | 27095996 | - | mRNA | protein_coding |
| -45835 | enst00000643460 | sg00000105991 | hoxa1-202 | 7 | 27093313 | 27095988 | - | mRNA | protein_coding |
| -46176 | enst00000495032 | sg00000233429 | hotairm1-205 | 7 | 27095647 | 27096327 | + | lnc_RNA | lncrna |
| 49818 | enst00000523331 | sg00000253508 | ac004080.2-201 | 7 | 27186573 | 27193448 | - | lnc_RNA | lncrna |
| 51970 | enst00000518136 | sg00000106031 | hoxa13-201 | 7 | 27193503 | 27195600 | - | lnc_RNA | processed_transcript |
| 54945 | enst00000421733 | sg00000243766 | hottip-201 | 7 | 27198575 | 27201236 | + | lnc_RNA | lncrna |
| 55615 | enst00000605136 | sg00000243766 | hottip-204 | 7 | 27199245 | 27201823 | + | lnc_RNA | lncrna |
| 56461 | enst00000649031 | sg00000106031 | hoxa13-202 | 7 | 27194364 | 27200091 | - | mRNA | protein_coding |
| 56807 | enst00000472494 | sg00000243766 | hottip-202 | 7 | 27200437 | 27202822 | + | lnc_RNA | lncrna |
| 56835 | enst00000620415 | sg00000276609 | ac004080.9-201 | 7 | 27200465 | 27200521 | + | ncRNA | misc_rna |
| 58214 | enst00000521028 | sg00000243766 | hottip-203 | 7 | 27201844 | 27207259 | + | lnc_RNA | lncrna |
| 58214 | enst00000616633 | sg00000278708 | ac004080.16-201 | 7 | 27201844 | 27202219 | + | ncRNA | misc_rna |
| 58672 | enst00000619957 | sg00000277469 | ac004080.10-201 | 7 | 27202302 | 27202638 | + | ncRNA | misc_rna |
| 62509 | enst00000618195 | sg00000277553 | ac004080.11-201 | 7 | 27206139 | 27206303 | + | ncRNA | misc_rna |
| 69335 | enst00000656679 | sg00000286323 | ac004080.17-201 | 7 | 27210801 | 27212965 | - | lnc_RNA | lncrna |
| -93654 | enst00000396362 | sg00000213786 | nhp2p2-201 | 7 | 27048169 | 27048628 | + | pseudogenic_transcript | processed_pseudogene |
| 97598 | enst00000523608 | sg00000253308 | ac004080.1-201 | 7 | 27239243 | 27241228 | - | lnc_RNA | lncrna |
| 99070 | enst00000222761 | sg00000106038 | evx1-201 | 7 | 27242700 | 27246425 | + | mRNA | protein_coding |
| 99172 | enst00000496902 | sg00000106038 | evx1-202 | 7 | 27242802 | 27247830 | + | mRNA | protein_coding |
| 99332 | enst00000519050 | sg00000253405 | evx1-as-202 | 7 | 27241930 | 27242962 | - | lnc_RNA | lncrna |
| 99738 | enst00000580535 | sg00000106038 | evx1-204 | 7 | 27243368 | 27247176 | + | mRNA | protein_coding |
| 100329 | enst00000519218 | sg00000253405 | evx1-as-203 | 7 | 27241950 | 27243959 | - | lnc_RNA | lncrna |
| 103599 | enst00000517726 | sg00000253405 | evx1-as-201 | 7 | 27241429 | 27247229 | - | lnc_RNA | lncrna |
| 103738 | enst00000518886 | sg00000106038 | evx1-203 | 7 | 27247368 | 27250493 | + | lnc_RNA | processed_transcript |
| -118086 | enst00000425942 | sg00000214869 | tpm3p4-201 | 7 | 27023737 | 27024907 | + | pseudogenic_transcript | processed_pseudogene |
| 126048 | enst00000446039 | sg00000213783 | rpl35p4-201 | 7 | 27269357 | 27269678 | - | pseudogenic_transcript | processed_pseudogene |
| -146584 | enst00000432747 | sg00000005020 | skap2-202 | 7 | 26738840 | 26995239 | - | mRNA | protein_coding |
| -158456 | enst00000417997 | sg00000226059 | hmgb3p20-201 | 7 | 26982768 | 26983367 | - | pseudogenic_transcript | processed_pseudogene |
| 185904 | enst00000446472 | sg00000236569 | hnrnpa1p73-201 | 7 | 27328607 | 27329534 | - | pseudogenic_transcript | processed_pseudogene |
| 217961 | enst00000664129 | sg00000224322 | ac004009.1-203 | 7 | 27361591 | 27410358 | + | lnc_RNA | lncrna |
| 217998 | enst00000656126 | sg00000224322 | ac004009.1-202 | 7 | 27361628 | 27410358 | + | lnc_RNA | lncrna |
| 218213 | enst00000412413 | sg00000224322 | ac004009.1-201 | 7 | 27361843 | 27409938 | + | lnc_RNA | lncrna |
| -219713 | enst00000441433 | sg00000213787 | rpl7ap38-201 | 7 | 26922110 | 26922912 | + | pseudogenic_transcript | processed_pseudogene |
| 236932 | enst00000624160 | sg00000279655 | ac004009.3-201 | 7 | 27380562 | 27381206 | + | unconfirmed_transcript | tec |
| 268534 | enst00000623016 | sg00000279429 | ac004009.2-201 | 7 | 27412164 | 27412891 | + | unconfirmed_transcript | tec |
| -276710 | enst00000481204 | sg00000005020 | skap2-204 | 7 | 26844029 | 26865113 | - | lnc_RNA | processed_transcript |
| -277233 | enst00000345317 | sg00000005020 | skap2-201 | 7 | 26667068 | 26864590 | - | mRNA | protein_coding |
| -277236 | enst00000497511 | sg00000005020 | skap2-209 | 7 | 26746567 | 26864587 | - | lnc_RNA | processed_transcript |
| -277238 | enst00000487720 | sg00000005020 | skap2-205 | 7 | 26844030 | 26864585 | - | lnc_RNA | processed_transcript |
| -283664 | enst00000490456 | sg00000005020 | skap2-207 | 7 | 26739887 | 26858159 | - | lnc_RNA | processed_transcript |
| -284145 | enst00000468712 | sg00000005020 | skap2-203 | 7 | 26726682 | 26857678 | - | lnc_RNA | retained_intron |
| -286672 | enst00000495802 | sg00000005020 | skap2-208 | 7 | 26726889 | 26855151 | - | lnc_RNA | processed_transcript |
| 315219 | enst00000453115 | sg00000233830 | eif4hp1-201 | 7 | 27458163 | 27458849 | - | pseudogenic_transcript | processed_pseudogene |
| 318136 | enst00000423961 | sg00000213781 | psmc1p2-201 | 7 | 27461766 | 27462969 | + | pseudogenic_transcript | processed_pseudogene |
| 349135 | enst00000450406 | sg00000235574 | ac073150.1-201 | 7 | 27491682 | 27492765 | - | pseudogenic_transcript | processed_pseudogene |
| -399348 | enst00000489977 | sg00000005020 | skap2-206 | 7 | 26690307 | 26742475 | - | lnc_RNA | processed_transcript |
| 473844 | enst00000665298 | sg00000286478 | ac007130.1-201 | 7 | 27617474 | 27627496 | + | 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