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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 |
|---|---|---|---|---|---|---|---|---|
| #146 | 13 | 113820374 | 113821613 | 1239 | 3 | 37 | 7.06823e-16 | 4.81463e-14 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 1581 | enst00000608763 | sg00000183087 | gas6-204 | 13 | 113820549 | 113823194 | - | lnc_RNA | retained_intron |
| -4744 | enst00000458001 | sg00000233695 | gas6-as1-201 | 13 | 113815630 | 113845744 | + | lnc_RNA | lncrna |
| 12128 | enst00000480426 | sg00000183087 | gas6-203 | 13 | 113820549 | 113833741 | - | lnc_RNA | retained_intron |
| 14431 | enst00000610073 | sg00000183087 | gas6-205 | 13 | 113820552 | 113836044 | - | lnc_RNA | retained_intron |
| -17324 | enst00000467169 | sg00000184497 | tmem255b-203 | 13 | 113803050 | 113811953 | + | lnc_RNA | processed_transcript |
| -20486 | enst00000498692 | sg00000184497 | tmem255b-206 | 13 | 113799888 | 113804890 | + | lnc_RNA | processed_transcript |
| 20877 | enst00000611082 | sg00000233695 | gas6-as1-202 | 13 | 113842490 | 113844306 | + | lnc_RNA | lncrna |
| 42402 | enst00000476291 | sg00000183087 | gas6-202 | 13 | 113847677 | 113864015 | - | lnc_RNA | processed_transcript |
| 42463 | enst00000327773 | sg00000183087 | gas6-201 | 13 | 113820549 | 113864076 | - | mRNA | protein_coding |
| 42499 | enst00000669254 | sg00000272695 | gas6-dt-203 | 13 | 113864112 | 113866834 | + | lnc_RNA | lncrna |
| 42505 | enst00000655351 | sg00000272695 | gas6-dt-202 | 13 | 113864118 | 113866618 | + | lnc_RNA | lncrna |
| 42555 | enst00000608651 | sg00000272695 | gas6-dt-201 | 13 | 113864168 | 113866833 | + | lnc_RNA | lncrna |
| -52238 | enst00000375348 | sg00000184497 | tmem255b-201 | 13 | 113768136 | 113799857 | + | lnc_RNA | processed_transcript |
| -54210 | enst00000483678 | sg00000184497 | tmem255b-204 | 13 | 113766164 | 113769815 | + | lnc_RNA | processed_transcript |
| 55995 | enst00000449453 | sg00000237699 | bx072579.1-201 | 13 | 113877608 | 113879376 | + | lnc_RNA | lncrna |
| 56800 | enst00000648342 | sg00000237699 | bx072579.1-202 | 13 | 113878413 | 113879367 | + | lnc_RNA | lncrna |
| 59763 | enst00000671045 | sg00000226921 | linc00454-209 | 13 | 113878630 | 113881376 | - | lnc_RNA | lncrna |
| 60317 | enst00000608044 | sg00000226921 | linc00454-204 | 13 | 113879004 | 113881930 | - | lnc_RNA | lncrna |
| 60589 | enst00000610194 | sg00000226921 | linc00454-207 | 13 | 113879011 | 113882202 | - | lnc_RNA | lncrna |
| -61134 | enst00000488362 | sg00000184497 | tmem255b-205 | 13 | 113759240 | 113799660 | + | mRNA | protein_coding |
| -61148 | enst00000375353 | sg00000184497 | tmem255b-202 | 13 | 113759226 | 113816995 | + | mRNA | protein_coding |
| 61715 | enst00000609493 | sg00000226921 | linc00454-205 | 13 | 113879004 | 113883328 | - | lnc_RNA | lncrna |
| 61865 | enst00000425483 | sg00000226921 | linc00454-201 | 13 | 113880382 | 113883478 | - | lnc_RNA | lncrna |
| 61920 | enst00000442500 | sg00000226921 | linc00454-203 | 13 | 113878628 | 113883533 | - | lnc_RNA | lncrna |
| 61944 | enst00000430978 | sg00000226921 | linc00454-202 | 13 | 113878489 | 113883557 | - | lnc_RNA | lncrna |
| 62036 | enst00000661456 | sg00000226921 | linc00454-208 | 13 | 113878628 | 113883649 | - | lnc_RNA | lncrna |
| 62038 | enst00000609861 | sg00000226921 | linc00454-206 | 13 | 113878628 | 113883651 | - | lnc_RNA | lncrna |
| 62054 | enst00000455857 | sg00000274766 | bx072579.2-201 | 13 | 113883667 | 113885335 | + | lnc_RNA | lncrna |
| 62090 | enst00000655130 | sg00000274766 | bx072579.2-204 | 13 | 113883703 | 113887149 | + | lnc_RNA | lncrna |
| 62094 | enst00000657154 | sg00000274766 | bx072579.2-203 | 13 | 113883707 | 113887147 | + | lnc_RNA | lncrna |
| 62124 | enst00000666964 | sg00000274766 | bx072579.2-202 | 13 | 113883737 | 113887142 | + | lnc_RNA | lncrna |
| 66693 | enst00000609661 | sg00000229373 | linc00452-202 | 13 | 113888306 | 113923512 | + | lnc_RNA | lncrna |
| -69285 | enst00000625151 | sg00000279770 | linc00552-201 | 13 | 113748511 | 113751089 | - | unconfirmed_transcript | tec |
| 73490 | enst00000426859 | sg00000229373 | linc00452-201 | 13 | 113895103 | 113921317 | + | lnc_RNA | lncrna |
| -85899 | enst00000606140 | sg00000185974 | grk1-203 | 13 | 113734475 | 113737735 | + | lnc_RNA | retained_intron |
| -93888 | enst00000545304 | sg00000185974 | grk1-202 | 13 | 113726486 | 113735236 | + | lnc_RNA | processed_transcript |
| 94328 | enst00000671032 | sg00000229373 | linc00452-203 | 13 | 113915941 | 113920995 | + | lnc_RNA | lncrna |
| 107231 | enst00000562710 | sg00000260910 | linc00565-201 | 13 | 113926514 | 113928844 | - | lnc_RNA | lncrna |
| 148796 | enst00000637024 | sg00000283199 | c13orf46-202 | 13 | 113956549 | 113970409 | - | lnc_RNA | processed_transcript |
| 152463 | enst00000636427 | sg00000283199 | c13orf46-201 | 13 | 113953705 | 113974076 | - | mRNA | protein_coding |
| -153155 | enst00000335678 | sg00000185974 | grk1-201 | 13 | 113667219 | 113737736 | + | mRNA | protein_coding |
| -162176 | enst00000335288 | sg00000186009 | atp4b-201 | 13 | 113648804 | 113658198 | - | mRNA | protein_coding |
| -183223 | enst00000494812 | sg00000198176 | tfdp1-207 | 13 | 113637151 | 113640684 | + | lnc_RNA | processed_transcript |
| 214580 | enst00000542651 | sg00000185989 | rasa3-202 | 13 | 114021409 | 114036193 | - | lnc_RNA | processed_transcript |
| -234948 | enst00000453989 | sg00000198176 | tfdp1-203 | 13 | 113585426 | 113633287 | + | mRNA | protein_coding |
| -235041 | enst00000408980 | sg00000198176 | tfdp1-202 | 13 | 113585333 | 113635996 | + | mRNA | protein_coding |
| -235101 | enst00000544902 | sg00000198176 | tfdp1-208 | 13 | 113585273 | 113640310 | + | mRNA | nonsense_mediated_decay |
| -235621 | enst00000375370 | sg00000198176 | tfdp1-201 | 13 | 113584753 | 113641473 | + | mRNA | protein_coding |
| -235631 | enst00000465174 | sg00000198176 | tfdp1-205 | 13 | 113584743 | 113633999 | + | lnc_RNA | processed_transcript |
| -235641 | enst00000464794 | sg00000198176 | tfdp1-204 | 13 | 113584733 | 113586180 | + | lnc_RNA | processed_transcript |
| -235653 | enst00000475254 | sg00000198176 | tfdp1-206 | 13 | 113584721 | 113633285 | + | lnc_RNA | processed_transcript |
| -272041 | enst00000619336 | sg00000150403 | tmco3-209 | 13 | 113548333 | 113552214 | + | mRNA | nonsense_mediated_decay |
| -272071 | enst00000620021 | sg00000150403 | tmco3-210 | 13 | 113548303 | 113554590 | + | mRNA | protein_coding |
| -273225 | enst00000491166 | sg00000150403 | tmco3-208 | 13 | 113547149 | 113549638 | + | lnc_RNA | processed_transcript |
| -274619 | enst00000460039 | sg00000150403 | tmco3-203 | 13 | 113545755 | 113549915 | + | lnc_RNA | processed_transcript |
| 287207 | enst00000454005 | sg00000232487 | rasa3-it1-201 | 13 | 114107569 | 114108820 | - | lnc_RNA | lncrna |
| -293114 | enst00000619092 | sg00000276248 | al442125.1-201 | 13 | 113527260 | 113530621 | + | lnc_RNA | lncrna |
| -299828 | enst00000465556 | sg00000150403 | tmco3-205 | 13 | 113520546 | 113539482 | + | lnc_RNA | processed_transcript |
| -308627 | enst00000619338 | sg00000276916 | al442125.2-201 | 13 | 113511747 | 113514473 | + | lnc_RNA | lncrna |
| 311010 | enst00000334062 | sg00000185989 | rasa3-201 | 13 | 113977783 | 114132623 | - | mRNA | protein_coding |
| -320350 | enst00000622371 | sg00000150403 | tmco3-211 | 13 | 113500024 | 113506062 | + | mRNA | protein_coding |
| -320353 | enst00000462877 | sg00000150403 | tmco3-204 | 13 | 113500021 | 113520661 | + | mRNA | protein_coding |
| -324503 | enst00000473287 | sg00000150403 | tmco3-206 | 13 | 113495871 | 113498645 | + | mRNA | protein_coding |
| -329278 | enst00000474393 | sg00000150403 | tmco3-207 | 13 | 113491096 | 113535286 | + | mRNA | protein_coding |
| -329331 | enst00000375391 | sg00000150403 | tmco3-201 | 13 | 113491043 | 113550229 | + | mRNA | protein_coding |
| -329353 | enst00000434316 | sg00000150403 | tmco3-202 | 13 | 113491021 | 113550229 | + | mRNA | protein_coding |
| -329423 | enst00000496873 | sg00000150401 | dcun1d2-211 | 13 | 113474210 | 113490951 | - | mRNA | protein_coding |
| -329663 | enst00000478244 | sg00000150401 | dcun1d2-208 | 13 | 113455819 | 113490711 | - | mRNA | protein_coding |
| -329683 | enst00000439909 | sg00000150401 | dcun1d2-204 | 13 | 113480648 | 113490691 | - | mRNA | protein_coding |
| -329683 | enst00000332592 | sg00000150401 | dcun1d2-201 | 13 | 113455819 | 113490691 | - | mRNA | protein_coding |
| -329683 | enst00000375403 | sg00000150401 | dcun1d2-202 | 13 | 113455819 | 113490691 | - | mRNA | nonsense_mediated_decay |
| -329766 | enst00000438545 | sg00000150401 | dcun1d2-203 | 13 | 113459312 | 113490608 | - | mRNA | nonsense_mediated_decay |
| -329880 | enst00000465710 | sg00000150401 | dcun1d2-206 | 13 | 113483963 | 113490494 | - | mRNA | protein_coding |
| 333078 | enst00000643687 | sg00000283361 | cfap97d2-205 | 13 | 114154691 | 114179420 | + | mRNA | protein_coding |
| -336184 | enst00000465938 | sg00000150401 | dcun1d2-207 | 13 | 113474197 | 113484190 | - | mRNA | protein_coding |
| -336378 | enst00000460318 | sg00000150401 | dcun1d2-205 | 13 | 113480466 | 113483996 | - | lnc_RNA | processed_transcript |
| -341296 | enst00000365477 | sg00000202347 | rnu1-16p-201 | 13 | 113478915 | 113479078 | - | snRNA | snrna |
| -344984 | enst00000453584 | sg00000233613 | dcun1d2-as-202 | 13 | 113475390 | 113476135 | + | lnc_RNA | lncrna |
| -351473 | enst00000414992 | sg00000233613 | dcun1d2-as-201 | 13 | 113468901 | 113476135 | + | lnc_RNA | lncrna |
| -357286 | enst00000491647 | sg00000150401 | dcun1d2-210 | 13 | 113461055 | 113463088 | - | lnc_RNA | retained_intron |
| 357625 | enst00000635974 | sg00000283361 | cfap97d2-203 | 13 | 114179238 | 114222770 | + | lnc_RNA | processed_transcript |
| 357637 | enst00000635901 | sg00000283361 | cfap97d2-202 | 13 | 114179250 | 114223084 | + | mRNA | protein_coding |
| 357718 | enst00000646158 | sg00000283361 | cfap97d2-206 | 13 | 114179331 | 114222518 | + | mRNA | protein_coding |
| 357718 | enst00000636692 | sg00000283361 | cfap97d2-204 | 13 | 114179331 | 114222776 | + | mRNA | protein_coding |
| -360831 | enst00000482038 | sg00000150401 | dcun1d2-209 | 13 | 113457797 | 113459543 | - | lnc_RNA | retained_intron |
| -366850 | enst00000612156 | sg00000153531 | adprhl1-204 | 13 | 113399610 | 113453524 | - | mRNA | protein_coding |
| -366850 | enst00000375418 | sg00000153531 | adprhl1-202 | 13 | 113422633 | 113453524 | - | mRNA | protein_coding |
| -371097 | enst00000413169 | sg00000153531 | adprhl1-203 | 13 | 113425052 | 113449277 | - | mRNA | protein_coding |
| -371232 | enst00000356501 | sg00000153531 | adprhl1-201 | 13 | 113421940 | 113449142 | - | mRNA | protein_coding |
| 378091 | enst00000635874 | sg00000283361 | cfap97d2-201 | 13 | 114199704 | 114222600 | + | lnc_RNA | processed_transcript |
| 394222 | enst00000637433 | sg00000283347 | al160396.1-201 | 13 | 114175485 | 114215835 | - | lnc_RNA | lncrna |
| 413274 | enst00000628084 | sg00000130177 | cdc16-211 | 13 | 114234887 | 114272675 | + | mRNA | protein_coding |
| 413274 | enst00000360383 | sg00000130177 | cdc16-204 | 13 | 114234887 | 114272675 | + | mRNA | protein_coding |
| 413284 | enst00000356221 | sg00000130177 | cdc16-203 | 13 | 114234897 | 114272723 | + | mRNA | protein_coding |
| 413321 | enst00000650489 | sg00000130177 | cdc16-212 | 13 | 114234934 | 114272657 | + | mRNA | nonsense_mediated_decay |
| 413366 | enst00000375310 | sg00000130177 | cdc16-206 | 13 | 114234979 | 114272675 | + | mRNA | protein_coding |
| 413405 | enst00000494766 | sg00000130177 | cdc16-210 | 13 | 114235018 | 114242675 | + | lnc_RNA | retained_intron |
| 413448 | enst00000375308 | sg00000130177 | cdc16-205 | 13 | 114235061 | 114272675 | + | mRNA | protein_coding |
| 413448 | enst00000252457 | sg00000130177 | cdc16-201 | 13 | 114235061 | 114272675 | + | mRNA | protein_coding |
| 413468 | enst00000252458 | sg00000130177 | cdc16-202 | 13 | 114235081 | 114272723 | + | mRNA | protein_coding |
| 422892 | enst00000582191 | sg00000264539 | mir548ar-201 | 13 | 114244505 | 114244561 | + | miRNA | mirna |
| 422949 | enst00000484907 | sg00000130177 | cdc16-208 | 13 | 114244562 | 114262979 | + | lnc_RNA | retained_intron |
| 424130 | enst00000494581 | sg00000130177 | cdc16-209 | 13 | 114245743 | 114247237 | + | lnc_RNA | processed_transcript |
| 442599 | enst00000461716 | sg00000130177 | cdc16-207 | 13 | 114264212 | 114272485 | + | lnc_RNA | processed_transcript |
| 452215 | enst00000580432 | sg00000265450 | mir4502-201 | 13 | 114273828 | 114273908 | + | miRNA | mirna |
| 455710 | enst00000649577 | sg00000285672 | al160396.2-201 | 13 | 114275326 | 114277323 | - | lnc_RNA | lncrna |
| -456226 | enst00000375430 | sg00000139835 | grtp1-202 | 13 | 113324845 | 113364148 | - | mRNA | protein_coding |
| -456226 | enst00000620217 | sg00000139835 | grtp1-205 | 13 | 113324164 | 113364148 | - | mRNA | protein_coding |
| -456243 | enst00000476439 | sg00000139835 | grtp1-204 | 13 | 113359617 | 113364131 | - | lnc_RNA | processed_transcript |
| -456244 | enst00000375431 | sg00000139835 | grtp1-203 | 13 | 113324163 | 113364130 | - | mRNA | protein_coding |
| 459988 | enst00000375299 | sg00000169062 | upf3a-202 | 13 | 114281601 | 114305817 | + | mRNA | protein_coding |
| 459990 | enst00000492270 | sg00000169062 | upf3a-209 | 13 | 114281603 | 114282270 | + | mRNA | protein_coding |
| 460015 | enst00000351487 | sg00000169062 | upf3a-201 | 13 | 114281628 | 114305808 | + | mRNA | protein_coding |
| 460024 | enst00000618700 | sg00000169062 | upf3a-211 | 13 | 114281637 | 114283729 | + | lnc_RNA | retained_intron |
| 460032 | enst00000484246 | sg00000169062 | upf3a-208 | 13 | 114281645 | 114291757 | + | lnc_RNA | processed_transcript |
| 460107 | enst00000480362 | sg00000169062 | upf3a-206 | 13 | 114281720 | 114304949 | + | lnc_RNA | processed_transcript |
| 460312 | enst00000474056 | sg00000169062 | upf3a-203 | 13 | 114281925 | 114301792 | + | lnc_RNA | processed_transcript |
| 460340 | enst00000493727 | sg00000169062 | upf3a-210 | 13 | 114281953 | 114301756 | + | lnc_RNA | processed_transcript |
| 463464 | enst00000619079 | sg00000169062 | upf3a-212 | 13 | 114285077 | 114287617 | + | lnc_RNA | retained_intron |
| 464362 | enst00000481131 | sg00000169062 | upf3a-207 | 13 | 114285975 | 114291718 | + | lnc_RNA | processed_transcript |
| 464761 | enst00000479712 | sg00000169062 | upf3a-205 | 13 | 114286374 | 114291744 | + | lnc_RNA | processed_transcript |
| 464772 | enst00000475218 | sg00000169062 | upf3a-204 | 13 | 114286385 | 114305808 | + | lnc_RNA | processed_transcript |
| -464938 | enst00000326039 | sg00000139835 | grtp1-201 | 13 | 113325062 | 113355436 | - | mRNA | protein_coding |
| -468558 | enst00000423246 | sg00000225083 | grtp1-as1-202 | 13 | 113351816 | 113361868 | + | lnc_RNA | lncrna |
| -468701 | enst00000419199 | sg00000225083 | grtp1-as1-201 | 13 | 113351673 | 113355734 | + | lnc_RNA | lncrna |
| -468729 | enst00000669000 | sg00000225083 | grtp1-as1-203 | 13 | 113351645 | 113356010 | + | lnc_RNA | lncrna |
| -480416 | enst00000621449 | sg00000276434 | al136221.1-201 | 13 | 113339450 | 113339958 | - | lnc_RNA | lncrna |
| 485033 | enst00000392050 | sg00000226158 | clcp2-201 | 13 | 114306646 | 114307066 | + | pseudogenic_transcript | processed_pseudogene |
| 492869 | enst00000646956 | sg00000198824 | champ1-208 | 13 | 114314482 | 114337626 | + | lnc_RNA | processed_transcript |
| 492875 | enst00000463003 | sg00000198824 | champ1-202 | 13 | 114314488 | 114324279 | + | mRNA | protein_coding |
| 492877 | enst00000645174 | sg00000198824 | champ1-206 | 13 | 114314490 | 114324208 | + | mRNA | protein_coding |
| 492890 | enst00000361283 | sg00000198824 | champ1-201 | 13 | 114314503 | 114327322 | + | mRNA | protein_coding |
| 492908 | enst00000646155 | sg00000198824 | champ1-207 | 13 | 114314521 | 114337626 | + | lnc_RNA | processed_transcript |
| 492918 | enst00000478022 | sg00000198824 | champ1-203 | 13 | 114314531 | 114322441 | + | lnc_RNA | processed_transcript |
| 492935 | enst00000644294 | sg00000198824 | champ1-205 | 13 | 114314548 | 114324425 | + | mRNA | protein_coding |
| -498607 | enst00000471046 | sg00000185896 | lamp1-202 | 13 | 113321767 | 113322594 | + | lnc_RNA | processed_transcript |
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