PycoMeth
Documentation
GitHub
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 |
|---|---|---|---|---|---|---|---|---|
| #129 | 13 | 113729703 | 113730407 | 704 | 3 | 36 | 2.06485e-16 | 1.59186e-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 |
|---|---|---|---|---|---|---|---|---|---|
| -3217 | enst00000545304 | sg00000185974 | grk1-202 | 13 | 113726486 | 113735236 | + | lnc_RNA | processed_transcript |
| 4068 | enst00000606140 | sg00000185974 | grk1-203 | 13 | 113734475 | 113737735 | + | lnc_RNA | retained_intron |
| 20682 | enst00000625151 | sg00000279770 | linc00552-201 | 13 | 113748511 | 113751089 | - | unconfirmed_transcript | tec |
| 28819 | enst00000375353 | sg00000184497 | tmem255b-202 | 13 | 113759226 | 113816995 | + | mRNA | protein_coding |
| 28833 | enst00000488362 | sg00000184497 | tmem255b-205 | 13 | 113759240 | 113799660 | + | mRNA | protein_coding |
| 35757 | enst00000483678 | sg00000184497 | tmem255b-204 | 13 | 113766164 | 113769815 | + | lnc_RNA | processed_transcript |
| 37729 | enst00000375348 | sg00000184497 | tmem255b-201 | 13 | 113768136 | 113799857 | + | lnc_RNA | processed_transcript |
| -62484 | enst00000335678 | sg00000185974 | grk1-201 | 13 | 113667219 | 113737736 | + | mRNA | protein_coding |
| 69481 | enst00000498692 | sg00000184497 | tmem255b-206 | 13 | 113799888 | 113804890 | + | lnc_RNA | processed_transcript |
| -71505 | enst00000335288 | sg00000186009 | atp4b-201 | 13 | 113648804 | 113658198 | - | mRNA | protein_coding |
| 72643 | enst00000467169 | sg00000184497 | tmem255b-203 | 13 | 113803050 | 113811953 | + | lnc_RNA | processed_transcript |
| 85223 | enst00000458001 | sg00000233695 | gas6-as1-201 | 13 | 113815630 | 113845744 | + | lnc_RNA | lncrna |
| -92552 | enst00000494812 | sg00000198176 | tfdp1-207 | 13 | 113637151 | 113640684 | + | lnc_RNA | processed_transcript |
| 92787 | enst00000608763 | sg00000183087 | gas6-204 | 13 | 113820549 | 113823194 | - | lnc_RNA | retained_intron |
| 103334 | enst00000480426 | sg00000183087 | gas6-203 | 13 | 113820549 | 113833741 | - | lnc_RNA | retained_intron |
| 105637 | enst00000610073 | sg00000183087 | gas6-205 | 13 | 113820552 | 113836044 | - | lnc_RNA | retained_intron |
| 112083 | enst00000611082 | sg00000233695 | gas6-as1-202 | 13 | 113842490 | 113844306 | + | lnc_RNA | lncrna |
| 133608 | enst00000476291 | sg00000183087 | gas6-202 | 13 | 113847677 | 113864015 | - | lnc_RNA | processed_transcript |
| 133669 | enst00000327773 | sg00000183087 | gas6-201 | 13 | 113820549 | 113864076 | - | mRNA | protein_coding |
| 133705 | enst00000669254 | sg00000272695 | gas6-dt-203 | 13 | 113864112 | 113866834 | + | lnc_RNA | lncrna |
| 133711 | enst00000655351 | sg00000272695 | gas6-dt-202 | 13 | 113864118 | 113866618 | + | lnc_RNA | lncrna |
| 133761 | enst00000608651 | sg00000272695 | gas6-dt-201 | 13 | 113864168 | 113866833 | + | lnc_RNA | lncrna |
| -144277 | enst00000453989 | sg00000198176 | tfdp1-203 | 13 | 113585426 | 113633287 | + | mRNA | protein_coding |
| -144370 | enst00000408980 | sg00000198176 | tfdp1-202 | 13 | 113585333 | 113635996 | + | mRNA | protein_coding |
| -144430 | enst00000544902 | sg00000198176 | tfdp1-208 | 13 | 113585273 | 113640310 | + | mRNA | nonsense_mediated_decay |
| -144950 | enst00000375370 | sg00000198176 | tfdp1-201 | 13 | 113584753 | 113641473 | + | mRNA | protein_coding |
| -144960 | enst00000465174 | sg00000198176 | tfdp1-205 | 13 | 113584743 | 113633999 | + | lnc_RNA | processed_transcript |
| -144970 | enst00000464794 | sg00000198176 | tfdp1-204 | 13 | 113584733 | 113586180 | + | lnc_RNA | processed_transcript |
| -144982 | enst00000475254 | sg00000198176 | tfdp1-206 | 13 | 113584721 | 113633285 | + | lnc_RNA | processed_transcript |
| 147201 | enst00000449453 | sg00000237699 | bx072579.1-201 | 13 | 113877608 | 113879376 | + | lnc_RNA | lncrna |
| 148006 | enst00000648342 | sg00000237699 | bx072579.1-202 | 13 | 113878413 | 113879367 | + | lnc_RNA | lncrna |
| 150969 | enst00000671045 | sg00000226921 | linc00454-209 | 13 | 113878630 | 113881376 | - | lnc_RNA | lncrna |
| 151523 | enst00000608044 | sg00000226921 | linc00454-204 | 13 | 113879004 | 113881930 | - | lnc_RNA | lncrna |
| 151795 | enst00000610194 | sg00000226921 | linc00454-207 | 13 | 113879011 | 113882202 | - | lnc_RNA | lncrna |
| 152921 | enst00000609493 | sg00000226921 | linc00454-205 | 13 | 113879004 | 113883328 | - | lnc_RNA | lncrna |
| 153071 | enst00000425483 | sg00000226921 | linc00454-201 | 13 | 113880382 | 113883478 | - | lnc_RNA | lncrna |
| 153126 | enst00000442500 | sg00000226921 | linc00454-203 | 13 | 113878628 | 113883533 | - | lnc_RNA | lncrna |
| 153150 | enst00000430978 | sg00000226921 | linc00454-202 | 13 | 113878489 | 113883557 | - | lnc_RNA | lncrna |
| 153242 | enst00000661456 | sg00000226921 | linc00454-208 | 13 | 113878628 | 113883649 | - | lnc_RNA | lncrna |
| 153244 | enst00000609861 | sg00000226921 | linc00454-206 | 13 | 113878628 | 113883651 | - | lnc_RNA | lncrna |
| 153260 | enst00000455857 | sg00000274766 | bx072579.2-201 | 13 | 113883667 | 113885335 | + | lnc_RNA | lncrna |
| 153296 | enst00000655130 | sg00000274766 | bx072579.2-204 | 13 | 113883703 | 113887149 | + | lnc_RNA | lncrna |
| 153300 | enst00000657154 | sg00000274766 | bx072579.2-203 | 13 | 113883707 | 113887147 | + | lnc_RNA | lncrna |
| 153330 | enst00000666964 | sg00000274766 | bx072579.2-202 | 13 | 113883737 | 113887142 | + | lnc_RNA | lncrna |
| 157899 | enst00000609661 | sg00000229373 | linc00452-202 | 13 | 113888306 | 113923512 | + | lnc_RNA | lncrna |
| 164696 | enst00000426859 | sg00000229373 | linc00452-201 | 13 | 113895103 | 113921317 | + | lnc_RNA | lncrna |
| -181370 | enst00000619336 | sg00000150403 | tmco3-209 | 13 | 113548333 | 113552214 | + | mRNA | nonsense_mediated_decay |
| -181400 | enst00000620021 | sg00000150403 | tmco3-210 | 13 | 113548303 | 113554590 | + | mRNA | protein_coding |
| -182554 | enst00000491166 | sg00000150403 | tmco3-208 | 13 | 113547149 | 113549638 | + | lnc_RNA | processed_transcript |
| -183948 | enst00000460039 | sg00000150403 | tmco3-203 | 13 | 113545755 | 113549915 | + | lnc_RNA | processed_transcript |
| 185534 | enst00000671032 | sg00000229373 | linc00452-203 | 13 | 113915941 | 113920995 | + | lnc_RNA | lncrna |
| 198437 | enst00000562710 | sg00000260910 | linc00565-201 | 13 | 113926514 | 113928844 | - | lnc_RNA | lncrna |
| -202443 | enst00000619092 | sg00000276248 | al442125.1-201 | 13 | 113527260 | 113530621 | + | lnc_RNA | lncrna |
| -209157 | enst00000465556 | sg00000150403 | tmco3-205 | 13 | 113520546 | 113539482 | + | lnc_RNA | processed_transcript |
| -217956 | enst00000619338 | sg00000276916 | al442125.2-201 | 13 | 113511747 | 113514473 | + | lnc_RNA | lncrna |
| -229679 | enst00000622371 | sg00000150403 | tmco3-211 | 13 | 113500024 | 113506062 | + | mRNA | protein_coding |
| -229682 | enst00000462877 | sg00000150403 | tmco3-204 | 13 | 113500021 | 113520661 | + | mRNA | protein_coding |
| -233832 | enst00000473287 | sg00000150403 | tmco3-206 | 13 | 113495871 | 113498645 | + | mRNA | protein_coding |
| -238607 | enst00000474393 | sg00000150403 | tmco3-207 | 13 | 113491096 | 113535286 | + | mRNA | protein_coding |
| -238660 | enst00000375391 | sg00000150403 | tmco3-201 | 13 | 113491043 | 113550229 | + | mRNA | protein_coding |
| -238682 | enst00000434316 | sg00000150403 | tmco3-202 | 13 | 113491021 | 113550229 | + | mRNA | protein_coding |
| -238752 | enst00000496873 | sg00000150401 | dcun1d2-211 | 13 | 113474210 | 113490951 | - | mRNA | protein_coding |
| -238992 | enst00000478244 | sg00000150401 | dcun1d2-208 | 13 | 113455819 | 113490711 | - | mRNA | protein_coding |
| -239012 | enst00000332592 | sg00000150401 | dcun1d2-201 | 13 | 113455819 | 113490691 | - | mRNA | protein_coding |
| -239012 | enst00000375403 | sg00000150401 | dcun1d2-202 | 13 | 113455819 | 113490691 | - | mRNA | nonsense_mediated_decay |
| -239012 | enst00000439909 | sg00000150401 | dcun1d2-204 | 13 | 113480648 | 113490691 | - | mRNA | protein_coding |
| -239095 | enst00000438545 | sg00000150401 | dcun1d2-203 | 13 | 113459312 | 113490608 | - | mRNA | nonsense_mediated_decay |
| -239209 | enst00000465710 | sg00000150401 | dcun1d2-206 | 13 | 113483963 | 113490494 | - | mRNA | protein_coding |
| 240002 | enst00000637024 | sg00000283199 | c13orf46-202 | 13 | 113956549 | 113970409 | - | lnc_RNA | processed_transcript |
| 243669 | enst00000636427 | sg00000283199 | c13orf46-201 | 13 | 113953705 | 113974076 | - | mRNA | protein_coding |
| -245513 | enst00000465938 | sg00000150401 | dcun1d2-207 | 13 | 113474197 | 113484190 | - | mRNA | protein_coding |
| -245707 | enst00000460318 | sg00000150401 | dcun1d2-205 | 13 | 113480466 | 113483996 | - | lnc_RNA | processed_transcript |
| -250625 | enst00000365477 | sg00000202347 | rnu1-16p-201 | 13 | 113478915 | 113479078 | - | snRNA | snrna |
| -254313 | enst00000453584 | sg00000233613 | dcun1d2-as-202 | 13 | 113475390 | 113476135 | + | lnc_RNA | lncrna |
| -260802 | enst00000414992 | sg00000233613 | dcun1d2-as-201 | 13 | 113468901 | 113476135 | + | lnc_RNA | lncrna |
| -266615 | enst00000491647 | sg00000150401 | dcun1d2-210 | 13 | 113461055 | 113463088 | - | lnc_RNA | retained_intron |
| -270160 | enst00000482038 | sg00000150401 | dcun1d2-209 | 13 | 113457797 | 113459543 | - | lnc_RNA | retained_intron |
| -276179 | enst00000612156 | sg00000153531 | adprhl1-204 | 13 | 113399610 | 113453524 | - | mRNA | protein_coding |
| -276179 | enst00000375418 | sg00000153531 | adprhl1-202 | 13 | 113422633 | 113453524 | - | mRNA | protein_coding |
| -280426 | enst00000413169 | sg00000153531 | adprhl1-203 | 13 | 113425052 | 113449277 | - | mRNA | protein_coding |
| -280561 | enst00000356501 | sg00000153531 | adprhl1-201 | 13 | 113421940 | 113449142 | - | mRNA | protein_coding |
| 305786 | enst00000542651 | sg00000185989 | rasa3-202 | 13 | 114021409 | 114036193 | - | lnc_RNA | processed_transcript |
| -365555 | enst00000375430 | sg00000139835 | grtp1-202 | 13 | 113324845 | 113364148 | - | mRNA | protein_coding |
| -365555 | enst00000620217 | sg00000139835 | grtp1-205 | 13 | 113324164 | 113364148 | - | mRNA | protein_coding |
| -365572 | enst00000476439 | sg00000139835 | grtp1-204 | 13 | 113359617 | 113364131 | - | lnc_RNA | processed_transcript |
| -365573 | enst00000375431 | sg00000139835 | grtp1-203 | 13 | 113324163 | 113364130 | - | mRNA | protein_coding |
| -374267 | enst00000326039 | sg00000139835 | grtp1-201 | 13 | 113325062 | 113355436 | - | mRNA | protein_coding |
| -377887 | enst00000423246 | sg00000225083 | grtp1-as1-202 | 13 | 113351816 | 113361868 | + | lnc_RNA | lncrna |
| -378030 | enst00000419199 | sg00000225083 | grtp1-as1-201 | 13 | 113351673 | 113355734 | + | lnc_RNA | lncrna |
| -378058 | enst00000669000 | sg00000225083 | grtp1-as1-203 | 13 | 113351645 | 113356010 | + | lnc_RNA | lncrna |
| 378413 | enst00000454005 | sg00000232487 | rasa3-it1-201 | 13 | 114107569 | 114108820 | - | lnc_RNA | lncrna |
| -389745 | enst00000621449 | sg00000276434 | al136221.1-201 | 13 | 113339450 | 113339958 | - | lnc_RNA | lncrna |
| 402216 | enst00000334062 | sg00000185989 | rasa3-201 | 13 | 113977783 | 114132623 | - | mRNA | protein_coding |
| -407936 | enst00000471046 | sg00000185896 | lamp1-202 | 13 | 113321767 | 113322594 | + | lnc_RNA | processed_transcript |
| 424284 | enst00000643687 | sg00000283361 | cfap97d2-205 | 13 | 114154691 | 114179420 | + | mRNA | protein_coding |
| -424771 | enst00000472564 | sg00000185896 | lamp1-203 | 13 | 113304932 | 113323430 | + | lnc_RNA | retained_intron |
| -432464 | enst00000332556 | sg00000185896 | lamp1-201 | 13 | 113297239 | 113323672 | + | mRNA | protein_coding |
| 448831 | enst00000635974 | sg00000283361 | cfap97d2-203 | 13 | 114179238 | 114222770 | + | lnc_RNA | processed_transcript |
| 448843 | enst00000635901 | sg00000283361 | cfap97d2-202 | 13 | 114179250 | 114223084 | + | mRNA | protein_coding |
| 448924 | enst00000636692 | sg00000283361 | cfap97d2-204 | 13 | 114179331 | 114222776 | + | mRNA | protein_coding |
| 448924 | enst00000646158 | sg00000283361 | cfap97d2-206 | 13 | 114179331 | 114222518 | + | mRNA | protein_coding |
| -453087 | enst00000455730 | sg00000232662 | ldhbp1-201 | 13 | 113276616 | 113277734 | + | pseudogenic_transcript | processed_pseudogene |
| -466783 | enst00000614354 | sg00000277942 | mir8075-201 | 13 | 113262920 | 113262999 | + | miRNA | mirna |
| 469297 | enst00000635874 | sg00000283361 | cfap97d2-201 | 13 | 114199704 | 114222600 | + | lnc_RNA | processed_transcript |
| -483747 | enst00000472083 | sg00000139842 | cul4a-207 | 13 | 113245956 | 113263559 | + | lnc_RNA | processed_transcript |
| 485428 | enst00000637433 | sg00000283347 | al160396.1-201 | 13 | 114175485 | 114215835 | - | lnc_RNA | lncrna |
| -485480 | enst00000470067 | sg00000139842 | cul4a-206 | 13 | 113244223 | 113254775 | + | 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