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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 |
|---|---|---|---|---|---|---|---|---|
| #93 | 1 | 203075448 | 203076659 | 1211 | 3 | 41 | 5.13466e-18 | 5.49077e-16 |
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 | enst00000594572 | sg00000143847 | ppfia4-206 | 1 | 203076003 | 203076981 | + | lnc_RNA | processed_transcript |
| -8003 | enst00000597023 | sg00000143847 | ppfia4-208 | 1 | 203067445 | 203068600 | + | lnc_RNA | retained_intron |
| 9353 | enst00000241651 | sg00000122180 | myog-201 | 1 | 203083129 | 203086012 | - | mRNA | protein_coding |
| -12489 | enst00000486360 | sg00000143847 | ppfia4-205 | 1 | 203062959 | 203078735 | + | lnc_RNA | retained_intron |
| 13995 | enst00000309502 | sg00000163485 | adora1-201 | 1 | 203090654 | 203167404 | + | mRNA | protein_coding |
| -14082 | enst00000594656 | sg00000143847 | ppfia4-207 | 1 | 203061366 | 203067765 | + | lnc_RNA | retained_intron |
| -21702 | enst00000599514 | sg00000143847 | ppfia4-209 | 1 | 203053746 | 203056806 | + | mRNA | protein_coding |
| -21745 | enst00000600447 | sg00000143847 | ppfia4-212 | 1 | 203053703 | 203055557 | + | lnc_RNA | retained_intron |
| -24208 | enst00000599966 | sg00000143847 | ppfia4-210 | 1 | 203051240 | 203076953 | + | mRNA | protein_coding |
| -24265 | enst00000272198 | sg00000143847 | ppfia4-201 | 1 | 203051183 | 203078736 | + | mRNA | protein_coding |
| -29982 | enst00000600426 | sg00000143847 | ppfia4-211 | 1 | 203045466 | 203076497 | + | mRNA | protein_coding |
| -30039 | enst00000601609 | sg00000143847 | ppfia4-213 | 1 | 203045409 | 203046507 | + | lnc_RNA | retained_intron |
| -40964 | enst00000295706 | sg00000143847 | ppfia4-202 | 1 | 203034484 | 203078735 | + | mRNA | protein_coding |
| -40964 | enst00000447715 | sg00000143847 | ppfia4-204 | 1 | 203034484 | 203078740 | + | mRNA | protein_coding |
| -48950 | enst00000367240 | sg00000143847 | ppfia4-203 | 1 | 203026498 | 203078736 | + | mRNA | protein_coding |
| 50406 | enst00000367236 | sg00000163485 | adora1-204 | 1 | 203127065 | 203167405 | + | mRNA | protein_coding |
| 51049 | enst00000640524 | sg00000163485 | adora1-209 | 1 | 203127708 | 203165089 | + | mRNA | protein_coding |
| 51067 | enst00000337894 | sg00000163485 | adora1-202 | 1 | 203127726 | 203167405 | + | mRNA | protein_coding |
| 51295 | enst00000421055 | sg00000234775 | ac105940.2-201 | 1 | 203127259 | 203127954 | - | lnc_RNA | lncrna |
| 51647 | enst00000367235 | sg00000163485 | adora1-203 | 1 | 203128306 | 203166749 | + | mRNA | protein_coding |
| 51708 | enst00000665660 | sg00000234775 | ac105940.2-202 | 1 | 203115468 | 203128367 | - | lnc_RNA | lncrna |
| 51714 | enst00000618295 | sg00000163485 | adora1-208 | 1 | 203128373 | 203166062 | + | mRNA | protein_coding |
| 52975 | enst00000464019 | sg00000163485 | adora1-205 | 1 | 203129634 | 203165741 | + | lnc_RNA | processed_transcript |
| -59608 | enst00000488097 | sg00000163444 | tmem183a-204 | 1 | 203015840 | 203020801 | + | lnc_RNA | retained_intron |
| -66708 | enst00000463015 | sg00000163444 | tmem183a-202 | 1 | 203008740 | 203015572 | + | lnc_RNA | retained_intron |
| -67674 | enst00000468449 | sg00000163444 | tmem183a-203 | 1 | 203007774 | 203017919 | + | lnc_RNA | processed_transcript |
| -68045 | enst00000543891 | sg00000163444 | tmem183a-205 | 1 | 203007403 | 203016094 | + | lnc_RNA | retained_intron |
| -68074 | enst00000367242 | sg00000163444 | tmem183a-201 | 1 | 203007374 | 203024848 | + | mRNA | protein_coding |
| 73973 | enst00000472535 | sg00000163485 | adora1-207 | 1 | 203150632 | 203166749 | + | lnc_RNA | processed_transcript |
| -75710 | enst00000427395 | sg00000231547 | ac096632.2-201 | 1 | 202999738 | 203000352 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 75920 | enst00000434265 | sg00000224671 | ac105940.1-201 | 1 | 203144694 | 203152579 | - | lnc_RNA | lncrna |
| 75987 | enst00000467253 | sg00000163485 | adora1-206 | 1 | 203152646 | 203166115 | + | lnc_RNA | processed_transcript |
| -86866 | enst00000438139 | sg00000234761 | mgat4fp-202 | 1 | 202986557 | 202988582 | - | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -86966 | enst00000417729 | sg00000234761 | mgat4fp-201 | 1 | 202987277 | 202988482 | - | lnc_RNA | processed_transcript |
| 99124 | enst00000621380 | sg00000133055 | mybph-202 | 1 | 203167811 | 203175783 | - | mRNA | protein_coding |
| 99167 | enst00000255416 | sg00000133055 | mybph-201 | 1 | 203167811 | 203175826 | - | mRNA | protein_coding |
| 103474 | enst00000478742 | sg00000133048 | chi3l1-205 | 1 | 203179134 | 203180133 | - | lnc_RNA | retained_intron |
| 105475 | enst00000473185 | sg00000133048 | chi3l1-204 | 1 | 203178931 | 203182134 | - | lnc_RNA | retained_intron |
| 106146 | enst00000404436 | sg00000133048 | chi3l1-202 | 1 | 203178981 | 203182805 | - | mRNA | protein_coding |
| 106182 | enst00000472064 | sg00000133048 | chi3l1-203 | 1 | 203179998 | 203182841 | - | lnc_RNA | retained_intron |
| -108173 | enst00000473599 | sg00000159348 | cyb5r1-203 | 1 | 202965371 | 202967275 | - | lnc_RNA | processed_transcript |
| -108191 | enst00000367249 | sg00000159348 | cyb5r1-201 | 1 | 202961873 | 202967257 | - | mRNA | protein_coding |
| -108205 | enst00000482572 | sg00000159348 | cyb5r1-205 | 1 | 202962547 | 202967243 | - | lnc_RNA | processed_transcript |
| -108223 | enst00000478009 | sg00000159348 | cyb5r1-204 | 1 | 202965887 | 202967225 | - | lnc_RNA | processed_transcript |
| -108888 | enst00000446185 | sg00000159348 | cyb5r1-202 | 1 | 202962926 | 202966560 | - | mRNA | protein_coding |
| 110045 | enst00000255409 | sg00000133048 | chi3l1-201 | 1 | 203178931 | 203186704 | - | mRNA | protein_coding |
| -110064 | enst00000497655 | sg00000159348 | cyb5r1-207 | 1 | 202961876 | 202965384 | - | lnc_RNA | processed_transcript |
| -111889 | enst00000483915 | sg00000159348 | cyb5r1-206 | 1 | 202962550 | 202963559 | - | lnc_RNA | processed_transcript |
| -116876 | enst00000417068 | sg00000159346 | adipor1-203 | 1 | 202943764 | 202958572 | - | mRNA | protein_coding |
| -117136 | enst00000340990 | sg00000159346 | adipor1-201 | 1 | 202940832 | 202958312 | - | mRNA | protein_coding |
| -117163 | enst00000426229 | sg00000159346 | adipor1-204 | 1 | 202944983 | 202958285 | - | mRNA | protein_coding |
| -117184 | enst00000367254 | sg00000159346 | adipor1-202 | 1 | 202941490 | 202958264 | - | mRNA | protein_coding |
| -130652 | enst00000495562 | sg00000159346 | adipor1-205 | 1 | 202940826 | 202944796 | - | lnc_RNA | retained_intron |
| 141362 | enst00000479483 | sg00000133063 | chit1-204 | 1 | 203212835 | 203218021 | - | lnc_RNA | processed_transcript |
| 145651 | enst00000506427 | sg00000133063 | chit1-208 | 1 | 203219574 | 203222310 | - | lnc_RNA | processed_transcript |
| -146812 | enst00000367258 | sg00000117153 | klhl12-201 | 1 | 202909010 | 202928636 | - | mRNA | protein_coding |
| -148214 | enst00000367261 | sg00000117153 | klhl12-203 | 1 | 202891120 | 202927234 | - | mRNA | protein_coding |
| 152986 | enst00000491855 | sg00000133063 | chit1-206 | 1 | 203216670 | 203229645 | - | mRNA | nonsense_mediated_decay |
| 153012 | enst00000255427 | sg00000133063 | chit1-201 | 1 | 203216670 | 203229671 | - | mRNA | protein_coding |
| 153012 | enst00000503786 | sg00000133063 | chit1-207 | 1 | 203216948 | 203229671 | - | mRNA | nonsense_mediated_decay |
| 153014 | enst00000367229 | sg00000133063 | chit1-202 | 1 | 203216079 | 203229673 | - | mRNA | protein_coding |
| -160468 | enst00000362601 | sg00000199471 | ac096632.1-201 | 1 | 202914880 | 202914980 | - | ncRNA | misc_rna |
| -163636 | enst00000430583 | sg00000230280 | hnrnpa1p59-201 | 1 | 202911812 | 202912729 | + | pseudogenic_transcript | processed_pseudogene |
| -166287 | enst00000367259 | sg00000117153 | klhl12-202 | 1 | 202891116 | 202909161 | - | mRNA | protein_coding |
| 179084 | enst00000412758 | sg00000236523 | npm1p40-201 | 1 | 203255743 | 203256475 | + | pseudogenic_transcript | processed_pseudogene |
| 184203 | enst00000513472 | sg00000133063 | chit1-209 | 1 | 203223588 | 203260862 | - | lnc_RNA | processed_transcript |
| -186299 | enst00000367262 | sg00000183155 | rabif-201 | 1 | 202878282 | 202889149 | - | mRNA | protein_coding |
| 196150 | enst00000484834 | sg00000133063 | chit1-205 | 1 | 203212827 | 203272809 | - | lnc_RNA | processed_transcript |
| 196562 | enst00000666545 | sg00000231507 | linc01353-205 | 1 | 203273221 | 203288712 | + | lnc_RNA | lncrna |
| 196982 | enst00000460619 | sg00000133063 | chit1-203 | 1 | 203240330 | 203273641 | - | lnc_RNA | processed_transcript |
| -202154 | enst00000438944 | sg00000234996 | ac098934.2-202 | 1 | 202873294 | 202874326 | + | pseudogenic_transcript | transcribed_processed_pseudogene |
| 205762 | enst00000657300 | sg00000231507 | linc01353-203 | 1 | 203282421 | 203288804 | + | lnc_RNA | lncrna |
| 209816 | enst00000412772 | sg00000231507 | linc01353-201 | 1 | 203286475 | 203288801 | + | lnc_RNA | lncrna |
| 209818 | enst00000662282 | sg00000231507 | linc01353-204 | 1 | 203286477 | 203288707 | + | lnc_RNA | lncrna |
| 211111 | enst00000433008 | sg00000231507 | linc01353-202 | 1 | 203287770 | 203288534 | + | lnc_RNA | lncrna |
| -213694 | enst00000456105 | sg00000234996 | ac098934.2-201 | 1 | 202861754 | 202875241 | + | lnc_RNA | processed_transcript |
| -213828 | enst00000430114 | sg00000214796 | ac098934.1-204 | 1 | 202857928 | 202861620 | - | lnc_RNA | processed_transcript |
| -213840 | enst00000443294 | sg00000214796 | ac098934.1-201 | 1 | 202851828 | 202861608 | - | lnc_RNA | processed_transcript |
| -216226 | enst00000449915 | sg00000214796 | ac098934.1-202 | 1 | 202852962 | 202859222 | - | lnc_RNA | processed_transcript |
| -216349 | enst00000442868 | sg00000214796 | ac098934.1-203 | 1 | 202852991 | 202859099 | - | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 227889 | enst00000425698 | sg00000233791 | linc01136-201 | 1 | 203300514 | 203304548 | - | lnc_RNA | lncrna |
| 228600 | enst00000432511 | sg00000233791 | linc01136-202 | 1 | 203301166 | 203305259 | - | lnc_RNA | lncrna |
| 228650 | enst00000457348 | sg00000233791 | linc01136-203 | 1 | 203298758 | 203305309 | - | lnc_RNA | lncrna |
| 228832 | enst00000475157 | sg00000159388 | btg2-202 | 1 | 203305491 | 203309569 | + | mRNA | nonsense_mediated_decay |
| 228860 | enst00000290551 | sg00000159388 | btg2-201 | 1 | 203305519 | 203309602 | + | mRNA | protein_coding |
| 242440 | enst00000365430 | sg00000202300 | rnu6-487p-201 | 1 | 203318996 | 203319099 | - | snRNA | snrna |
| -250262 | enst00000549576 | sg00000184774 | mgat4ep-202 | 1 | 202825186 | 202826320 | + | pseudogenic_transcript | transcribed_unitary_pseudogene |
| -255182 | enst00000330493 | sg00000184774 | mgat4ep-201 | 1 | 202820266 | 202827225 | + | lnc_RNA | processed_transcript |
| -264486 | enst00000417262 | sg00000228288 | pcat6-201 | 1 | 202810962 | 202811913 | + | lnc_RNA | lncrna |
| -264486 | enst00000425295 | sg00000228288 | pcat6-202 | 1 | 202810962 | 202811913 | + | lnc_RNA | lncrna |
| -264493 | enst00000660963 | sg00000228288 | pcat6-204 | 1 | 202810955 | 202811912 | + | lnc_RNA | lncrna |
| -264494 | enst00000553157 | sg00000228288 | pcat6-203 | 1 | 202810954 | 202812156 | + | lnc_RNA | lncrna |
| -264619 | enst00000564127 | sg00000260021 | ac098934.4-201 | 1 | 202810238 | 202810829 | - | lnc_RNA | lncrna |
| -266961 | enst00000650368 | sg00000117139 | kdm5b-235 | 1 | 202770097 | 202808487 | - | mRNA | protein_coding |
| -266961 | enst00000648056 | sg00000117139 | kdm5b-215 | 1 | 202727448 | 202808487 | - | mRNA | protein_coding |
| -266967 | enst00000367264 | sg00000117139 | kdm5b-202 | 1 | 202727435 | 202808481 | - | mRNA | protein_coding |
| -266967 | enst00000648473 | sg00000117139 | kdm5b-220 | 1 | 202727445 | 202808481 | - | mRNA | protein_coding |
| -266967 | enst00000650417 | sg00000117139 | kdm5b-236 | 1 | 202728481 | 202808481 | - | mRNA | nonsense_mediated_decay |
| -266975 | enst00000648338 | sg00000117139 | kdm5b-217 | 1 | 202724887 | 202808473 | - | mRNA | protein_coding |
| -266978 | enst00000648469 | sg00000117139 | kdm5b-219 | 1 | 202728291 | 202808470 | - | mRNA | protein_coding |
| -266999 | enst00000650493 | sg00000117139 | kdm5b-238 | 1 | 202773189 | 202808449 | - | mRNA | protein_coding |
| -267009 | enst00000649200 | sg00000117139 | kdm5b-226 | 1 | 202770926 | 202808439 | - | mRNA | protein_coding |
| -267015 | enst00000648958 | sg00000117139 | kdm5b-224 | 1 | 202764074 | 202808433 | - | lnc_RNA | retained_intron |
| -267027 | enst00000649770 | sg00000117139 | kdm5b-233 | 1 | 202727675 | 202808421 | - | mRNA | protein_coding |
| -267027 | enst00000367265 | sg00000117139 | kdm5b-203 | 1 | 202724495 | 202808421 | - | mRNA | protein_coding |
| -267032 | enst00000650569 | sg00000117139 | kdm5b-240 | 1 | 202727445 | 202808416 | - | mRNA | protein_coding |
| -267232 | enst00000648354 | sg00000117139 | kdm5b-218 | 1 | 202772695 | 202808216 | - | mRNA | protein_coding |
| -267323 | enst00000602511 | sg00000117139 | kdm5b-210 | 1 | 202767031 | 202808125 | - | mRNA | nonsense_mediated_decay |
| -267334 | enst00000648738 | sg00000117139 | kdm5b-222 | 1 | 202758440 | 202808114 | - | mRNA | protein_coding |
| -267396 | enst00000647757 | sg00000117139 | kdm5b-214 | 1 | 202727412 | 202808052 | - | lnc_RNA | processed_transcript |
| -267399 | enst00000649542 | sg00000117139 | kdm5b-232 | 1 | 202727405 | 202808049 | - | lnc_RNA | processed_transcript |
| -268100 | enst00000235790 | sg00000117139 | kdm5b-201 | 1 | 202729905 | 202807348 | - | mRNA | protein_coding |
| -268243 | enst00000467487 | sg00000117139 | kdm5b-205 | 1 | 202774630 | 202807205 | - | lnc_RNA | processed_transcript |
| -268697 | enst00000470573 | sg00000117139 | kdm5b-206 | 1 | 202773217 | 202806751 | - | lnc_RNA | processed_transcript |
| 274427 | enst00000461936 | sg00000122176 | fmod-202 | 1 | 203342183 | 203351086 | - | lnc_RNA | processed_transcript |
| 274429 | enst00000493296 | sg00000122176 | fmod-203 | 1 | 203341337 | 203351088 | - | lnc_RNA | processed_transcript |
| 274463 | enst00000354955 | sg00000122176 | fmod-201 | 1 | 203340628 | 203351122 | - | mRNA | protein_coding |
| 275099 | enst00000647586 | sg00000122176 | fmod-204 | 1 | 203340661 | 203351758 | - | mRNA | protein_coding |
| 276992 | enst00000381357 | sg00000229652 | al359837.1-201 | 1 | 203353365 | 203353651 | - | pseudogenic_transcript | processed_pseudogene |
| -279418 | enst00000444461 | sg00000226148 | slc25a39p1-201 | 1 | 202796030 | 202797094 | + | pseudogenic_transcript | processed_pseudogene |
| -297867 | enst00000650422 | sg00000117139 | kdm5b-237 | 1 | 202735505 | 202777581 | - | lnc_RNA | retained_intron |
| -308030 | enst00000430450 | sg00000235449 | ac098934.3-201 | 1 | 202767229 | 202767418 | - | pseudogenic_transcript | processed_pseudogene |
| -308239 | enst00000648744 | sg00000117139 | kdm5b-223 | 1 | 202760530 | 202767209 | - | lnc_RNA | retained_intron |
| -312503 | enst00000649321 | sg00000117139 | kdm5b-228 | 1 | 202754997 | 202762945 | - | lnc_RNA | retained_intron |
| -314925 | enst00000648099 | sg00000117139 | kdm5b-216 | 1 | 202758269 | 202760523 | - | lnc_RNA | retained_intron |
| -316124 | enst00000647754 | sg00000117139 | kdm5b-213 | 1 | 202748397 | 202759324 | - | lnc_RNA | retained_intron |
| -316496 | enst00000456180 | sg00000117139 | kdm5b-204 | 1 | 202753031 | 202758952 | - | lnc_RNA | processed_transcript |
| -320078 | enst00000649929 | sg00000117139 | kdm5b-234 | 1 | 202745555 | 202755370 | - | mRNA | protein_coding |
| 323922 | enst00000605576 | sg00000271588 | larp7p1-201 | 1 | 203400266 | 203400581 | - | pseudogenic_transcript | processed_pseudogene |
| -324746 | enst00000649089 | sg00000117139 | kdm5b-225 | 1 | 202728698 | 202750702 | - | mRNA | nonsense_mediated_decay |
| -327883 | enst00000649230 | sg00000117139 | kdm5b-227 | 1 | 202727494 | 202747565 | - | lnc_RNA | retained_intron |
| -328844 | enst00000498276 | sg00000117139 | kdm5b-209 | 1 | 202728448 | 202746604 | - | lnc_RNA | retained_intron |
| -329536 | enst00000649400 | sg00000117139 | kdm5b-231 | 1 | 202727417 | 202745912 | - | lnc_RNA | retained_intron |
| -332144 | enst00000650506 | sg00000117139 | kdm5b-239 | 1 | 202727583 | 202743304 | - | lnc_RNA | retained_intron |
| -339208 | enst00000649388 | sg00000117139 | kdm5b-230 | 1 | 202735172 | 202736240 | - | lnc_RNA | retained_intron |
| -341133 | enst00000472822 | sg00000117139 | kdm5b-207 | 1 | 202727404 | 202734315 | - | lnc_RNA | retained_intron |
| -341176 | enst00000647657 | sg00000117139 | kdm5b-211 | 1 | 202728615 | 202734272 | - | lnc_RNA | retained_intron |
| -342021 | enst00000647747 | sg00000117139 | kdm5b-212 | 1 | 202727427 | 202733427 | - | lnc_RNA | retained_intron |
| -343392 | enst00000491153 | sg00000117139 | kdm5b-208 | 1 | 202728204 | 202732056 | - | lnc_RNA | retained_intron |
| -344904 | enst00000649339 | sg00000117139 | kdm5b-229 | 1 | 202727404 | 202730544 | - | lnc_RNA | retained_intron |
| -345733 | enst00000648676 | sg00000117139 | kdm5b-221 | 1 | 202724714 | 202729715 | - | mRNA | protein_coding |
| -364994 | enst00000367268 | sg00000143858 | syt2-202 | 1 | 202590596 | 202710454 | - | mRNA | protein_coding |
| 399147 | enst00000343110 | sg00000188783 | prelp-201 | 1 | 203475806 | 203491352 | + | mRNA | protein_coding |
| 417494 | enst00000367222 | sg00000188770 | optc-201 | 1 | 203494153 | 203508949 | + | mRNA | protein_coding |
| 419311 | enst00000448911 | sg00000188770 | optc-202 | 1 | 203495970 | 203499709 | + | mRNA | protein_coding |
| -431995 | enst00000367267 | sg00000143858 | syt2-201 | 1 | 202590596 | 202643453 | - | mRNA | protein_coding |
| -443020 | enst00000411431 | sg00000225620 | ac104463.1-201 | 1 | 202632428 | 202632911 | + | lnc_RNA | lncrna |
| -471180 | enst00000428573 | sg00000226862 | ac104463.2-201 | 1 | 202604268 | 202605293 | + | 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