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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 |
|---|---|---|---|---|---|---|---|---|
| #54 | 5 | 6773361 | 6774577 | 1216 | 3 | 46 | 5.13658e-21 | 9.45986e-19 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 1241 | enst00000648399 | sg00000251365 | linc02236-203 | 5 | 6775818 | 6833120 | + | lnc_RNA | lncrna |
| 2505 | enst00000660855 | sg00000251365 | linc02236-206 | 5 | 6777082 | 6786687 | + | lnc_RNA | lncrna |
| 4881 | enst00000606566 | sg00000272071 | ac122710.2-201 | 5 | 6779458 | 6779998 | + | lnc_RNA | lncrna |
| -7467 | enst00000649262 | sg00000251365 | linc02236-204 | 5 | 6765894 | 6776669 | + | lnc_RNA | lncrna |
| -7470 | enst00000506093 | sg00000251365 | linc02236-201 | 5 | 6765891 | 6771953 | + | lnc_RNA | lncrna |
| 21303 | enst00000508881 | sg00000251365 | linc02236-202 | 5 | 6795880 | 6826728 | + | lnc_RNA | lncrna |
| -22981 | enst00000514410 | sg00000112941 | tent4a-204 | 5 | 6750380 | 6751489 | + | lnc_RNA | retained_intron |
| -23806 | enst00000505457 | sg00000112941 | tent4a-202 | 5 | 6749555 | 6750816 | + | lnc_RNA | retained_intron |
| -27373 | enst00000514697 | sg00000112941 | tent4a-205 | 5 | 6745988 | 6755486 | + | lnc_RNA | retained_intron |
| -27446 | enst00000511764 | sg00000112941 | tent4a-203 | 5 | 6745915 | 6749657 | + | lnc_RNA | retained_intron |
| 51983 | enst00000652281 | sg00000251365 | linc02236-205 | 5 | 6826560 | 6827822 | + | lnc_RNA | lncrna |
| 53344 | enst00000636094 | sg00000283420 | mir4278-201 | 5 | 6827853 | 6827921 | - | miRNA | mirna |
| -58572 | enst00000631941 | sg00000112941 | tent4a-207 | 5 | 6714789 | 6755030 | + | mRNA | protein_coding |
| -58729 | enst00000515721 | sg00000112941 | tent4a-206 | 5 | 6714632 | 6737624 | + | mRNA | protein_coding |
| -59929 | enst00000230859 | sg00000112941 | tent4a-201 | 5 | 6713432 | 6757044 | + | mRNA | protein_coding |
| 64883 | enst00000648809 | sg00000250974 | linc02196-202 | 5 | 6839460 | 7180267 | + | lnc_RNA | lncrna |
| -65650 | enst00000503989 | sg00000248677 | linc02102-201 | 5 | 6686325 | 6707711 | - | lnc_RNA | lncrna |
| -66690 | enst00000667865 | sg00000248677 | linc02102-204 | 5 | 6702174 | 6706671 | - | lnc_RNA | lncrna |
| -67089 | enst00000514788 | sg00000248677 | linc02102-202 | 5 | 6705150 | 6706272 | - | lnc_RNA | lncrna |
| -67386 | enst00000664592 | sg00000248677 | linc02102-203 | 5 | 6702168 | 6705975 | - | lnc_RNA | lncrna |
| 73885 | enst00000363373 | sg00000200243 | rn7skp79-201 | 5 | 6848127 | 6848462 | - | ncRNA | misc_rna |
| 93977 | enst00000655466 | sg00000250060 | ac122710.1-202 | 5 | 6868554 | 6888087 | + | lnc_RNA | lncrna |
| 93982 | enst00000510622 | sg00000250060 | ac122710.1-201 | 5 | 6868559 | 6886787 | + | lnc_RNA | lncrna |
| -139905 | enst00000504286 | sg00000145545 | srd5a1-202 | 5 | 6633456 | 6653527 | + | lnc_RNA | processed_transcript |
| -139921 | enst00000274192 | sg00000145545 | srd5a1-201 | 5 | 6633440 | 6674386 | + | mRNA | protein_coding |
| -139934 | enst00000510531 | sg00000145545 | srd5a1-203 | 5 | 6633427 | 6668849 | + | mRNA | nonsense_mediated_decay |
| -139934 | enst00000513117 | sg00000145545 | srd5a1-204 | 5 | 6633427 | 6668972 | + | mRNA | nonsense_mediated_decay |
| -140070 | enst00000504374 | sg00000037474 | nsun2-203 | 5 | 6599240 | 6633291 | - | mRNA | nonsense_mediated_decay |
| -140317 | enst00000264670 | sg00000037474 | nsun2-201 | 5 | 6599239 | 6633044 | - | mRNA | protein_coding |
| -140319 | enst00000506139 | sg00000037474 | nsun2-206 | 5 | 6599569 | 6633042 | - | mRNA | protein_coding |
| -147723 | enst00000505264 | sg00000037474 | nsun2-204 | 5 | 6620116 | 6625638 | - | lnc_RNA | processed_transcript |
| -151872 | enst00000505892 | sg00000037474 | nsun2-205 | 5 | 6599241 | 6621489 | - | lnc_RNA | retained_intron |
| 159093 | enst00000512838 | sg00000250974 | linc02196-201 | 5 | 6933670 | 7214054 | + | lnc_RNA | lncrna |
| -166104 | enst00000514127 | sg00000037474 | nsun2-209 | 5 | 6600030 | 6607257 | - | mRNA | nonsense_mediated_decay |
| -166435 | enst00000507888 | sg00000037474 | nsun2-207 | 5 | 6604801 | 6606926 | - | lnc_RNA | retained_intron |
| -168479 | enst00000513888 | sg00000037474 | nsun2-208 | 5 | 6599400 | 6604882 | - | lnc_RNA | retained_intron |
| -168653 | enst00000502932 | sg00000037474 | nsun2-202 | 5 | 6603869 | 6604708 | - | lnc_RNA | retained_intron |
| -187589 | enst00000507582 | sg00000250056 | linc01018-202 | 5 | 6585772 | 6587925 | + | lnc_RNA | lncrna |
| -189745 | enst00000659556 | sg00000250056 | linc01018-211 | 5 | 6583616 | 6592871 | + | lnc_RNA | lncrna |
| -189756 | enst00000669289 | sg00000250056 | linc01018-221 | 5 | 6583605 | 6600283 | + | lnc_RNA | lncrna |
| -189789 | enst00000658850 | sg00000250056 | linc01018-208 | 5 | 6583572 | 6588498 | + | lnc_RNA | lncrna |
| -190058 | enst00000657872 | sg00000250056 | linc01018-206 | 5 | 6583303 | 6588481 | + | lnc_RNA | lncrna |
| -190058 | enst00000659719 | sg00000250056 | linc01018-212 | 5 | 6583303 | 6589013 | + | lnc_RNA | lncrna |
| -190058 | enst00000671065 | sg00000250056 | linc01018-222 | 5 | 6583303 | 6589141 | + | lnc_RNA | lncrna |
| -190058 | enst00000658539 | sg00000250056 | linc01018-207 | 5 | 6583303 | 6593567 | + | lnc_RNA | lncrna |
| -190058 | enst00000659245 | sg00000250056 | linc01018-210 | 5 | 6583303 | 6589175 | + | lnc_RNA | lncrna |
| -190061 | enst00000661215 | sg00000250056 | linc01018-214 | 5 | 6583300 | 6600288 | + | lnc_RNA | lncrna |
| -190088 | enst00000660957 | sg00000250056 | linc01018-213 | 5 | 6583273 | 6589195 | + | lnc_RNA | lncrna |
| -190088 | enst00000664093 | sg00000250056 | linc01018-215 | 5 | 6583273 | 6589222 | + | lnc_RNA | lncrna |
| -190091 | enst00000667172 | sg00000250056 | linc01018-218 | 5 | 6583270 | 6586945 | + | lnc_RNA | lncrna |
| -190684 | enst00000667226 | sg00000250056 | linc01018-219 | 5 | 6582677 | 6589206 | + | lnc_RNA | lncrna |
| -191191 | enst00000665924 | sg00000250056 | linc01018-216 | 5 | 6582170 | 6589200 | + | lnc_RNA | lncrna |
| -191208 | enst00000652158 | sg00000250056 | linc01018-205 | 5 | 6582153 | 6588480 | + | lnc_RNA | lncrna |
| -191215 | enst00000666121 | sg00000250056 | linc01018-217 | 5 | 6582146 | 6589200 | + | lnc_RNA | lncrna |
| -191219 | enst00000668899 | sg00000250056 | linc01018-220 | 5 | 6582142 | 6588497 | + | lnc_RNA | lncrna |
| -191220 | enst00000659049 | sg00000250056 | linc01018-209 | 5 | 6582141 | 6589206 | + | lnc_RNA | lncrna |
| -191223 | enst00000505626 | sg00000250056 | linc01018-201 | 5 | 6582138 | 6588499 | + | lnc_RNA | lncrna |
| -191225 | enst00000507628 | sg00000250056 | linc01018-203 | 5 | 6582136 | 6587670 | + | lnc_RNA | lncrna |
| -191225 | enst00000513844 | sg00000250056 | linc01018-204 | 5 | 6582136 | 6586604 | + | lnc_RNA | lncrna |
| 215387 | enst00000651243 | sg00000250974 | linc02196-203 | 5 | 6989964 | 7219291 | + | lnc_RNA | lncrna |
| -240161 | enst00000603257 | sg00000271230 | ac027334.1-201 | 5 | 6532891 | 6533200 | - | pseudogenic_transcript | processed_pseudogene |
| 272650 | enst00000390956 | sg00000212258 | rna5sp176-201 | 5 | 7047227 | 7047336 | + | pseudogenic_transcript | rrna_pseudogene |
| 294774 | enst00000660096 | sg00000287790 | ac025756.1-201 | 5 | 7065091 | 7069351 | - | lnc_RNA | lncrna |
| -324502 | enst00000399816 | sg00000215218 | ube2ql1-201 | 5 | 6448859 | 6496723 | + | mRNA | protein_coding |
| -394687 | enst00000653641 | sg00000287031 | ac093307.1-201 | 5 | 6378674 | 6411690 | + | lnc_RNA | lncrna |
| -394790 | enst00000504058 | sg00000133398 | med10-203 | 5 | 6376812 | 6378571 | - | lnc_RNA | retained_intron |
| -394814 | enst00000255764 | sg00000133398 | med10-201 | 5 | 6371874 | 6378547 | - | mRNA | protein_coding |
| -398550 | enst00000503112 | sg00000133398 | med10-202 | 5 | 6372165 | 6374811 | - | lnc_RNA | retained_intron |
| -433477 | enst00000502644 | sg00000250490 | linc02145-201 | 5 | 6337239 | 6339884 | - | lnc_RNA | lncrna |
| -436069 | enst00000507444 | sg00000250490 | linc02145-202 | 5 | 6310441 | 6337292 | - | lnc_RNA | lncrna |
| 454780 | enst00000650863 | sg00000286254 | ac091889.1-201 | 5 | 7226156 | 7229357 | - | lnc_RNA | lncrna |
| 465204 | enst00000422908 | sg00000237611 | ac091951.2-201 | 5 | 7239781 | 7240018 | + | ncRNA | misc_rna |
| -483504 | enst00000510526 | sg00000250730 | hmgb3p3-201 | 5 | 6289857 | 6290624 | + | pseudogenic_transcript | processed_pseudogene |
| 498215 | enst00000649201 | sg00000285689 | ac091951.5-201 | 5 | 7272792 | 7276923 | + | 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