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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 |
|---|---|---|---|---|---|---|---|---|
| #100 | 10 | 48450148 | 48451244 | 1096 | 3 | 39 | 1.59786e-17 | 1.58907e-15 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 383 | enst00000477708 | sg00000128805 | arhgap22-210 | 10 | 48446036 | 48451627 | - | mRNA | protein_coding |
| -4328 | enst00000624848 | sg00000279822 | ac016397.2-201 | 10 | 48443836 | 48445820 | - | unconfirmed_transcript | tec |
| 15452 | enst00000489984 | sg00000128805 | arhgap22-211 | 10 | 48454157 | 48466696 | - | lnc_RNA | processed_transcript |
| -20255 | enst00000459755 | sg00000107643 | mapk8-211 | 10 | 48429893 | 48435877 | + | lnc_RNA | retained_intron |
| -24294 | enst00000482840 | sg00000107643 | mapk8-216 | 10 | 48425854 | 48426612 | + | lnc_RNA | processed_transcript |
| -24959 | enst00000469110 | sg00000107643 | mapk8-212 | 10 | 48425189 | 48436440 | + | lnc_RNA | retained_intron |
| -25579 | enst00000471272 | sg00000107643 | mapk8-214 | 10 | 48424569 | 48427410 | + | lnc_RNA | retained_intron |
| -25629 | enst00000469879 | sg00000107643 | mapk8-213 | 10 | 48424519 | 48434898 | + | lnc_RNA | processed_transcript |
| 27962 | enst00000515523 | sg00000128805 | arhgap22-215 | 10 | 48453301 | 48479206 | - | lnc_RNA | processed_transcript |
| 42405 | enst00000417247 | sg00000128805 | arhgap22-204 | 10 | 48446037 | 48493649 | - | mRNA | protein_coding |
| -48487 | enst00000374174 | sg00000107643 | mapk8-202 | 10 | 48401661 | 48425831 | + | lnc_RNA | processed_transcript |
| -48500 | enst00000374176 | sg00000107643 | mapk8-203 | 10 | 48401648 | 48439360 | + | mRNA | protein_coding |
| -48505 | enst00000374182 | sg00000107643 | mapk8-205 | 10 | 48401643 | 48439360 | + | mRNA | protein_coding |
| -48536 | enst00000360332 | sg00000107643 | mapk8-201 | 10 | 48401612 | 48439357 | + | mRNA | protein_coding |
| 60345 | enst00000505718 | sg00000248682 | arhgap22-it1-201 | 10 | 48510525 | 48511589 | - | lnc_RNA | lncrna |
| 72992 | enst00000374170 | sg00000128805 | arhgap22-202 | 10 | 48446036 | 48524236 | - | mRNA | protein_coding |
| 95469 | enst00000412463 | sg00000231906 | ac016397.1-201 | 10 | 48546472 | 48546713 | - | pseudogenic_transcript | processed_pseudogene |
| 105434 | enst00000374172 | sg00000128805 | arhgap22-203 | 10 | 48446036 | 48556678 | - | mRNA | protein_coding |
| 131803 | enst00000511570 | sg00000128805 | arhgap22-214 | 10 | 48575322 | 48583047 | - | lnc_RNA | processed_transcript |
| 131881 | enst00000493012 | sg00000128805 | arhgap22-213 | 10 | 48532484 | 48583125 | - | lnc_RNA | processed_transcript |
| -141932 | enst00000476134 | sg00000107643 | mapk8-215 | 10 | 48308216 | 48410328 | + | mRNA | protein_coding |
| -143122 | enst00000426557 | sg00000107643 | mapk8-208 | 10 | 48307026 | 48410144 | + | mRNA | protein_coding |
| -143395 | enst00000374179 | sg00000107643 | mapk8-204 | 10 | 48306753 | 48439360 | + | mRNA | protein_coding |
| -143458 | enst00000374189 | sg00000107643 | mapk8-206 | 10 | 48306690 | 48439360 | + | mRNA | protein_coding |
| -143468 | enst00000429041 | sg00000107643 | mapk8-209 | 10 | 48306680 | 48420246 | + | mRNA | nonsense_mediated_decay |
| -143493 | enst00000432379 | sg00000107643 | mapk8-210 | 10 | 48306655 | 48410146 | + | mRNA | protein_coding |
| -143509 | enst00000395611 | sg00000107643 | mapk8-207 | 10 | 48306639 | 48439357 | + | mRNA | protein_coding |
| 153708 | enst00000417912 | sg00000128805 | arhgap22-205 | 10 | 48446340 | 48604952 | - | mRNA | protein_coding |
| 153711 | enst00000491108 | sg00000128805 | arhgap22-212 | 10 | 48574702 | 48604955 | - | lnc_RNA | processed_transcript |
| 153844 | enst00000471013 | sg00000128805 | arhgap22-209 | 10 | 48453357 | 48605088 | - | lnc_RNA | processed_transcript |
| 153849 | enst00000249601 | sg00000128805 | arhgap22-201 | 10 | 48446034 | 48605093 | - | mRNA | protein_coding |
| -157449 | enst00000425165 | sg00000225482 | rps6p14-201 | 10 | 48292699 | 48293417 | + | pseudogenic_transcript | processed_pseudogene |
| 173849 | enst00000514425 | sg00000251413 | ac068898.2-201 | 10 | 48624004 | 48625093 | - | lnc_RNA | lncrna |
| -175452 | enst00000374201 | sg00000170324 | frmpd2-202 | 10 | 48156562 | 48274696 | - | mRNA | protein_coding |
| -175459 | enst00000637395 | sg00000170324 | frmpd2-214 | 10 | 48155312 | 48274689 | - | mRNA | nonsense_mediated_decay |
| -175474 | enst00000486151 | sg00000170324 | frmpd2-207 | 10 | 48177293 | 48274674 | - | lnc_RNA | retained_intron |
| -175581 | enst00000636244 | sg00000170324 | frmpd2-213 | 10 | 48155673 | 48274567 | - | mRNA | protein_coding |
| -198391 | enst00000305531 | sg00000170324 | frmpd2-201 | 10 | 48156559 | 48251757 | - | mRNA | protein_coding |
| -198495 | enst00000468556 | sg00000170324 | frmpd2-204 | 10 | 48242046 | 48251653 | - | lnc_RNA | retained_intron |
| -198537 | enst00000492045 | sg00000170324 | frmpd2-209 | 10 | 48248543 | 48251611 | - | lnc_RNA | retained_intron |
| 201077 | enst00000464445 | sg00000128805 | arhgap22-208 | 10 | 48582721 | 48652321 | - | lnc_RNA | retained_intron |
| 201372 | enst00000435790 | sg00000128805 | arhgap22-206 | 10 | 48446242 | 48652616 | - | mRNA | protein_coding |
| -203623 | enst00000649379 | sg00000285786 | ac074325.1-201 | 10 | 48246525 | 48248512 | + | lnc_RNA | lncrna |
| 205021 | enst00000460425 | sg00000128805 | arhgap22-207 | 10 | 48446558 | 48656265 | - | mRNA | nonsense_mediated_decay |
| 221180 | enst00000440750 | sg00000236800 | ac068898.1-201 | 10 | 48664199 | 48672424 | - | lnc_RNA | lncrna |
| 233632 | enst00000360890 | sg00000128815 | wdfy4-202 | 10 | 48684876 | 48736242 | + | mRNA | protein_coding |
| 233632 | enst00000325239 | sg00000128815 | wdfy4-201 | 10 | 48684876 | 48982956 | + | mRNA | protein_coding |
| -248494 | enst00000505547 | sg00000170324 | frmpd2-211 | 10 | 48199668 | 48201654 | - | lnc_RNA | retained_intron |
| -248700 | enst00000494505 | sg00000170324 | frmpd2-210 | 10 | 48187194 | 48201448 | - | lnc_RNA | processed_transcript |
| -257210 | enst00000635925 | sg00000170324 | frmpd2-212 | 10 | 48153088 | 48192938 | - | lnc_RNA | retained_intron |
| -271258 | enst00000463706 | sg00000170324 | frmpd2-203 | 10 | 48158893 | 48178890 | - | lnc_RNA | processed_transcript |
| -273803 | enst00000477710 | sg00000170324 | frmpd2-206 | 10 | 48174895 | 48176345 | - | lnc_RNA | retained_intron |
| -273936 | enst00000474573 | sg00000170324 | frmpd2-205 | 10 | 48156558 | 48176212 | - | lnc_RNA | processed_transcript |
| -275005 | enst00000491130 | sg00000170324 | frmpd2-208 | 10 | 48156767 | 48175143 | - | lnc_RNA | retained_intron |
| 294884 | enst00000434320 | sg00000228754 | rpl13ap19-201 | 10 | 48745545 | 48746128 | - | pseudogenic_transcript | processed_pseudogene |
| -330693 | enst00000614090 | sg00000278561 | ptpn20cp-201 | 10 | 48064308 | 48119455 | - | pseudogenic_transcript | unprocessed_pseudogene |
| 351494 | enst00000374161 | sg00000128815 | wdfy4-203 | 10 | 48802738 | 48824169 | + | lnc_RNA | processed_transcript |
| -390132 | enst00000602440 | sg00000270025 | bms1p7-201 | 10 | 48050282 | 48060016 | - | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 394701 | enst00000664118 | sg00000286993 | ac035139.2-201 | 10 | 48835541 | 48845945 | - | lnc_RNA | lncrna |
| -409686 | enst00000516340 | sg00000252149 | rna5sp315-201 | 10 | 48040462 | 48040577 | + | pseudogenic_transcript | rrna_pseudogene |
| -418508 | enst00000603888 | sg00000265018 | agap12p-202 | 10 | 48010132 | 48031640 | - | lnc_RNA | processed_transcript |
| -418549 | enst00000585227 | sg00000265018 | agap12p-201 | 10 | 48009873 | 48031599 | - | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 426778 | enst00000423256 | sg00000228403 | ac035139.1-201 | 10 | 48878022 | 48878649 | + | lnc_RNA | lncrna |
| -450357 | enst00000617224 | sg00000276430 | fam25c-201 | 10 | 47995322 | 47999791 | - | mRNA | protein_coding |
| -458271 | enst00000668134 | sg00000276850 | ac245041.2-205 | 10 | 47985515 | 47991877 | - | lnc_RNA | lncrna |
| -458298 | enst00000610809 | sg00000276850 | ac245041.2-204 | 10 | 47985519 | 47991850 | - | lnc_RNA | lncrna |
| -458348 | enst00000479781 | sg00000276850 | ac245041.2-201 | 10 | 47908064 | 47991800 | - | lnc_RNA | lncrna |
| 462988 | enst00000374160 | sg00000165383 | lrrc18-201 | 10 | 48909483 | 48914232 | - | mRNA | protein_coding |
| -464161 | enst00000618306 | sg00000276850 | ac245041.2-203 | 10 | 47934348 | 47985987 | - | lnc_RNA | lncrna |
| -464182 | enst00000613389 | sg00000276850 | ac245041.2-202 | 10 | 47934345 | 47985966 | - | lnc_RNA | lncrna |
| -476652 | enst00000619523 | sg00000273760 | ac245041.1-201 | 10 | 47970043 | 47973496 | - | lnc_RNA | lncrna |
| 483969 | enst00000430438 | sg00000241577 | ac060234.3-201 | 10 | 48883955 | 48935213 | - | lnc_RNA | lncrna |
| 494803 | enst00000465910 | sg00000128815 | wdfy4-204 | 10 | 48946047 | 48982956 | + | lnc_RNA | retained_intron |
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