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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 |
|---|---|---|---|---|---|---|---|---|
| #187 | 5 | 173228696 | 173229703 | 1007 | 3 | 33 | 2.12901e-14 | 1.13224e-12 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| -2273 | enst00000521552 | sg00000254200 | rpl7ap33-201 | 5 | 173225836 | 173226423 | - | pseudogenic_transcript | processed_pseudogene |
| 5503 | enst00000329198 | sg00000183072 | nkx2-5-201 | 5 | 173232109 | 173235206 | - | mRNA | protein_coding |
| 5503 | enst00000521848 | sg00000183072 | nkx2-5-204 | 5 | 173232895 | 173235206 | - | mRNA | protein_coding |
| 5561 | enst00000424406 | sg00000183072 | nkx2-5-202 | 5 | 173232893 | 173235264 | - | mRNA | protein_coding |
| 5608 | enst00000517440 | sg00000183072 | nkx2-5-203 | 5 | 173234048 | 173235311 | - | mRNA | protein_coding |
| 24587 | enst00000364407 | sg00000201277 | ac008412.1-201 | 5 | 173254190 | 173254290 | - | ncRNA | misc_rna |
| 62916 | enst00000516360 | sg00000252169 | rna5sp200-201 | 5 | 173292517 | 173292619 | - | pseudogenic_transcript | rrna_pseudogene |
| -68720 | enst00000519459 | sg00000113734 | bnip1-205 | 5 | 173159976 | 173161877 | + | mRNA | protein_coding |
| -83657 | enst00000521251 | sg00000253172 | ac008378.2-201 | 5 | 173144162 | 173145039 | - | lnc_RNA | lncrna |
| -84150 | enst00000393770 | sg00000113734 | bnip1-204 | 5 | 173144546 | 173164057 | + | mRNA | protein_coding |
| -84159 | enst00000352523 | sg00000113734 | bnip1-203 | 5 | 173144537 | 173164341 | + | mRNA | protein_coding |
| -84181 | enst00000351486 | sg00000113734 | bnip1-202 | 5 | 173144515 | 173164387 | + | mRNA | protein_coding |
| -84254 | enst00000231668 | sg00000113734 | bnip1-201 | 5 | 173144442 | 173164340 | + | mRNA | protein_coding |
| 94583 | enst00000520593 | sg00000113739 | stc2-204 | 5 | 173318178 | 173324286 | - | lnc_RNA | processed_transcript |
| 97094 | enst00000518455 | sg00000113739 | stc2-202 | 5 | 173323310 | 173326797 | - | mRNA | protein_coding |
| 98350 | enst00000520648 | sg00000113739 | stc2-205 | 5 | 173322969 | 173328053 | - | mRNA | protein_coding |
| 98744 | enst00000519511 | sg00000113739 | stc2-203 | 5 | 173325834 | 173328447 | - | lnc_RNA | retained_intron |
| 99800 | enst00000265087 | sg00000113739 | stc2-201 | 5 | 173314713 | 173329503 | - | mRNA | protein_coding |
| 117752 | enst00000614530 | sg00000274994 | mir8056-201 | 5 | 173347455 | 173347536 | + | miRNA | mirna |
| 132537 | enst00000362349 | sg00000199219 | rnu6-500p-201 | 5 | 173362134 | 173362240 | - | snRNA | snrna |
| -142486 | enst00000518654 | sg00000253439 | cdc42p5-201 | 5 | 173085342 | 173086210 | - | pseudogenic_transcript | processed_pseudogene |
| 154238 | enst00000663262 | sg00000253968 | ac016573.1-202 | 5 | 173383941 | 173451591 | + | lnc_RNA | lncrna |
| 154256 | enst00000655905 | sg00000253968 | ac016573.1-203 | 5 | 173383959 | 173451591 | + | lnc_RNA | lncrna |
| 154260 | enst00000657357 | sg00000253968 | ac016573.1-204 | 5 | 173383963 | 173451591 | + | lnc_RNA | lncrna |
| 154260 | enst00000654783 | sg00000253968 | ac016573.1-206 | 5 | 173383963 | 173451591 | + | lnc_RNA | lncrna |
| 154260 | enst00000667613 | sg00000253968 | ac016573.1-205 | 5 | 173383963 | 173451591 | + | lnc_RNA | lncrna |
| -171302 | enst00000523161 | sg00000164463 | crebrf-206 | 5 | 173057394 | 173086569 | + | mRNA | protein_coding |
| -171352 | enst00000517882 | sg00000164463 | crebrf-202 | 5 | 173057344 | 173060455 | + | lnc_RNA | processed_transcript |
| -172306 | enst00000520464 | sg00000164463 | crebrf-204 | 5 | 173056390 | 173124581 | + | lnc_RNA | retained_intron |
| -172328 | enst00000520420 | sg00000164463 | crebrf-203 | 5 | 173056368 | 173091536 | + | mRNA | protein_coding |
| -172344 | enst00000522692 | sg00000164463 | crebrf-205 | 5 | 173056352 | 173092330 | + | mRNA | protein_coding |
| -172344 | enst00000296953 | sg00000164463 | crebrf-201 | 5 | 173056352 | 173139284 | + | mRNA | protein_coding |
| -176141 | enst00000384481 | sg00000207210 | ac008378.1-201 | 5 | 173052452 | 173052555 | - | ncRNA | misc_rna |
| 184332 | enst00000523205 | sg00000253968 | ac016573.1-201 | 5 | 173414035 | 173451165 | + | lnc_RNA | lncrna |
| -207968 | enst00000391100 | sg00000212402 | snora74b-201 | 5 | 173020728 | 173020928 | + | snoRNA | snorna |
| 233781 | enst00000519400 | sg00000253141 | ac008632.1-201 | 5 | 173463484 | 173470851 | + | lnc_RNA | lncrna |
| 233805 | enst00000662094 | sg00000253141 | ac008632.1-203 | 5 | 173463508 | 173470851 | + | lnc_RNA | lncrna |
| 239979 | enst00000518605 | sg00000253141 | ac008632.1-202 | 5 | 173469682 | 173484584 | + | lnc_RNA | lncrna |
| -242016 | enst00000521201 | sg00000254328 | ac008429.4-201 | 5 | 172986680 | 172987198 | + | pseudogenic_transcript | processed_pseudogene |
| -244865 | enst00000517669 | sg00000113732 | atp6v0e1-202 | 5 | 172983831 | 173020557 | + | mRNA | protein_coding |
| -244880 | enst00000265093 | sg00000113732 | atp6v0e1-201 | 5 | 172983816 | 173034892 | + | mRNA | protein_coding |
| -244915 | enst00000519911 | sg00000113732 | atp6v0e1-204 | 5 | 172983781 | 173034884 | + | mRNA | protein_coding |
| -244925 | enst00000519374 | sg00000113732 | atp6v0e1-203 | 5 | 172983771 | 173035445 | + | mRNA | protein_coding |
| -253185 | enst00000523057 | sg00000253785 | ac008429.2-201 | 5 | 172975511 | 172976374 | + | pseudogenic_transcript | processed_pseudogene |
| -268931 | enst00000519156 | sg00000037241 | rpl26l1-202 | 5 | 172959765 | 172969487 | + | mRNA | protein_coding |
| -269176 | enst00000519522 | sg00000037241 | rpl26l1-204 | 5 | 172959520 | 172959989 | + | mRNA | protein_coding |
| -269236 | enst00000519239 | sg00000037241 | rpl26l1-203 | 5 | 172959460 | 172969718 | + | mRNA | protein_coding |
| -269272 | enst00000265100 | sg00000037241 | rpl26l1-201 | 5 | 172959424 | 172969771 | + | mRNA | protein_coding |
| -269304 | enst00000518894 | sg00000204758 | ac008429.1-203 | 5 | 172955765 | 172959392 | - | lnc_RNA | lncrna |
| -269319 | enst00000518818 | sg00000204758 | ac008429.1-202 | 5 | 172955154 | 172959377 | - | lnc_RNA | lncrna |
| -269803 | enst00000521476 | sg00000037241 | rpl26l1-206 | 5 | 172958893 | 172969721 | + | mRNA | protein_coding |
| -269918 | enst00000520067 | sg00000204758 | ac008429.1-201 | 5 | 172954786 | 172958778 | - | lnc_RNA | lncrna |
| -269932 | enst00000667351 | sg00000204758 | ac008429.1-204 | 5 | 172955591 | 172958764 | - | lnc_RNA | lncrna |
| -269967 | enst00000519974 | sg00000037241 | rpl26l1-205 | 5 | 172958729 | 172969716 | + | mRNA | protein_coding |
| -273789 | enst00000519755 | sg00000254295 | ac008429.3-201 | 5 | 172954907 | 172957162 | + | lnc_RNA | lncrna |
| -295034 | enst00000523215 | sg00000113719 | ergic1-211 | 5 | 172933662 | 172952680 | + | lnc_RNA | retained_intron |
| -297603 | enst00000520399 | sg00000113719 | ergic1-208 | 5 | 172931093 | 172938007 | + | lnc_RNA | retained_intron |
| -304593 | enst00000523366 | sg00000113719 | ergic1-213 | 5 | 172924103 | 172927099 | + | lnc_RNA | processed_transcript |
| -306551 | enst00000521392 | sg00000113719 | ergic1-210 | 5 | 172922145 | 172932511 | + | lnc_RNA | processed_transcript |
| -308332 | enst00000523650 | sg00000113719 | ergic1-214 | 5 | 172920364 | 172932536 | + | lnc_RNA | processed_transcript |
| -319029 | enst00000519796 | sg00000113719 | ergic1-205 | 5 | 172909667 | 172932478 | + | mRNA | nonsense_mediated_decay |
| -322636 | enst00000519567 | sg00000113719 | ergic1-204 | 5 | 172906060 | 172926563 | + | lnc_RNA | processed_transcript |
| -323456 | enst00000326654 | sg00000113719 | ergic1-201 | 5 | 172905240 | 172918335 | + | mRNA | protein_coding |
| -323479 | enst00000518247 | sg00000113719 | ergic1-203 | 5 | 172905217 | 172924080 | + | mRNA | protein_coding |
| 332775 | enst00000519821 | sg00000253768 | ac008663.1-201 | 5 | 173562478 | 173573199 | + | lnc_RNA | lncrna |
| 345235 | enst00000520300 | sg00000254164 | ac008663.3-201 | 5 | 173574938 | 173576275 | + | lnc_RNA | lncrna |
| 348572 | enst00000663273 | sg00000253955 | ac008663.2-205 | 5 | 173578275 | 173581554 | + | lnc_RNA | lncrna |
| 348826 | enst00000653394 | sg00000253955 | ac008663.2-203 | 5 | 173578529 | 173580874 | + | lnc_RNA | lncrna |
| 349940 | enst00000517299 | sg00000253955 | ac008663.2-201 | 5 | 173579643 | 173585068 | + | lnc_RNA | lncrna |
| 349946 | enst00000519897 | sg00000253955 | ac008663.2-202 | 5 | 173579649 | 173581612 | + | lnc_RNA | lncrna |
| 349983 | enst00000659572 | sg00000253955 | ac008663.2-204 | 5 | 173579686 | 173580872 | + | lnc_RNA | lncrna |
| 380037 | enst00000518658 | sg00000145919 | bod1-207 | 5 | 173608060 | 173609740 | - | lnc_RNA | retained_intron |
| 385149 | enst00000462674 | sg00000145919 | bod1-203 | 5 | 173609357 | 173614852 | - | mRNA | protein_coding |
| 386655 | enst00000477985 | sg00000145919 | bod1-205 | 5 | 173607799 | 173616358 | - | mRNA | protein_coding |
| 386885 | enst00000285908 | sg00000145919 | bod1-201 | 5 | 173607521 | 173616588 | - | mRNA | protein_coding |
| 386947 | enst00000311086 | sg00000145919 | bod1-202 | 5 | 173607145 | 173616650 | - | mRNA | protein_coding |
| 386950 | enst00000480951 | sg00000145919 | bod1-206 | 5 | 173607933 | 173616653 | - | mRNA | protein_coding |
| 386956 | enst00000471339 | sg00000145919 | bod1-204 | 5 | 173609568 | 173616659 | - | lnc_RNA | processed_transcript |
| -394285 | enst00000523291 | sg00000113719 | ergic1-212 | 5 | 172834411 | 172920571 | + | mRNA | protein_coding |
| -394311 | enst00000520642 | sg00000113719 | ergic1-209 | 5 | 172834385 | 172924061 | + | mRNA | nonsense_mediated_decay |
| -394361 | enst00000520326 | sg00000113719 | ergic1-207 | 5 | 172834335 | 172924024 | + | lnc_RNA | processed_transcript |
| -394377 | enst00000519860 | sg00000113719 | ergic1-206 | 5 | 172834319 | 172898585 | + | mRNA | protein_coding |
| -394445 | enst00000393784 | sg00000113719 | ergic1-202 | 5 | 172834251 | 172952683 | + | mRNA | protein_coding |
| -412066 | enst00000660336 | sg00000253628 | ac110011.1-203 | 5 | 172816630 | 172819919 | + | lnc_RNA | lncrna |
| -412075 | enst00000518260 | sg00000253628 | ac110011.1-201 | 5 | 172816621 | 172819958 | + | lnc_RNA | lncrna |
| -412104 | enst00000657724 | sg00000253628 | ac110011.1-202 | 5 | 172816592 | 172819931 | + | lnc_RNA | lncrna |
| 412816 | enst00000523242 | sg00000253959 | linc01863-201 | 5 | 173642519 | 173658194 | + | lnc_RNA | lncrna |
| -443272 | enst00000604389 | sg00000270243 | ac022217.5-201 | 5 | 172785262 | 172785424 | - | pseudogenic_transcript | processed_pseudogene |
| -448602 | enst00000384014 | sg00000206741 | ac022217.1-201 | 5 | 172779982 | 172780094 | - | ncRNA | misc_rna |
| -451987 | enst00000652842 | sg00000253736 | ac022217.4-203 | 5 | 172776709 | 172777898 | + | lnc_RNA | lncrna |
| -452231 | enst00000650258 | sg00000253736 | ac022217.4-202 | 5 | 172776465 | 172782334 | + | lnc_RNA | lncrna |
| -457501 | enst00000239223 | sg00000120129 | dusp1-201 | 5 | 172768096 | 172771195 | - | mRNA | protein_coding |
| 459756 | enst00000521373 | sg00000253428 | linc01942-201 | 5 | 173689459 | 173705849 | + | lnc_RNA | lncrna |
| -465438 | enst00000521069 | sg00000213386 | ac022217.2-201 | 5 | 172762521 | 172763258 | - | pseudogenic_transcript | processed_pseudogene |
| -465716 | enst00000523005 | sg00000253736 | ac022217.4-201 | 5 | 172762980 | 172777774 | + | lnc_RNA | lncrna |
| -470433 | enst00000518941 | sg00000253295 | ac022217.3-202 | 5 | 172758263 | 172762517 | + | lnc_RNA | lncrna |
| -473239 | enst00000666787 | sg00000253295 | ac022217.3-201 | 5 | 172755457 | 172762587 | + | lnc_RNA | lncrna |
| 485258 | enst00000665162 | sg00000253686 | linc01484-206 | 5 | 173708142 | 173714961 | - | lnc_RNA | lncrna |
| 489989 | enst00000521128 | sg00000253686 | linc01484-203 | 5 | 173710440 | 173719692 | - | lnc_RNA | lncrna |
| 490200 | enst00000669486 | sg00000253686 | linc01484-209 | 5 | 173708106 | 173719903 | - | 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