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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 |
|---|---|---|---|---|---|---|---|---|
| #142 | 8 | 41566734 | 41567976 | 1242 | 3 | 38 | 6.03875e-16 | 4.22925e-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 |
|---|---|---|---|---|---|---|---|---|---|
| 0 | enst00000665362 | sg00000287535 | ac009630.4-201 | 8 | 41566858 | 41568641 | + | lnc_RNA | lncrna |
| 9211 | enst00000521184 | sg00000158669 | gpat4-208 | 8 | 41577187 | 41598614 | + | lnc_RNA | processed_transcript |
| 10212 | enst00000520258 | sg00000158669 | gpat4-206 | 8 | 41578188 | 41598925 | + | lnc_RNA | processed_transcript |
| 10224 | enst00000396987 | sg00000158669 | gpat4-201 | 8 | 41578200 | 41625001 | + | mRNA | protein_coding |
| 10239 | enst00000519853 | sg00000158669 | gpat4-203 | 8 | 41578215 | 41610812 | + | mRNA | protein_coding |
| 10439 | enst00000520223 | sg00000158669 | gpat4-205 | 8 | 41578415 | 41599226 | + | mRNA | protein_coding |
| 10445 | enst00000523081 | sg00000253133 | ac009630.1-201 | 8 | 41509593 | 41578421 | - | lnc_RNA | lncrna |
| 16796 | enst00000521121 | sg00000158669 | gpat4-207 | 8 | 41584772 | 41598665 | + | lnc_RNA | processed_transcript |
| -21690 | enst00000524133 | sg00000253174 | ac009630.2-201 | 8 | 41540381 | 41545044 | - | lnc_RNA | lncrna |
| -21965 | enst00000578500 | sg00000253174 | ac009630.2-202 | 8 | 41542047 | 41544769 | - | lnc_RNA | lncrna |
| -24930 | enst00000518430 | sg00000147536 | gins4-202 | 8 | 41541804 | 41542409 | + | lnc_RNA | retained_intron |
| -30376 | enst00000522642 | sg00000147536 | gins4-208 | 8 | 41536358 | 41540004 | + | lnc_RNA | retained_intron |
| 31072 | enst00000521806 | sg00000158669 | gpat4-210 | 8 | 41599048 | 41612236 | + | mRNA | nonsense_mediated_decay |
| -37473 | enst00000276533 | sg00000147536 | gins4-201 | 8 | 41529261 | 41545030 | + | mRNA | protein_coding |
| -37485 | enst00000523277 | sg00000147536 | gins4-209 | 8 | 41529249 | 41545030 | + | mRNA | protein_coding |
| -37497 | enst00000518671 | sg00000147536 | gins4-203 | 8 | 41529237 | 41542402 | + | mRNA | protein_coding |
| -37504 | enst00000520736 | sg00000147536 | gins4-207 | 8 | 41529230 | 41536452 | + | lnc_RNA | retained_intron |
| -37507 | enst00000520631 | sg00000147536 | gins4-205 | 8 | 41529227 | 41537301 | + | lnc_RNA | retained_intron |
| -37513 | enst00000520710 | sg00000147536 | gins4-206 | 8 | 41529221 | 41538036 | + | mRNA | protein_coding |
| -37516 | enst00000520354 | sg00000147536 | gins4-204 | 8 | 41529218 | 41542239 | + | mRNA | nonsense_mediated_decay |
| 42280 | enst00000519921 | sg00000158669 | gpat4-204 | 8 | 41610256 | 41615048 | + | lnc_RNA | retained_intron |
| 42802 | enst00000523906 | sg00000158669 | gpat4-211 | 8 | 41610778 | 41618813 | + | lnc_RNA | retained_intron |
| 50556 | enst00000521349 | sg00000158669 | gpat4-209 | 8 | 41618532 | 41621373 | + | lnc_RNA | retained_intron |
| 50730 | enst00000518628 | sg00000158669 | gpat4-202 | 8 | 41618706 | 41621394 | + | lnc_RNA | retained_intron |
| 53526 | enst00000581909 | sg00000264578 | ac009630.3-201 | 8 | 41609692 | 41621502 | - | lnc_RNA | lncrna |
| -55494 | enst00000520711 | sg00000253943 | krt18p37-201 | 8 | 41511240 | 41512521 | + | pseudogenic_transcript | processed_pseudogene |
| -60919 | enst00000523128 | sg00000147533 | golga7-206 | 8 | 41505815 | 41509831 | + | lnc_RNA | retained_intron |
| -64165 | enst00000521417 | sg00000147533 | golga7-205 | 8 | 41502569 | 41510139 | + | lnc_RNA | processed_transcript |
| -76122 | enst00000523420 | sg00000147533 | golga7-207 | 8 | 41490612 | 41509673 | + | lnc_RNA | processed_transcript |
| -76152 | enst00000357743 | sg00000147533 | golga7-201 | 8 | 41490582 | 41510980 | + | mRNA | protein_coding |
| -76172 | enst00000405786 | sg00000147533 | golga7-202 | 8 | 41490562 | 41510974 | + | mRNA | protein_coding |
| -76252 | enst00000520817 | sg00000147533 | golga7-204 | 8 | 41490482 | 41510980 | + | mRNA | protein_coding |
| -76338 | enst00000518270 | sg00000147533 | golga7-203 | 8 | 41490396 | 41509769 | + | mRNA | protein_coding |
| 79383 | enst00000524115 | sg00000165066 | nkx6-3-202 | 8 | 41645178 | 41647359 | - | mRNA | protein_coding |
| 82841 | enst00000518699 | sg00000165066 | nkx6-3-201 | 8 | 41645177 | 41650817 | - | mRNA | protein_coding |
| 92468 | enst00000637446 | sg00000283450 | mir486-2-201 | 8 | 41660444 | 41660507 | + | miRNA | mirna |
| 92532 | enst00000612171 | sg00000274705 | mir486-1-201 | 8 | 41660441 | 41660508 | - | miRNA | mirna |
| 93015 | enst00000522388 | sg00000253389 | ac113133.1-201 | 8 | 41660991 | 41665566 | + | lnc_RNA | lncrna |
| 93310 | enst00000585088 | sg00000253389 | ac113133.1-202 | 8 | 41661286 | 41663986 | + | lnc_RNA | lncrna |
| 93332 | enst00000520418 | sg00000253389 | ac113133.1-203 | 8 | 41661308 | 41664248 | + | lnc_RNA | lncrna |
| 97231 | enst00000335651 | sg00000029534 | ank1-204 | 8 | 41661527 | 41665207 | - | mRNA | protein_coding |
| 97285 | enst00000522231 | sg00000029534 | ank1-211 | 8 | 41655301 | 41665261 | - | mRNA | protein_coding |
| 97298 | enst00000348036 | sg00000029534 | ank1-206 | 8 | 41655686 | 41665274 | - | mRNA | protein_coding |
| 97298 | enst00000314214 | sg00000029534 | ank1-203 | 8 | 41655324 | 41665274 | - | mRNA | protein_coding |
| 97310 | enst00000522543 | sg00000029534 | ank1-212 | 8 | 41655301 | 41665286 | - | mRNA | protein_coding |
| 97854 | enst00000518715 | sg00000029534 | ank1-208 | 8 | 41655440 | 41665830 | - | lnc_RNA | processed_transcript |
| 122309 | enst00000518061 | sg00000029534 | ank1-207 | 8 | 41668341 | 41690285 | - | mRNA | nonsense_mediated_decay |
| 125953 | enst00000645531 | sg00000029534 | ank1-214 | 8 | 41655375 | 41693929 | - | mRNA | protein_coding |
| 129870 | enst00000524227 | sg00000029534 | ank1-213 | 8 | 41660989 | 41697846 | - | lnc_RNA | retained_intron |
| -131436 | enst00000521725 | sg00000253396 | ac016868.1-201 | 8 | 41435298 | 41440419 | + | lnc_RNA | lncrna |
| 138203 | enst00000520299 | sg00000029534 | ank1-209 | 8 | 41655324 | 41706179 | - | mRNA | protein_coding |
| -140079 | enst00000459126 | sg00000238936 | snord65b-201 | 8 | 41426655 | 41426727 | + | snoRNA | snorna |
| 229617 | enst00000521407 | sg00000029534 | ank1-210 | 8 | 41788882 | 41797593 | - | lnc_RNA | processed_transcript |
| 229646 | enst00000347528 | sg00000029534 | ank1-205 | 8 | 41653220 | 41797622 | - | mRNA | protein_coding |
| 229646 | enst00000289734 | sg00000029534 | ank1-202 | 8 | 41653225 | 41797622 | - | mRNA | protein_coding |
| 235373 | enst00000384373 | sg00000207101 | ac027702.1-201 | 8 | 41803349 | 41803450 | + | ncRNA | misc_rna |
| -257261 | enst00000220772 | sg00000104332 | sfrp1-201 | 8 | 41261962 | 41309473 | - | mRNA | protein_coding |
| -259744 | enst00000379845 | sg00000104332 | sfrp1-202 | 8 | 41261964 | 41306990 | - | mRNA | protein_coding |
| 261958 | enst00000563810 | sg00000260588 | ac027702.2-201 | 8 | 41828165 | 41829934 | - | lnc_RNA | lncrna |
| -268571 | enst00000384125 | sg00000206852 | rnu6-895p-201 | 8 | 41298163 | 41298265 | + | snRNA | snrna |
| 272363 | enst00000465197 | sg00000241834 | rn7sl149p-201 | 8 | 41840059 | 41840339 | - | ncRNA | misc_rna |
| -289731 | enst00000517495 | sg00000253509 | ac104393.1-201 | 8 | 41275115 | 41277003 | - | lnc_RNA | lncrna |
| -295303 | enst00000479278 | sg00000239281 | rps29p2-201 | 8 | 41271431 | 41271566 | + | pseudogenic_transcript | processed_pseudogene |
| -295591 | enst00000579992 | sg00000263372 | mir548ao-201 | 8 | 41271048 | 41271143 | - | miRNA | mirna |
| 328786 | enst00000265709 | sg00000029534 | ank1-201 | 8 | 41653225 | 41896762 | - | mRNA | protein_coding |
| 373900 | enst00000648224 | sg00000083168 | kat6a-212 | 8 | 41938345 | 41941876 | - | lnc_RNA | retained_intron |
| 376884 | enst00000650495 | sg00000083168 | kat6a-217 | 8 | 41934789 | 41944860 | - | lnc_RNA | retained_intron |
| 390387 | enst00000418721 | sg00000083168 | kat6a-204 | 8 | 41934774 | 41958363 | - | lnc_RNA | retained_intron |
| 406758 | enst00000649817 | sg00000083168 | kat6a-214 | 8 | 41930762 | 41974734 | - | mRNA | protein_coding |
| 409159 | enst00000647746 | sg00000083168 | kat6a-209 | 8 | 41964351 | 41977135 | - | mRNA | protein_coding |
| 409514 | enst00000463961 | sg00000083168 | kat6a-206 | 8 | 41974800 | 41977490 | - | lnc_RNA | retained_intron |
| 475599 | enst00000459551 | sg00000238966 | ac090571.1-201 | 8 | 42043504 | 42043575 | - | snoRNA | snorna |
| 484008 | enst00000647809 | sg00000083168 | kat6a-210 | 8 | 41946513 | 42051984 | - | lnc_RNA | retained_intron |
| 484011 | enst00000470574 | sg00000083168 | kat6a-207 | 8 | 41973498 | 42051987 | - | lnc_RNA | retained_intron |
| 484011 | enst00000648030 | sg00000083168 | kat6a-211 | 8 | 41973404 | 42051987 | - | lnc_RNA | retained_intron |
| 484011 | enst00000648335 | sg00000083168 | kat6a-213 | 8 | 41933188 | 42051987 | - | mRNA | protein_coding |
| 484011 | enst00000649827 | sg00000083168 | kat6a-215 | 8 | 41934400 | 42051987 | - | mRNA | nonsense_mediated_decay |
| 484011 | enst00000265713 | sg00000083168 | kat6a-201 | 8 | 41929479 | 42051987 | - | mRNA | protein_coding |
| 484011 | enst00000485568 | sg00000083168 | kat6a-208 | 8 | 41942049 | 42051987 | - | mRNA | protein_coding |
| 484011 | enst00000426524 | sg00000083168 | kat6a-205 | 8 | 42045878 | 42051987 | - | mRNA | protein_coding |
| 484014 | enst00000396930 | sg00000083168 | kat6a-202 | 8 | 41930761 | 42051990 | - | mRNA | protein_coding |
| 484018 | enst00000650356 | sg00000083168 | kat6a-216 | 8 | 41973422 | 42051994 | - | lnc_RNA | retained_intron |
| 484018 | enst00000406337 | sg00000083168 | kat6a-203 | 8 | 41929479 | 42051994 | - | mRNA | protein_coding |
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