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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 |
|---|---|---|---|---|---|---|---|---|
| #171 | X | 40091300 | 40092577 | 1277 | 3 | 39 | 9.72109e-15 | 5.65358e-13 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 4035 | enst00000673391 | sg00000183337 | bcor-215 | X | 40051272 | 40096612 | - | mRNA | protein_coding |
| 4826 | enst00000397354 | sg00000183337 | bcor-205 | X | 40051246 | 40097403 | - | mRNA | protein_coding |
| 5381 | enst00000378444 | sg00000183337 | bcor-202 | X | 40051251 | 40097958 | - | mRNA | protein_coding |
| 5402 | enst00000672922 | sg00000183337 | bcor-214 | X | 40074683 | 40097979 | - | mRNA | protein_coding |
| -13331 | enst00000490976 | sg00000183337 | bcor-211 | X | 40071906 | 40077969 | - | lnc_RNA | retained_intron |
| -13343 | enst00000615339 | sg00000183337 | bcor-212 | X | 40071944 | 40077957 | - | mRNA | protein_coding |
| -17544 | enst00000427012 | sg00000183337 | bcor-209 | X | 40051312 | 40073756 | - | mRNA | protein_coding |
| -23180 | enst00000378463 | sg00000183337 | bcor-204 | X | 40049815 | 40068120 | - | lnc_RNA | processed_transcript |
| -26751 | enst00000413905 | sg00000183337 | bcor-208 | X | 40049815 | 40064549 | - | mRNA | protein_coding |
| -28363 | enst00000442018 | sg00000183337 | bcor-210 | X | 40051255 | 40062937 | - | mRNA | protein_coding |
| -35067 | enst00000672265 | sg00000183337 | bcor-213 | X | 40051318 | 40056233 | - | lnc_RNA | retained_intron |
| 54052 | enst00000412952 | sg00000183337 | bcor-207 | X | 40077844 | 40146629 | - | mRNA | protein_coding |
| -82024 | enst00000447651 | sg00000223486 | ac092198.1-201 | X | 40009276 | 40012182 | + | lnc_RNA | lncrna |
| 84506 | enst00000406200 | sg00000183337 | bcor-206 | X | 40062955 | 40177083 | - | mRNA | protein_coding |
| 84752 | enst00000378455 | sg00000183337 | bcor-203 | X | 40051246 | 40177329 | - | mRNA | protein_coding |
| 84752 | enst00000342274 | sg00000183337 | bcor-201 | X | 40051248 | 40177329 | - | mRNA | protein_coding |
| 170340 | enst00000452690 | sg00000236393 | ac091806.1-201 | X | 40262917 | 40287720 | + | lnc_RNA | lncrna |
| 170389 | enst00000447570 | sg00000236393 | ac091806.1-202 | X | 40262966 | 40267222 | + | lnc_RNA | lncrna |
| 170432 | enst00000653973 | sg00000236393 | ac091806.1-203 | X | 40263009 | 40299061 | + | lnc_RNA | lncrna |
| -182991 | enst00000649640 | sg00000285709 | al592164.2-201 | X | 39908309 | 39914419 | + | lnc_RNA | lncrna |
| -225876 | enst00000442125 | sg00000214047 | rps11p7-201 | X | 39865424 | 39865888 | + | pseudogenic_transcript | processed_pseudogene |
| -242942 | enst00000562814 | sg00000261435 | al592164.1-201 | X | 39837536 | 39848358 | - | lnc_RNA | lncrna |
| -253739 | enst00000583319 | sg00000263972 | mir1587-201 | X | 39837561 | 39837613 | + | miRNA | mirna |
| 268149 | enst00000418838 | sg00000214045 | ac091807.2-201 | X | 40359183 | 40360726 | - | pseudogenic_transcript | processed_pseudogene |
| -299396 | enst00000603131 | sg00000270759 | ac091810.1-201 | X | 39791580 | 39791904 | - | pseudogenic_transcript | processed_pseudogene |
| -303164 | enst00000452570 | sg00000228232 | gapdhp1-201 | X | 39787132 | 39788136 | - | pseudogenic_transcript | processed_pseudogene |
| -304477 | enst00000581157 | sg00000264618 | rn7sl732p-201 | X | 39786524 | 39786823 | - | ncRNA | misc_rna |
| 400267 | enst00000383950 | sg00000206677 | ac091807.1-201 | X | 40492844 | 40492941 | + | ncRNA | misc_rna |
| 422318 | enst00000441098 | sg00000235685 | ac092473.1-201 | X | 40514895 | 40515508 | + | pseudogenic_transcript | processed_pseudogene |
| -430084 | enst00000580135 | sg00000263730 | mir3937-201 | X | 39661216 | 39661321 | + | miRNA | mirna |
| 442986 | enst00000459221 | sg00000238730 | rnu7-164p-201 | X | 40535502 | 40535563 | - | snRNA | snrna |
| 486795 | enst00000436783 | sg00000182220 | atp6ap2-203 | X | 40579372 | 40597661 | + | mRNA | protein_coding |
| 488317 | enst00000636409 | sg00000182220 | atp6ap2-215 | X | 40580894 | 40606588 | + | mRNA | protein_coding |
| 488323 | enst00000487051 | sg00000182220 | atp6ap2-207 | X | 40580900 | 40592502 | + | lnc_RNA | retained_intron |
| 488333 | enst00000637327 | sg00000182220 | atp6ap2-224 | X | 40580910 | 40606606 | + | mRNA | protein_coding |
| 488360 | enst00000637526 | sg00000182220 | atp6ap2-226 | X | 40580937 | 40606466 | + | mRNA | protein_coding |
| 488360 | enst00000635774 | sg00000182220 | atp6ap2-209 | X | 40580937 | 40606539 | + | mRNA | nonsense_mediated_decay |
| 488363 | enst00000636639 | sg00000182220 | atp6ap2-218 | X | 40580940 | 40606618 | + | mRNA | nonsense_mediated_decay |
| 488366 | enst00000636787 | sg00000182220 | atp6ap2-219 | X | 40580943 | 40606598 | + | mRNA | nonsense_mediated_decay |
| 488372 | enst00000638153 | sg00000182220 | atp6ap2-233 | X | 40580949 | 40605945 | + | mRNA | protein_coding |
| 488381 | enst00000378438 | sg00000182220 | atp6ap2-201 | X | 40580958 | 40606619 | + | mRNA | protein_coding |
| 488383 | enst00000636970 | sg00000182220 | atp6ap2-220 | X | 40580960 | 40606010 | + | mRNA | protein_coding |
| 488389 | enst00000635734 | sg00000182220 | atp6ap2-208 | X | 40580966 | 40606588 | + | mRNA | nonsense_mediated_decay |
| 488393 | enst00000636196 | sg00000182220 | atp6ap2-211 | X | 40580970 | 40606024 | + | mRNA | protein_coding |
| 488393 | enst00000636251 | sg00000182220 | atp6ap2-213 | X | 40580970 | 40606617 | + | mRNA | protein_coding |
| 488393 | enst00000637482 | sg00000182220 | atp6ap2-225 | X | 40580970 | 40606619 | + | mRNA | protein_coding |
| 488393 | enst00000636574 | sg00000182220 | atp6ap2-216 | X | 40580970 | 40606635 | + | mRNA | nonsense_mediated_decay |
| 488393 | enst00000636580 | sg00000182220 | atp6ap2-217 | X | 40580970 | 40606848 | + | mRNA | protein_coding |
| 488405 | enst00000486558 | sg00000182220 | atp6ap2-206 | X | 40580982 | 40605594 | + | mRNA | nonsense_mediated_decay |
| 488405 | enst00000423649 | sg00000182220 | atp6ap2-202 | X | 40580982 | 40605945 | + | mRNA | protein_coding |
| 488418 | enst00000637954 | sg00000182220 | atp6ap2-230 | X | 40580995 | 40592470 | + | lnc_RNA | retained_intron |
| 488421 | enst00000636287 | sg00000182220 | atp6ap2-214 | X | 40580998 | 40606637 | + | mRNA | protein_coding |
| 488459 | enst00000447485 | sg00000182220 | atp6ap2-204 | X | 40581036 | 40605946 | + | mRNA | protein_coding |
| 496421 | enst00000637955 | sg00000182220 | atp6ap2-231 | X | 40588998 | 40605955 | + | mRNA | protein_coding |
| 498682 | enst00000635829 | sg00000182220 | atp6ap2-210 | X | 40591259 | 40606588 | + | lnc_RNA | retained_intron |
| 498693 | enst00000637614 | sg00000182220 | atp6ap2-227 | X | 40591270 | 40605815 | + | 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