PycoMeth
Documentation
GitHub
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 |
|---|---|---|---|---|---|---|---|---|
| #10 | 8 | 140097670 | 140099673 | 2003 | 3 | 76 | 2.3023e-29 | 2.28964e-26 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 870 | enst00000631594 | sg00000282164 | peg13-201 | 8 | 140094894 | 140100543 | - | lnc_RNA | lncrna |
| -15517 | enst00000523777 | sg00000167632 | trappc9-214 | 8 | 139732162 | 140082153 | - | lnc_RNA | processed_transcript |
| -57914 | enst00000617244 | sg00000274064 | ac040978.1-201 | 8 | 140039756 | 140041037 | + | pseudogenic_transcript | processed_pseudogene |
| -89079 | enst00000524162 | sg00000167632 | trappc9-215 | 8 | 139732093 | 140008591 | - | lnc_RNA | processed_transcript |
| 138820 | enst00000517667 | sg00000167632 | trappc9-203 | 8 | 139988740 | 140238493 | - | lnc_RNA | processed_transcript |
| 163057 | enst00000518839 | sg00000167632 | trappc9-205 | 8 | 140215910 | 140262730 | - | lnc_RNA | processed_transcript |
| 163058 | enst00000520532 | sg00000167632 | trappc9-207 | 8 | 139988823 | 140262731 | - | lnc_RNA | processed_transcript |
| -166498 | enst00000507535 | sg00000250733 | c8orf17-201 | 8 | 139931172 | 139933942 | + | unconfirmed_transcript | tec |
| -166498 | enst00000625034 | sg00000250733 | c8orf17-202 | 8 | 139931172 | 139933946 | + | unconfirmed_transcript | tec |
| 176080 | enst00000634178 | sg00000167632 | trappc9-216 | 8 | 140252571 | 140275753 | - | mRNA | protein_coding |
| -182871 | enst00000521883 | sg00000253574 | ac021744.1-202 | 8 | 139914799 | 139916620 | + | lnc_RNA | lncrna |
| -186432 | enst00000518354 | sg00000253574 | ac021744.1-201 | 8 | 139911238 | 139916620 | + | lnc_RNA | lncrna |
| -188912 | enst00000519482 | sg00000167632 | trappc9-206 | 8 | 139731044 | 139908758 | - | lnc_RNA | processed_transcript |
| -188975 | enst00000518723 | sg00000167632 | trappc9-204 | 8 | 139904432 | 139908695 | - | lnc_RNA | retained_intron |
| 191578 | enst00000521667 | sg00000167632 | trappc9-210 | 8 | 139730892 | 140291251 | - | lnc_RNA | retained_intron |
| 203162 | enst00000521167 | sg00000167632 | trappc9-209 | 8 | 140283987 | 140302835 | - | lnc_RNA | processed_transcript |
| -216375 | enst00000522504 | sg00000167632 | trappc9-213 | 8 | 139730996 | 139881295 | - | lnc_RNA | processed_transcript |
| -291437 | enst00000521700 | sg00000167632 | trappc9-211 | 8 | 139731006 | 139806233 | - | lnc_RNA | processed_transcript |
| 335524 | enst00000521944 | sg00000167632 | trappc9-212 | 8 | 140405293 | 140435197 | - | lnc_RNA | retained_intron |
| 351257 | enst00000520857 | sg00000167632 | trappc9-208 | 8 | 139730345 | 140450930 | - | mRNA | protein_coding |
| 358071 | enst00000438773 | sg00000167632 | trappc9-202 | 8 | 139730343 | 140457744 | - | mRNA | protein_coding |
| 358906 | enst00000389328 | sg00000167632 | trappc9-201 | 8 | 139730343 | 140458579 | - | mRNA | protein_coding |
| 358906 | enst00000648948 | sg00000167632 | trappc9-217 | 8 | 139727725 | 140458579 | - | mRNA | protein_coding |
| -393561 | enst00000648164 | sg00000169427 | kcnk9-208 | 8 | 139617121 | 139704109 | - | mRNA | protein_coding |
| -394547 | enst00000520439 | sg00000169427 | kcnk9-203 | 8 | 139617121 | 139703123 | - | mRNA | protein_coding |
| -394577 | enst00000650269 | sg00000169427 | kcnk9-212 | 8 | 139601097 | 139703093 | - | mRNA | protein_coding |
| -394629 | enst00000522317 | sg00000169427 | kcnk9-204 | 8 | 139600838 | 139703041 | - | mRNA | nonsense_mediated_decay |
| -394672 | enst00000303015 | sg00000169427 | kcnk9-201 | 8 | 139612561 | 139702998 | - | mRNA | protein_coding |
| -394714 | enst00000649473 | sg00000169427 | kcnk9-210 | 8 | 139600839 | 139702956 | - | mRNA | nonsense_mediated_decay |
| 408370 | enst00000564464 | sg00000259891 | ac107375.1-201 | 8 | 140505813 | 140508043 | - | lnc_RNA | lncrna |
| 411638 | enst00000519533 | sg00000104472 | chrac1-203 | 8 | 140511311 | 140516467 | + | mRNA | protein_coding |
| 411649 | enst00000220913 | sg00000104472 | chrac1-201 | 8 | 140511322 | 140517154 | + | mRNA | protein_coding |
| 412245 | enst00000518971 | sg00000104472 | chrac1-202 | 8 | 140511918 | 140515185 | + | mRNA | protein_coding |
| 412309 | enst00000519618 | sg00000104472 | chrac1-204 | 8 | 140511982 | 140515765 | + | mRNA | protein_coding |
| 414621 | enst00000523569 | sg00000104472 | chrac1-205 | 8 | 140514294 | 140515541 | + | lnc_RNA | retained_intron |
| 433033 | enst00000520628 | sg00000123908 | ago2-207 | 8 | 140532094 | 140532706 | - | lnc_RNA | processed_transcript |
| 439776 | enst00000519347 | sg00000123908 | ago2-204 | 8 | 140535391 | 140539449 | - | lnc_RNA | retained_intron |
| 441784 | enst00000520412 | sg00000123908 | ago2-206 | 8 | 140532533 | 140541457 | - | lnc_RNA | retained_intron |
| -443320 | enst00000523477 | sg00000169427 | kcnk9-205 | 8 | 139600845 | 139654350 | - | lnc_RNA | processed_transcript |
| -443340 | enst00000647605 | sg00000169427 | kcnk9-207 | 8 | 139617159 | 139654330 | - | mRNA | protein_coding |
| -443340 | enst00000649696 | sg00000169427 | kcnk9-211 | 8 | 139600845 | 139654330 | - | mRNA | nonsense_mediated_decay |
| 456565 | enst00000521325 | sg00000123908 | ago2-208 | 8 | 140555408 | 140556238 | - | lnc_RNA | retained_intron |
| -463809 | enst00000648481 | sg00000169427 | kcnk9-209 | 8 | 139617206 | 139633861 | - | lnc_RNA | processed_transcript |
| 473139 | enst00000624190 | sg00000279766 | ac067931.1-201 | 8 | 140572142 | 140572812 | - | unconfirmed_transcript | tec |
| -481623 | enst00000519923 | sg00000169427 | kcnk9-202 | 8 | 139612326 | 139616047 | - | lnc_RNA | processed_transcript |
| 492011 | enst00000624905 | sg00000280326 | ac067931.2-201 | 8 | 140591684 | 140593201 | + | unconfirmed_transcript | tec |
| -495606 | enst00000523653 | sg00000169427 | kcnk9-206 | 8 | 139601078 | 139602064 | - | lnc_RNA | processed_transcript |
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