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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 |
|---|---|---|---|---|---|---|---|---|
| #69 | 2 | 176066755 | 176068252 | 1497 | 3 | 45 | 7.51812e-20 | 1.08359e-17 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 15661 | enst00000308618 | sg00000174279 | evx2-201 | 2 | 176077472 | 176083913 | - | mRNA | protein_coding |
| 24469 | enst00000392539 | sg00000128714 | hoxd13-201 | 2 | 176092721 | 176095944 | + | mRNA | protein_coding |
| 31543 | enst00000406506 | sg00000170178 | hoxd12-202 | 2 | 176099795 | 176102489 | + | mRNA | protein_coding |
| 31550 | enst00000404162 | sg00000170178 | hoxd12-201 | 2 | 176099802 | 176100760 | + | mRNA | protein_coding |
| 35964 | enst00000498438 | sg00000128713 | hoxd11-202 | 2 | 176104216 | 176109754 | + | lnc_RNA | processed_transcript |
| 39028 | enst00000249504 | sg00000128713 | hoxd11-201 | 2 | 176107280 | 176109754 | + | mRNA | protein_coding |
| 40538 | enst00000490088 | sg00000128710 | hoxd10-202 | 2 | 176108790 | 176119394 | + | lnc_RNA | processed_transcript |
| 40625 | enst00000549469 | sg00000128710 | hoxd10-203 | 2 | 176108877 | 176119243 | + | lnc_RNA | processed_transcript |
| 48327 | enst00000249501 | sg00000128710 | hoxd10-201 | 2 | 176116579 | 176119942 | + | mRNA | protein_coding |
| 54467 | enst00000249499 | sg00000128709 | hoxd9-201 | 2 | 176122719 | 176124937 | + | mRNA | protein_coding |
| 61442 | enst00000429017 | sg00000175879 | hoxd8-202 | 2 | 176129694 | 176132695 | + | mRNA | protein_coding |
| 61453 | enst00000313173 | sg00000175879 | hoxd8-201 | 2 | 176129705 | 176132695 | + | mRNA | protein_coding |
| 61770 | enst00000544999 | sg00000175879 | hoxd8-204 | 2 | 176130022 | 176132100 | + | mRNA | protein_coding |
| 62105 | enst00000450510 | sg00000175879 | hoxd8-203 | 2 | 176130357 | 176132000 | + | mRNA | protein_coding |
| -63916 | enst00000445472 | sg00000144320 | lnpk-205 | 2 | 175992239 | 176002839 | - | mRNA | protein_coding |
| -63969 | enst00000466445 | sg00000144320 | lnpk-206 | 2 | 175993181 | 176002786 | - | lnc_RNA | processed_transcript |
| -64461 | enst00000544803 | sg00000144320 | lnpk-212 | 2 | 175923897 | 176002294 | - | mRNA | protein_coding |
| -64476 | enst00000483230 | sg00000144320 | lnpk-210 | 2 | 175992231 | 176002279 | - | lnc_RNA | processed_transcript |
| -64481 | enst00000409660 | sg00000144320 | lnpk-203 | 2 | 175929173 | 176002274 | - | mRNA | protein_coding |
| -64488 | enst00000272748 | sg00000144320 | lnpk-201 | 2 | 175923882 | 176002267 | - | mRNA | protein_coding |
| -64492 | enst00000392540 | sg00000144320 | lnpk-202 | 2 | 175970764 | 176002263 | - | mRNA | protein_coding |
| 68360 | enst00000459979 | sg00000128652 | hoxd3-204 | 2 | 176136612 | 176139663 | + | lnc_RNA | processed_transcript |
| 68515 | enst00000651440 | sg00000237380 | hoxd-as2-203 | 2 | 176131969 | 176136767 | - | lnc_RNA | lncrna |
| 68705 | enst00000432796 | sg00000128652 | hoxd3-203 | 2 | 176136957 | 176169415 | + | mRNA | protein_coding |
| 68761 | enst00000440016 | sg00000237380 | hoxd-as2-202 | 2 | 176121611 | 176137013 | - | lnc_RNA | lncrna |
| 68846 | enst00000426965 | sg00000237380 | hoxd-as2-201 | 2 | 176134606 | 176137098 | - | lnc_RNA | lncrna |
| 82051 | enst00000385011 | sg00000207744 | mir10b-201 | 2 | 176150303 | 176150412 | + | miRNA | mirna |
| 83298 | enst00000306324 | sg00000170166 | hoxd4-201 | 2 | 176151550 | 176153226 | + | mRNA | protein_coding |
| 92639 | enst00000410016 | sg00000128652 | hoxd3-202 | 2 | 176160891 | 176173085 | + | mRNA | protein_coding |
| 95825 | enst00000249440 | sg00000128652 | hoxd3-201 | 2 | 176164077 | 176173102 | + | mRNA | protein_coding |
| 97464 | enst00000608941 | sg00000272729 | ac009336.1-201 | 2 | 176164164 | 176165716 | - | lnc_RNA | lncrna |
| 109316 | enst00000547207 | sg00000224189 | haglr-210 | 2 | 176176476 | 176177568 | - | lnc_RNA | lncrna |
| 109465 | enst00000426615 | sg00000226363 | haglros-201 | 2 | 176177717 | 176179008 | + | lnc_RNA | lncrna |
| 109790 | enst00000549329 | sg00000224189 | haglr-211 | 2 | 176176386 | 176178042 | - | lnc_RNA | lncrna |
| 109831 | enst00000552156 | sg00000224189 | haglr-212 | 2 | 176176472 | 176178083 | - | lnc_RNA | lncrna |
| 109832 | enst00000447538 | sg00000224189 | haglr-206 | 2 | 176176380 | 176178084 | - | lnc_RNA | lncrna |
| 109847 | enst00000413969 | sg00000224189 | haglr-201 | 2 | 176164051 | 176178099 | - | lnc_RNA | lncrna |
| 109873 | enst00000456876 | sg00000224189 | haglr-208 | 2 | 176176472 | 176178125 | - | lnc_RNA | lncrna |
| 109873 | enst00000546798 | sg00000224189 | haglr-209 | 2 | 176176386 | 176178125 | - | lnc_RNA | lncrna |
| 109886 | enst00000416928 | sg00000224189 | haglr-202 | 2 | 176173189 | 176178138 | - | lnc_RNA | lncrna |
| 110847 | enst00000669485 | sg00000224189 | haglr-217 | 2 | 176173031 | 176179099 | - | lnc_RNA | lncrna |
| -119245 | enst00000431754 | sg00000144320 | lnpk-204 | 2 | 175929969 | 175947510 | - | mRNA | nonsense_mediated_decay |
| 120017 | enst00000436126 | sg00000224189 | haglr-205 | 2 | 176176186 | 176188269 | - | lnc_RNA | lncrna |
| 120227 | enst00000425005 | sg00000224189 | haglr-204 | 2 | 176176480 | 176188479 | - | lnc_RNA | lncrna |
| 120279 | enst00000645228 | sg00000224189 | haglr-216 | 2 | 176174262 | 176188531 | - | lnc_RNA | lncrna |
| 120279 | enst00000452365 | sg00000224189 | haglr-207 | 2 | 176173002 | 176188531 | - | lnc_RNA | lncrna |
| 120294 | enst00000417086 | sg00000224189 | haglr-203 | 2 | 176175773 | 176188546 | - | lnc_RNA | lncrna |
| 120299 | enst00000642267 | sg00000224189 | haglr-213 | 2 | 176173233 | 176188551 | - | lnc_RNA | lncrna |
| 120339 | enst00000643050 | sg00000224189 | haglr-214 | 2 | 176173225 | 176188591 | - | lnc_RNA | lncrna |
| 120416 | enst00000331462 | sg00000128645 | hoxd1-201 | 2 | 176188668 | 176190907 | + | mRNA | protein_coding |
| 120591 | enst00000610524 | sg00000283880 | mir7704-201 | 2 | 176188843 | 176188901 | + | miRNA | mirna |
| 120706 | enst00000644334 | sg00000224189 | haglr-215 | 2 | 176173674 | 176188958 | - | lnc_RNA | lncrna |
| 124286 | enst00000623777 | sg00000279160 | ac009336.2-201 | 2 | 176189919 | 176192538 | - | unconfirmed_transcript | tec |
| -127001 | enst00000480788 | sg00000144320 | lnpk-209 | 2 | 175937478 | 175939754 | - | lnc_RNA | retained_intron |
| -127948 | enst00000489827 | sg00000144320 | lnpk-211 | 2 | 175937468 | 175938807 | - | lnc_RNA | retained_intron |
| -128419 | enst00000475515 | sg00000144320 | lnpk-207 | 2 | 175929946 | 175938336 | - | lnc_RNA | processed_transcript |
| -128899 | enst00000479012 | sg00000144320 | lnpk-208 | 2 | 175929939 | 175937856 | - | lnc_RNA | retained_intron |
| 133000 | enst00000405359 | sg00000218175 | ac016739.1-201 | 2 | 176200908 | 176201252 | - | pseudogenic_transcript | processed_pseudogene |
| -161253 | enst00000458254 | sg00000229779 | ac016751.1-201 | 2 | 175904371 | 175905502 | - | lnc_RNA | lncrna |
| -169419 | enst00000453206 | sg00000235047 | ac016751.2-201 | 2 | 175897336 | 175904232 | + | lnc_RNA | lncrna |
| 173859 | enst00000412645 | sg00000230384 | rpsap25-201 | 2 | 176242111 | 176242993 | + | pseudogenic_transcript | processed_pseudogene |
| 201143 | enst00000420864 | sg00000128654 | mtx2-202 | 2 | 176269395 | 176338025 | + | mRNA | nonsense_mediated_decay |
| 201190 | enst00000249442 | sg00000128654 | mtx2-201 | 2 | 176269442 | 176338025 | + | mRNA | protein_coding |
| 201200 | enst00000423461 | sg00000128654 | mtx2-203 | 2 | 176269452 | 176328322 | + | mRNA | nonsense_mediated_decay |
| 201218 | enst00000443241 | sg00000128654 | mtx2-204 | 2 | 176269470 | 176337679 | + | mRNA | protein_coding |
| 201250 | enst00000452865 | sg00000128654 | mtx2-205 | 2 | 176269502 | 176337630 | + | mRNA | protein_coding |
| -223868 | enst00000446218 | sg00000223976 | extl2p1-201 | 2 | 175842887 | 175843302 | + | pseudogenic_transcript | processed_pseudogene |
| 270385 | enst00000428657 | sg00000237260 | ppiap67-201 | 2 | 176338637 | 176339077 | + | pseudogenic_transcript | processed_pseudogene |
| 427003 | enst00000652995 | sg00000224577 | linc01117-203 | 2 | 176495255 | 176655967 | + | lnc_RNA | lncrna |
| 439450 | enst00000412153 | sg00000229434 | ac017048.1-201 | 2 | 176506245 | 176507702 | - | lnc_RNA | lncrna |
| 463431 | enst00000431455 | sg00000236231 | ac017048.2-201 | 2 | 176524879 | 176531683 | - | 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