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 |
|---|---|---|---|---|---|---|---|---|
| #15 | 20 | 20363429 | 20365644 | 2215 | 3 | 65 | 9.05495e-28 | 6.00343e-25 |
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 | enst00000623641 | sg00000280229 | al161658.1-201 | 20 | 20363691 | 20365657 | + | unconfirmed_transcript | tec |
| 2460 | enst00000310227 | sg00000173404 | insm1-201 | 20 | 20368104 | 20370949 | + | mRNA | protein_coding |
| -46674 | enst00000582087 | sg00000264879 | rn7sl690p-201 | 20 | 20316755 | 20316994 | + | ncRNA | misc_rna |
| -73127 | enst00000469994 | sg00000089101 | cfap61-212 | 20 | 20290302 | 20322814 | + | lnc_RNA | processed_transcript |
| -95620 | enst00000460400 | sg00000243810 | cfap61-as1-201 | 20 | 20258407 | 20267809 | - | lnc_RNA | lncrna |
| -100458 | enst00000488640 | sg00000089101 | cfap61-218 | 20 | 20262971 | 20290357 | + | lnc_RNA | processed_transcript |
| -109591 | enst00000445304 | sg00000229500 | rpl17p1-201 | 20 | 20253303 | 20253838 | - | pseudogenic_transcript | processed_pseudogene |
| -135183 | enst00000389656 | sg00000089101 | cfap61-207 | 20 | 20228246 | 20265616 | + | mRNA | protein_coding |
| -137342 | enst00000486624 | sg00000089101 | cfap61-217 | 20 | 20226087 | 20228614 | + | lnc_RNA | processed_transcript |
| -137968 | enst00000377308 | sg00000089101 | cfap61-206 | 20 | 20225461 | 20360698 | + | mRNA | nonsense_mediated_decay |
| -141489 | enst00000377293 | sg00000089101 | cfap61-203 | 20 | 20221940 | 20265833 | + | mRNA | protein_coding |
| -143262 | enst00000497372 | sg00000089101 | cfap61-221 | 20 | 20220167 | 20232926 | + | lnc_RNA | processed_transcript |
| -143300 | enst00000493330 | sg00000089101 | cfap61-219 | 20 | 20220129 | 20225322 | + | lnc_RNA | processed_transcript |
| 146956 | enst00000427175 | sg00000188559 | ralgapa2-203 | 20 | 20470933 | 20512600 | - | mRNA | protein_coding |
| 147014 | enst00000620717 | sg00000188559 | ralgapa2-206 | 20 | 20392768 | 20512658 | - | mRNA | protein_coding |
| -148167 | enst00000443692 | sg00000225417 | al049648.1-201 | 20 | 20214299 | 20215262 | - | lnc_RNA | lncrna |
| -166776 | enst00000476414 | sg00000089101 | cfap61-216 | 20 | 20196653 | 20251763 | + | lnc_RNA | processed_transcript |
| -166776 | enst00000468719 | sg00000089101 | cfap61-211 | 20 | 20196653 | 20251763 | + | lnc_RNA | processed_transcript |
| -178868 | enst00000471716 | sg00000089101 | cfap61-213 | 20 | 20184561 | 20196714 | + | lnc_RNA | processed_transcript |
| -194050 | enst00000431753 | sg00000089101 | cfap61-208 | 20 | 20169379 | 20228447 | + | mRNA | protein_coding |
| 239768 | enst00000495793 | sg00000188559 | ralgapa2-205 | 20 | 20591177 | 20605412 | - | mRNA | protein_coding |
| -267745 | enst00000470758 | sg00000241054 | al035454.1-201 | 20 | 20094401 | 20095684 | - | lnc_RNA | lncrna |
| 274256 | enst00000430436 | sg00000188559 | ralgapa2-204 | 20 | 20389552 | 20639900 | - | mRNA | protein_coding |
| 275162 | enst00000424981 | sg00000188559 | ralgapa2-202 | 20 | 20635351 | 20640806 | - | lnc_RNA | retained_intron |
| -277967 | enst00000442372 | sg00000089101 | cfap61-209 | 20 | 20085462 | 20166428 | + | mRNA | nonsense_mediated_decay |
| -289537 | enst00000472660 | sg00000089101 | cfap61-214 | 20 | 20073892 | 20098749 | + | mRNA | protein_coding |
| 294066 | enst00000393781 | sg00000213384 | eif4e2p1-201 | 20 | 20659710 | 20659964 | + | pseudogenic_transcript | processed_pseudogene |
| -306783 | enst00000451767 | sg00000089101 | cfap61-210 | 20 | 20056646 | 20172333 | + | mRNA | protein_coding |
| -307383 | enst00000377327 | sg00000101343 | crnkl1-201 | 20 | 20034368 | 20056046 | - | mRNA | protein_coding |
| -307383 | enst00000377340 | sg00000101343 | crnkl1-202 | 20 | 20034368 | 20056046 | - | mRNA | protein_coding |
| -307383 | enst00000490910 | sg00000101343 | crnkl1-204 | 20 | 20034368 | 20056046 | - | mRNA | nonsense_mediated_decay |
| -307383 | enst00000496549 | sg00000101343 | crnkl1-205 | 20 | 20034368 | 20056046 | - | mRNA | nonsense_mediated_decay |
| -310850 | enst00000475466 | sg00000089101 | cfap61-215 | 20 | 20052579 | 20075224 | + | mRNA | protein_coding |
| -310871 | enst00000494029 | sg00000089101 | cfap61-220 | 20 | 20052558 | 20074378 | + | mRNA | nonsense_mediated_decay |
| -310871 | enst00000377303 | sg00000089101 | cfap61-204 | 20 | 20052558 | 20075616 | + | mRNA | protein_coding |
| -310877 | enst00000377306 | sg00000089101 | cfap61-205 | 20 | 20052552 | 20172336 | + | mRNA | protein_coding |
| -310897 | enst00000245957 | sg00000089101 | cfap61-201 | 20 | 20052532 | 20360698 | + | mRNA | protein_coding |
| -310915 | enst00000340348 | sg00000089101 | cfap61-202 | 20 | 20052514 | 20166441 | + | mRNA | protein_coding |
| -310963 | enst00000536226 | sg00000101343 | crnkl1-207 | 20 | 20034374 | 20052466 | - | mRNA | protein_coding |
| -324818 | enst00000490258 | sg00000101343 | crnkl1-203 | 20 | 20036142 | 20038611 | - | lnc_RNA | retained_intron |
| -324977 | enst00000521379 | sg00000101343 | crnkl1-206 | 20 | 20036006 | 20038452 | - | lnc_RNA | processed_transcript |
| -345628 | enst00000481837 | sg00000173418 | naa20-206 | 20 | 20017801 | 20022655 | + | lnc_RNA | retained_intron |
| -346039 | enst00000398602 | sg00000173418 | naa20-203 | 20 | 20017390 | 20033655 | + | mRNA | protein_coding |
| -346067 | enst00000334982 | sg00000173418 | naa20-202 | 20 | 20017362 | 20033655 | + | mRNA | protein_coding |
| -346070 | enst00000480550 | sg00000173418 | naa20-205 | 20 | 20017359 | 20033629 | + | lnc_RNA | processed_transcript |
| -346081 | enst00000463154 | sg00000173418 | naa20-204 | 20 | 20017348 | 20033629 | + | lnc_RNA | processed_transcript |
| -346119 | enst00000484480 | sg00000173418 | naa20-207 | 20 | 20017310 | 20033629 | + | lnc_RNA | processed_transcript |
| -346119 | enst00000310450 | sg00000173418 | naa20-201 | 20 | 20017310 | 20033629 | + | mRNA | protein_coding |
| 347000 | enst00000202677 | sg00000188559 | ralgapa2-201 | 20 | 20389530 | 20712644 | - | mRNA | protein_coding |
| 355543 | enst00000603571 | sg00000270793 | llphp1-201 | 20 | 20721187 | 20721879 | + | pseudogenic_transcript | processed_pseudogene |
| 373087 | enst00000461220 | sg00000278525 | rn7sl607p-201 | 20 | 20738433 | 20738731 | - | ncRNA | misc_rna |
| -428304 | enst00000484638 | sg00000132669 | rin2-209 | 20 | 19935125 | 20002457 | + | lnc_RNA | processed_transcript |
| -473863 | enst00000440354 | sg00000132669 | rin2-205 | 20 | 19889566 | 20001348 | + | mRNA | protein_coding |
| -473863 | enst00000465815 | sg00000132669 | rin2-207 | 20 | 19889566 | 19895947 | + | lnc_RNA | processed_transcript |
| -474019 | enst00000488077 | sg00000132669 | rin2-210 | 20 | 19889410 | 19935550 | + | lnc_RNA | processed_transcript |
| -474042 | enst00000467569 | sg00000132669 | rin2-208 | 20 | 19889387 | 19970929 | + | lnc_RNA | processed_transcript |
| -474054 | enst00000459721 | sg00000132669 | rin2-206 | 20 | 19889375 | 19956807 | + | lnc_RNA | processed_transcript |
| -476908 | enst00000648440 | sg00000132669 | rin2-213 | 20 | 19886521 | 20002457 | + | mRNA | protein_coding |
| -476908 | enst00000255006 | sg00000132669 | rin2-201 | 20 | 19886521 | 20002459 | + | mRNA | protein_coding |
| 488998 | enst00000437558 | sg00000225803 | mrps11p1-201 | 20 | 20854121 | 20854642 | - | pseudogenic_transcript | processed_pseudogene |
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