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 |
|---|---|---|---|---|---|---|---|---|
| #18 | 2 | 66445077 | 66447024 | 1947 | 3 | 61 | 4.5619e-27 | 2.52045e-24 |
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 | enst00000475239 | sg00000143995 | meis1-208 | 2 | 66445193 | 66567500 | + | lnc_RNA | processed_transcript |
| -856 | enst00000666153 | sg00000230749 | meis1-as2-203 | 2 | 66441650 | 66444221 | - | lnc_RNA | lncrna |
| -2112 | enst00000606455 | sg00000143995 | meis1-217 | 2 | 66442965 | 66568714 | + | lnc_RNA | processed_transcript |
| -2302 | enst00000498705 | sg00000143995 | meis1-214 | 2 | 66442775 | 66512294 | + | lnc_RNA | retained_intron |
| -3241 | enst00000454595 | sg00000230749 | meis1-as2-202 | 2 | 66439443 | 66441836 | - | lnc_RNA | lncrna |
| -4370 | enst00000466811 | sg00000143995 | meis1-207 | 2 | 66440707 | 66454735 | + | lnc_RNA | processed_transcript |
| -4399 | enst00000437869 | sg00000143995 | meis1-205 | 2 | 66440678 | 66464220 | + | mRNA | protein_coding |
| -4765 | enst00000439433 | sg00000230749 | meis1-as2-201 | 2 | 66439088 | 66440312 | - | lnc_RNA | lncrna |
| -4980 | enst00000409622 | sg00000143995 | meis1-204 | 2 | 66440097 | 66512191 | + | lnc_RNA | processed_transcript |
| -5756 | enst00000495021 | sg00000143995 | meis1-212 | 2 | 66439321 | 66572759 | + | mRNA | protein_coding |
| -7684 | enst00000398506 | sg00000143995 | meis1-202 | 2 | 66437393 | 66573329 | + | mRNA | protein_coding |
| -8160 | enst00000490726 | sg00000143995 | meis1-210 | 2 | 66436917 | 66441440 | + | lnc_RNA | processed_transcript |
| -9519 | enst00000488550 | sg00000143995 | meis1-209 | 2 | 66435558 | 66572454 | + | mRNA | protein_coding |
| -9908 | enst00000491706 | sg00000143995 | meis1-211 | 2 | 66435169 | 66443772 | + | lnc_RNA | retained_intron |
| -9944 | enst00000560281 | sg00000143995 | meis1-216 | 2 | 66435133 | 66568536 | + | mRNA | protein_coding |
| -9952 | enst00000272369 | sg00000143995 | meis1-201 | 2 | 66435125 | 66573869 | + | mRNA | protein_coding |
| -11607 | enst00000454167 | sg00000226819 | meis1-as3-201 | 2 | 66426735 | 66433470 | - | lnc_RNA | lncrna |
| -11625 | enst00000496248 | sg00000143995 | meis1-213 | 2 | 66433452 | 66439967 | + | lnc_RNA | processed_transcript |
| 14774 | enst00000409517 | sg00000143995 | meis1-203 | 2 | 66461798 | 66572454 | + | lnc_RNA | processed_transcript |
| 49002 | enst00000542964 | sg00000143995 | meis1-215 | 2 | 66496026 | 66571251 | + | lnc_RNA | processed_transcript |
| -61771 | enst00000428647 | sg00000232164 | linc01873-201 | 2 | 66383306 | 66392450 | + | lnc_RNA | lncrna |
| 61903 | enst00000450027 | sg00000143995 | meis1-206 | 2 | 66508927 | 66568745 | + | lnc_RNA | processed_transcript |
| -86749 | enst00000577635 | sg00000264525 | mir4778-201 | 2 | 66358249 | 66358328 | - | miRNA | mirna |
| -117716 | enst00000449673 | sg00000225815 | ac092669.1-202 | 2 | 66327361 | 66328984 | + | lnc_RNA | lncrna |
| -117728 | enst00000412313 | sg00000225815 | ac092669.1-201 | 2 | 66327349 | 66328643 | + | lnc_RNA | lncrna |
| 127006 | enst00000433396 | sg00000232046 | linc01798-204 | 2 | 66574030 | 66695505 | + | lnc_RNA | lncrna |
| -208864 | enst00000411785 | sg00000227293 | ac118345.1-201 | 2 | 66235377 | 66236213 | - | lnc_RNA | lncrna |
| 242844 | enst00000423168 | sg00000232046 | linc01798-202 | 2 | 66689868 | 66695581 | + | lnc_RNA | lncrna |
| 244392 | enst00000435389 | sg00000232046 | linc01798-205 | 2 | 66691416 | 66696804 | + | lnc_RNA | lncrna |
| 244414 | enst00000428590 | sg00000232046 | linc01798-203 | 2 | 66691438 | 66715630 | + | lnc_RNA | lncrna |
| 244416 | enst00000653254 | sg00000232046 | linc01798-206 | 2 | 66691440 | 66731223 | + | lnc_RNA | lncrna |
| 244422 | enst00000412944 | sg00000232046 | linc01798-201 | 2 | 66691446 | 66730157 | + | lnc_RNA | lncrna |
| 256164 | enst00000670163 | sg00000237179 | linc01797-205 | 2 | 66699753 | 66703188 | - | lnc_RNA | lncrna |
| 256173 | enst00000432410 | sg00000237179 | linc01797-201 | 2 | 66697158 | 66703197 | - | lnc_RNA | lncrna |
| 256194 | enst00000451698 | sg00000237179 | linc01797-203 | 2 | 66696493 | 66703218 | - | lnc_RNA | lncrna |
| 256203 | enst00000433432 | sg00000237179 | linc01797-202 | 2 | 66697125 | 66703227 | - | lnc_RNA | lncrna |
| 256228 | enst00000660433 | sg00000237179 | linc01797-204 | 2 | 66696190 | 66703252 | - | lnc_RNA | lncrna |
| -312542 | enst00000668467 | sg00000204929 | ac007389.1-211 | 2 | 66132535 | 66135944 | + | lnc_RNA | lncrna |
| -359977 | enst00000666114 | sg00000204929 | ac007389.1-210 | 2 | 66085100 | 66200373 | + | lnc_RNA | lncrna |
| -366619 | enst00000607539 | sg00000204929 | ac007389.1-208 | 2 | 66078458 | 66084638 | + | lnc_RNA | lncrna |
| -368721 | enst00000652861 | sg00000204929 | ac007389.1-212 | 2 | 66076356 | 66133944 | + | lnc_RNA | lncrna |
| 375546 | enst00000455096 | sg00000224071 | ac009474.1-201 | 2 | 66820684 | 66822570 | - | pseudogenic_transcript | processed_pseudogene |
| 434198 | enst00000451383 | sg00000230355 | ac009474.2-201 | 2 | 66881087 | 66881222 | - | pseudogenic_transcript | processed_pseudogene |
| 457412 | enst00000426260 | sg00000230525 | linc01799-202 | 2 | 66904436 | 66971462 | + | lnc_RNA | lncrna |
| 458538 | enst00000659816 | sg00000230525 | linc01799-204 | 2 | 66905562 | 66971462 | + | lnc_RNA | lncrna |
| 458558 | enst00000657974 | sg00000230525 | linc01799-203 | 2 | 66905582 | 66971462 | + | lnc_RNA | lncrna |
| 473270 | enst00000664251 | sg00000230525 | linc01799-205 | 2 | 66920294 | 66947248 | + | lnc_RNA | lncrna |
| 474670 | enst00000411701 | sg00000230525 | linc01799-201 | 2 | 66921694 | 66958920 | + | lnc_RNA | lncrna |
| 475458 | enst00000444266 | sg00000232688 | linc01628-201 | 2 | 66921510 | 66922482 | - | 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