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 |
|---|---|---|---|---|---|---|---|---|
| #163 | 5 | 159104866 | 159105808 | 942 | 3 | 33 | 5.36873e-15 | 3.27559e-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 |
|---|---|---|---|---|---|---|---|---|---|
| 572 | enst00000624206 | sg00000279204 | ac134043.3-201 | 5 | 159106380 | 159108617 | + | unconfirmed_transcript | tec |
| -4184 | enst00000499583 | sg00000245812 | linc02202-201 | 5 | 159100682 | 159117478 | + | lnc_RNA | lncrna |
| -4244 | enst00000523301 | sg00000245812 | linc02202-203 | 5 | 159100622 | 159107217 | + | lnc_RNA | lncrna |
| -4383 | enst00000517335 | sg00000245812 | linc02202-202 | 5 | 159100483 | 159117323 | + | lnc_RNA | lncrna |
| -4950 | enst00000313708 | sg00000164330 | ebf1-201 | 5 | 158695920 | 159099916 | - | mRNA | protein_coding |
| -5105 | enst00000517373 | sg00000164330 | ebf1-203 | 5 | 158698689 | 159099761 | - | mRNA | protein_coding |
| -5109 | enst00000518836 | sg00000164330 | ebf1-205 | 5 | 158695920 | 159099757 | - | lnc_RNA | processed_transcript |
| -5173 | enst00000380654 | sg00000164330 | ebf1-202 | 5 | 158698664 | 159099693 | - | mRNA | protein_coding |
| -7243 | enst00000523315 | sg00000164330 | ebf1-209 | 5 | 159084666 | 159097623 | - | lnc_RNA | processed_transcript |
| -8260 | enst00000522192 | sg00000164330 | ebf1-208 | 5 | 158698885 | 159096606 | - | lnc_RNA | retained_intron |
| -8496 | enst00000519739 | sg00000164330 | ebf1-206 | 5 | 158695920 | 159096370 | - | lnc_RNA | retained_intron |
| -31072 | enst00000519890 | sg00000164330 | ebf1-207 | 5 | 158695920 | 159073794 | - | lnc_RNA | retained_intron |
| 55552 | enst00000519985 | sg00000145860 | rnf145-207 | 5 | 159157824 | 159161360 | - | lnc_RNA | processed_transcript |
| 55772 | enst00000518284 | sg00000145860 | rnf145-204 | 5 | 159157411 | 159161580 | - | lnc_RNA | processed_transcript |
| 57220 | enst00000518062 | sg00000145860 | rnf145-203 | 5 | 159161141 | 159163028 | - | lnc_RNA | retained_intron |
| 68233 | enst00000521266 | sg00000145860 | rnf145-210 | 5 | 159161484 | 159174041 | - | lnc_RNA | processed_transcript |
| -85737 | enst00000523464 | sg00000164330 | ebf1-210 | 5 | 158731044 | 159019129 | - | lnc_RNA | processed_transcript |
| 101826 | enst00000520638 | sg00000145860 | rnf145-209 | 5 | 159158521 | 159207634 | - | mRNA | protein_coding |
| 102018 | enst00000274542 | sg00000145860 | rnf145-201 | 5 | 159157409 | 159207826 | - | mRNA | protein_coding |
| 102265 | enst00000519865 | sg00000145860 | rnf145-206 | 5 | 159157409 | 159208073 | - | mRNA | protein_coding |
| 102324 | enst00000521606 | sg00000145860 | rnf145-211 | 5 | 159158291 | 159208132 | - | mRNA | protein_coding |
| 103743 | enst00000424310 | sg00000145860 | rnf145-202 | 5 | 159157409 | 159209551 | - | mRNA | protein_coding |
| 103790 | enst00000611185 | sg00000145860 | rnf145-212 | 5 | 159157413 | 159209598 | - | mRNA | protein_coding |
| 103983 | enst00000520548 | sg00000145860 | rnf145-208 | 5 | 159181960 | 159209791 | - | lnc_RNA | processed_transcript |
| 104113 | enst00000521204 | sg00000253256 | ac134043.2-201 | 5 | 159209921 | 159248796 | + | lnc_RNA | lncrna |
| 104245 | enst00000518802 | sg00000145860 | rnf145-205 | 5 | 159158299 | 159210053 | - | mRNA | protein_coding |
| -119060 | enst00000518425 | sg00000253456 | ac136424.1-201 | 5 | 158985806 | 158987199 | + | lnc_RNA | lncrna |
| -121860 | enst00000522582 | sg00000253811 | ac136424.2-201 | 5 | 158983006 | 158984789 | + | lnc_RNA | lncrna |
| 121907 | enst00000520323 | sg00000253315 | linc01932-201 | 5 | 159227715 | 159245127 | + | lnc_RNA | lncrna |
| 124386 | enst00000516649 | sg00000252458 | ac134043.1-201 | 5 | 159230194 | 159230322 | + | snoRNA | snorna |
| 157482 | enst00000296786 | sg00000164332 | ublcp1-201 | 5 | 159263290 | 159286036 | + | mRNA | protein_coding |
| 168580 | enst00000521738 | sg00000164332 | ublcp1-203 | 5 | 159274388 | 159275333 | + | lnc_RNA | retained_intron |
| 168734 | enst00000519276 | sg00000164332 | ublcp1-202 | 5 | 159274542 | 159286036 | + | lnc_RNA | retained_intron |
| 204937 | enst00000641961 | sg00000249738 | ac008691.1-201 | 5 | 159310745 | 159312634 | + | lnc_RNA | lncrna |
| 205125 | enst00000521472 | sg00000249738 | ac008691.1-202 | 5 | 159310933 | 159333182 | + | lnc_RNA | lncrna |
| 212234 | enst00000408674 | sg00000221601 | rnu4atac2p-201 | 5 | 159318042 | 159318167 | + | snRNA | snrna |
| 224679 | enst00000231228 | sg00000113302 | il12b-201 | 5 | 159314780 | 159330487 | - | mRNA | protein_coding |
| 225710 | enst00000515337 | sg00000249738 | ac008691.1-203 | 5 | 159331518 | 159362834 | + | lnc_RNA | lncrna |
| 226131 | enst00000641150 | sg00000249738 | ac008691.1-204 | 5 | 159331939 | 159416624 | + | lnc_RNA | lncrna |
| 240292 | enst00000635333 | sg00000249738 | ac008691.1-205 | 5 | 159346100 | 159451999 | + | lnc_RNA | lncrna |
| 248261 | enst00000648969 | sg00000249738 | ac008691.1-206 | 5 | 159354069 | 159426698 | + | lnc_RNA | lncrna |
| -264743 | enst00000622875 | sg00000164330 | ebf1-211 | 5 | 158695916 | 158840123 | - | mRNA | protein_coding |
| 315406 | enst00000636261 | sg00000249738 | ac008691.1-207 | 5 | 159421214 | 159557687 | + | lnc_RNA | lncrna |
| 360468 | enst00000518418 | sg00000253298 | linc01845-201 | 5 | 159448556 | 159466276 | - | lnc_RNA | lncrna |
| 360483 | enst00000658947 | sg00000253298 | linc01845-202 | 5 | 159458838 | 159466291 | - | lnc_RNA | lncrna |
| -396857 | enst00000518323 | sg00000164330 | ebf1-204 | 5 | 158698641 | 158708009 | - | lnc_RNA | processed_transcript |
| 405879 | enst00000637629 | sg00000283413 | ac008703.1-201 | 5 | 159484130 | 159511687 | - | lnc_RNA | lncrna |
| 447194 | enst00000636819 | sg00000249738 | ac008691.1-208 | 5 | 159553002 | 159805536 | + | lnc_RNA | lncrna |
| 447200 | enst00000636943 | sg00000249738 | ac008691.1-209 | 5 | 159553008 | 159557783 | + | lnc_RNA | lncrna |
| 471038 | enst00000642094 | sg00000249738 | ac008691.1-210 | 5 | 159576846 | 159587991 | + | lnc_RNA | lncrna |
| 481058 | enst00000641685 | sg00000249738 | ac008691.1-211 | 5 | 159586866 | 159614595 | + | 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