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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 |
|---|---|---|---|---|---|---|---|---|
| #138 | 2 | 70888459 | 70889814 | 1355 | 3 | 38 | 3.79392e-16 | 2.7341e-14 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| -588 | enst00000449073 | sg00000237751 | linc01143-201 | 2 | 70887871 | 70889959 | + | lnc_RNA | lncrna |
| 10341 | enst00000622578 | sg00000277764 | ac007040.3-201 | 2 | 70900155 | 70900351 | + | ncRNA | misc_rna |
| 10762 | enst00000234392 | sg00000116035 | vax2-201 | 2 | 70900576 | 70933446 | + | mRNA | protein_coding |
| 10984 | enst00000432367 | sg00000116035 | vax2-202 | 2 | 70900798 | 70965373 | + | mRNA | nonsense_mediated_decay |
| 31393 | enst00000646783 | sg00000116035 | vax2-203 | 2 | 70921207 | 70964458 | + | mRNA | nonsense_mediated_decay |
| 46086 | enst00000234396 | sg00000116039 | atp6v1b1-201 | 2 | 70935900 | 70965431 | + | mRNA | protein_coding |
| 46087 | enst00000454446 | sg00000116039 | atp6v1b1-205 | 2 | 70935901 | 70962900 | + | mRNA | protein_coding |
| 46107 | enst00000412314 | sg00000116039 | atp6v1b1-202 | 2 | 70935921 | 70965401 | + | mRNA | protein_coding |
| -52643 | enst00000410009 | sg00000116031 | cd207-201 | 2 | 70830211 | 70835816 | - | mRNA | protein_coding |
| 53560 | enst00000432098 | sg00000116039 | atp6v1b1-203 | 2 | 70943374 | 70961022 | + | lnc_RNA | retained_intron |
| 58738 | enst00000447639 | sg00000239322 | atp6v1b1-as1-202 | 2 | 70941817 | 70948552 | - | lnc_RNA | lncrna |
| 58796 | enst00000422761 | sg00000239322 | atp6v1b1-as1-201 | 2 | 70941827 | 70948610 | - | lnc_RNA | lncrna |
| 66420 | enst00000412558 | sg00000226186 | elocp21-201 | 2 | 70955899 | 70956234 | - | pseudogenic_transcript | processed_pseudogene |
| -67860 | enst00000272367 | sg00000152672 | clec4f-201 | 2 | 70808643 | 70820599 | - | mRNA | protein_coding |
| -67912 | enst00000426626 | sg00000152672 | clec4f-202 | 2 | 70808813 | 70820547 | - | mRNA | protein_coding |
| 67957 | enst00000463380 | sg00000116039 | atp6v1b1-206 | 2 | 70957771 | 70959966 | + | lnc_RNA | retained_intron |
| 70125 | enst00000495118 | sg00000116039 | atp6v1b1-207 | 2 | 70959939 | 70961820 | + | lnc_RNA | retained_intron |
| 73808 | enst00000433895 | sg00000116039 | atp6v1b1-204 | 2 | 70963622 | 70965119 | + | mRNA | protein_coding |
| 75770 | enst00000468558 | sg00000241159 | rn7sl160p-201 | 2 | 70965584 | 70965867 | + | ncRNA | misc_rna |
| -76985 | enst00000451333 | sg00000231386 | ac007395.1-201 | 2 | 70810798 | 70811474 | - | pseudogenic_transcript | processed_pseudogene |
| -85302 | enst00000447764 | sg00000228034 | hmgn2p21-201 | 2 | 70803157 | 70803426 | + | pseudogenic_transcript | processed_pseudogene |
| 88566 | enst00000272421 | sg00000144031 | ankrd53-201 | 2 | 70978380 | 70985499 | + | mRNA | protein_coding |
| 88638 | enst00000441349 | sg00000144031 | ankrd53-203 | 2 | 70978452 | 70985450 | + | mRNA | protein_coding |
| 88693 | enst00000457410 | sg00000144031 | ankrd53-204 | 2 | 70978507 | 70985341 | + | mRNA | protein_coding |
| 88816 | enst00000360589 | sg00000144031 | ankrd53-202 | 2 | 70978630 | 70985499 | + | mRNA | protein_coding |
| 89193 | enst00000483334 | sg00000144031 | ankrd53-206 | 2 | 70979007 | 70982695 | + | lnc_RNA | retained_intron |
| 89197 | enst00000496088 | sg00000144031 | ankrd53-207 | 2 | 70979011 | 70981967 | + | lnc_RNA | retained_intron |
| 92512 | enst00000460927 | sg00000144031 | ankrd53-205 | 2 | 70982326 | 70984225 | + | lnc_RNA | retained_intron |
| -97816 | enst00000332372 | sg00000183733 | figla-201 | 2 | 70777310 | 70790643 | - | mRNA | protein_coding |
| 99907 | enst00000478068 | sg00000144043 | tex261-205 | 2 | 70985944 | 70989721 | - | lnc_RNA | retained_intron |
| 104696 | enst00000416229 | sg00000228384 | ac007040.1-201 | 2 | 70994510 | 71002754 | + | lnc_RNA | lncrna |
| 104890 | enst00000466731 | sg00000144043 | tex261-203 | 2 | 70988600 | 70994704 | - | lnc_RNA | processed_transcript |
| 104935 | enst00000453130 | sg00000258881 | ac007040.2-202 | 2 | 70947540 | 70994749 | - | mRNA | nonsense_mediated_decay |
| 104989 | enst00000489894 | sg00000144043 | tex261-206 | 2 | 70989577 | 70994803 | - | lnc_RNA | retained_intron |
| 105018 | enst00000433258 | sg00000144043 | tex261-202 | 2 | 70988354 | 70994832 | - | mRNA | nonsense_mediated_decay |
| 105059 | enst00000473055 | sg00000144043 | tex261-204 | 2 | 70991789 | 70994873 | - | lnc_RNA | retained_intron |
| 105059 | enst00000272438 | sg00000144043 | tex261-201 | 2 | 70985942 | 70994873 | - | mRNA | protein_coding |
| 105522 | enst00000606025 | sg00000258881 | ac007040.2-201 | 2 | 70939318 | 70995336 | - | mRNA | protein_coding |
| -120234 | enst00000496178 | sg00000075340 | add2-213 | 2 | 70713070 | 70768225 | - | lnc_RNA | processed_transcript |
| -120247 | enst00000413157 | sg00000075340 | add2-205 | 2 | 70675093 | 70768212 | - | mRNA | protein_coding |
| -120259 | enst00000473232 | sg00000075340 | add2-211 | 2 | 70706413 | 70768200 | - | lnc_RNA | processed_transcript |
| -120259 | enst00000264436 | sg00000075340 | add2-201 | 2 | 70656784 | 70768200 | - | mRNA | protein_coding |
| -120261 | enst00000403045 | sg00000075340 | add2-203 | 2 | 70607618 | 70768198 | - | mRNA | nonsense_mediated_decay |
| -120262 | enst00000430656 | sg00000075340 | add2-208 | 2 | 70676403 | 70768197 | - | mRNA | protein_coding |
| -120263 | enst00000447731 | sg00000075340 | add2-209 | 2 | 70706357 | 70768196 | - | mRNA | protein_coding |
| -120282 | enst00000355733 | sg00000075340 | add2-202 | 2 | 70663483 | 70768177 | - | mRNA | protein_coding |
| -120744 | enst00000407644 | sg00000075340 | add2-204 | 2 | 70662130 | 70767715 | - | mRNA | protein_coding |
| -120990 | enst00000425976 | sg00000075340 | add2-207 | 2 | 70696291 | 70767469 | - | mRNA | protein_coding |
| 134313 | enst00000642062 | sg00000205847 | or7e91p-202 | 2 | 71024127 | 71029893 | + | lnc_RNA | processed_transcript |
| 139214 | enst00000400027 | sg00000205847 | or7e91p-201 | 2 | 71029028 | 71029893 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 147871 | enst00000503990 | sg00000234485 | or7e46p-201 | 2 | 71037685 | 71038703 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 165713 | enst00000456741 | sg00000234896 | or7e62p-201 | 2 | 71055527 | 71056003 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -170681 | enst00000415348 | sg00000075340 | add2-206 | 2 | 70692428 | 70717778 | - | mRNA | protein_coding |
| 174530 | enst00000531799 | sg00000124357 | nagk-226 | 2 | 71064344 | 71068381 | + | lnc_RNA | processed_transcript |
| 174929 | enst00000434990 | sg00000236469 | ac007881.2-201 | 2 | 71002531 | 71064743 | - | lnc_RNA | lncrna |
| 178311 | enst00000608897 | sg00000272735 | ac007881.3-201 | 2 | 71067519 | 71068125 | - | lnc_RNA | lncrna |
| 178464 | enst00000613852 | sg00000124357 | nagk-229 | 2 | 71068278 | 71078868 | + | mRNA | protein_coding |
| 178464 | enst00000497690 | sg00000124357 | nagk-221 | 2 | 71068278 | 71070619 | + | lnc_RNA | retained_intron |
| 178487 | enst00000455662 | sg00000124357 | nagk-208 | 2 | 71068301 | 71078868 | + | mRNA | protein_coding |
| 178494 | enst00000531934 | sg00000124357 | nagk-227 | 2 | 71068308 | 71076662 | + | mRNA | protein_coding |
| 178502 | enst00000455197 | sg00000124357 | nagk-207 | 2 | 71068316 | 71073594 | + | mRNA | nonsense_mediated_decay |
| 178774 | enst00000418807 | sg00000124357 | nagk-202 | 2 | 71068588 | 71079805 | + | mRNA | protein_coding |
| 178778 | enst00000443872 | sg00000124357 | nagk-204 | 2 | 71068592 | 71078585 | + | mRNA | protein_coding |
| 178805 | enst00000443938 | sg00000124357 | nagk-205 | 2 | 71068619 | 71078641 | + | mRNA | protein_coding |
| 178808 | enst00000484984 | sg00000124357 | nagk-217 | 2 | 71068622 | 71073131 | + | lnc_RNA | retained_intron |
| 178817 | enst00000493102 | sg00000124357 | nagk-220 | 2 | 71068631 | 71075807 | + | lnc_RNA | retained_intron |
| 178833 | enst00000450272 | sg00000124357 | nagk-206 | 2 | 71068647 | 71078613 | + | mRNA | nonsense_mediated_decay |
| 178834 | enst00000244204 | sg00000124357 | nagk-201 | 2 | 71068648 | 71079808 | + | mRNA | protein_coding |
| 178836 | enst00000480411 | sg00000124357 | nagk-216 | 2 | 71068650 | 71071138 | + | lnc_RNA | retained_intron |
| 178836 | enst00000475709 | sg00000124357 | nagk-213 | 2 | 71068650 | 71078636 | + | lnc_RNA | retained_intron |
| 178836 | enst00000465105 | sg00000124357 | nagk-210 | 2 | 71068650 | 71071019 | + | lnc_RNA | retained_intron |
| 178848 | enst00000533981 | sg00000124357 | nagk-228 | 2 | 71068662 | 71072690 | + | mRNA | protein_coding |
| 178851 | enst00000472519 | sg00000124357 | nagk-212 | 2 | 71068665 | 71078620 | + | lnc_RNA | retained_intron |
| 179164 | enst00000489309 | sg00000124357 | nagk-218 | 2 | 71068978 | 71078636 | + | lnc_RNA | retained_intron |
| 180486 | enst00000464638 | sg00000124357 | nagk-209 | 2 | 71070300 | 71075630 | + | lnc_RNA | retained_intron |
| 180688 | enst00000428360 | sg00000124357 | nagk-203 | 2 | 71070502 | 71072740 | + | lnc_RNA | processed_transcript |
| 180699 | enst00000524736 | sg00000124357 | nagk-224 | 2 | 71070513 | 71077636 | + | mRNA | nonsense_mediated_decay |
| 181735 | enst00000479854 | sg00000124357 | nagk-215 | 2 | 71071549 | 71076641 | + | lnc_RNA | retained_intron |
| 181977 | enst00000529236 | sg00000124357 | nagk-225 | 2 | 71071791 | 71077605 | + | mRNA | protein_coding |
| -182016 | enst00000522886 | sg00000075340 | add2-214 | 2 | 70673311 | 70706443 | - | mRNA | protein_coding |
| -182051 | enst00000456320 | sg00000075340 | add2-210 | 2 | 70674678 | 70706408 | - | mRNA | protein_coding |
| 182471 | enst00000478659 | sg00000124357 | nagk-214 | 2 | 71072285 | 71075651 | + | lnc_RNA | retained_intron |
| 183723 | enst00000524537 | sg00000124357 | nagk-223 | 2 | 71073537 | 71078633 | + | mRNA | protein_coding |
| 184806 | enst00000490998 | sg00000124357 | nagk-219 | 2 | 71074620 | 71078639 | + | lnc_RNA | retained_intron |
| 185602 | enst00000468601 | sg00000124357 | nagk-211 | 2 | 71075416 | 71078354 | + | lnc_RNA | retained_intron |
| 187717 | enst00000498022 | sg00000124357 | nagk-222 | 2 | 71077531 | 71078635 | + | lnc_RNA | retained_intron |
| -201317 | enst00000457851 | sg00000235035 | ac005234.1-201 | 2 | 70687142 | 70691824 | + | lnc_RNA | lncrna |
| -215111 | enst00000481675 | sg00000075340 | add2-212 | 2 | 70663498 | 70673348 | - | lnc_RNA | retained_intron |
| 223063 | enst00000653174 | sg00000288065 | ac007881.4-201 | 2 | 71112877 | 71117406 | + | lnc_RNA | lncrna |
| 228570 | enst00000462609 | sg00000124370 | mcee-203 | 2 | 71109814 | 71118384 | - | lnc_RNA | processed_transcript |
| 234637 | enst00000413592 | sg00000124370 | mcee-202 | 2 | 71109684 | 71124451 | - | mRNA | protein_coding |
| 240400 | enst00000494660 | sg00000124370 | mcee-205 | 2 | 71124206 | 71130214 | - | mRNA | protein_coding |
| 240415 | enst00000244217 | sg00000124370 | mcee-201 | 2 | 71109687 | 71130229 | - | mRNA | protein_coding |
| 240425 | enst00000486135 | sg00000124370 | mcee-204 | 2 | 71124206 | 71130239 | - | mRNA | protein_coding |
| 240818 | enst00000498451 | sg00000124383 | mphosph10-205 | 2 | 71130632 | 71139425 | + | mRNA | protein_coding |
| 240820 | enst00000244230 | sg00000124383 | mphosph10-201 | 2 | 71130634 | 71150101 | + | mRNA | protein_coding |
| 240820 | enst00000468427 | sg00000124383 | mphosph10-202 | 2 | 71130634 | 71133168 | + | lnc_RNA | processed_transcript |
| 254426 | enst00000476969 | sg00000124383 | mphosph10-203 | 2 | 71144240 | 71149287 | + | lnc_RNA | retained_intron |
| 258292 | enst00000493360 | sg00000124383 | mphosph10-204 | 2 | 71148106 | 71150101 | + | lnc_RNA | retained_intron |
| -258802 | enst00000663725 | sg00000286979 | ac005234.2-201 | 2 | 70629657 | 70648761 | + | lnc_RNA | lncrna |
| 288773 | enst00000437460 | sg00000233870 | ac007881.1-201 | 2 | 71178587 | 71178773 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -334266 | enst00000474101 | sg00000163235 | tgfa-209 | 2 | 70514859 | 70554193 | - | lnc_RNA | processed_transcript |
| -334486 | enst00000394241 | sg00000163235 | tgfa-202 | 2 | 70456339 | 70553973 | - | mRNA | protein_coding |
| -334633 | enst00000460808 | sg00000163235 | tgfa-208 | 2 | 70456366 | 70553826 | - | lnc_RNA | processed_transcript |
| -334633 | enst00000418333 | sg00000163235 | tgfa-203 | 2 | 70450173 | 70553826 | - | mRNA | protein_coding |
| -334633 | enst00000295400 | sg00000163235 | tgfa-201 | 2 | 70447284 | 70553826 | - | mRNA | protein_coding |
| -334687 | enst00000445399 | sg00000163235 | tgfa-206 | 2 | 70449319 | 70553772 | - | mRNA | protein_coding |
| -334821 | enst00000444975 | sg00000163235 | tgfa-205 | 2 | 70450772 | 70553638 | - | mRNA | protein_coding |
| -334969 | enst00000450929 | sg00000163235 | tgfa-207 | 2 | 70450656 | 70553490 | - | mRNA | protein_coding |
| 337289 | enst00000244221 | sg00000124374 | paip2b-201 | 2 | 71182738 | 71227103 | - | mRNA | protein_coding |
| 386747 | enst00000494621 | sg00000075292 | znf638-226 | 2 | 71276561 | 71365705 | + | mRNA | protein_coding |
| 386779 | enst00000410075 | sg00000075292 | znf638-204 | 2 | 71276593 | 71395670 | + | mRNA | protein_coding |
| 386779 | enst00000466975 | sg00000075292 | znf638-214 | 2 | 71276593 | 71365488 | + | mRNA | protein_coding |
| 386831 | enst00000466330 | sg00000075292 | znf638-213 | 2 | 71276645 | 71365613 | + | mRNA | protein_coding |
| -419964 | enst00000441238 | sg00000224606 | tgfa-it1-201 | 2 | 70467385 | 70468495 | - | lnc_RNA | lncrna |
| -422726 | enst00000419940 | sg00000163235 | tgfa-204 | 2 | 70449319 | 70465733 | - | mRNA | protein_coding |
| 441914 | enst00000437658 | sg00000075292 | znf638-206 | 2 | 71331728 | 71349545 | + | mRNA | protein_coding |
| 441946 | enst00000464375 | sg00000075292 | znf638-212 | 2 | 71331760 | 71365538 | + | mRNA | protein_coding |
| 441948 | enst00000475743 | sg00000075292 | znf638-216 | 2 | 71331762 | 71365514 | + | mRNA | protein_coding |
| 441950 | enst00000409544 | sg00000075292 | znf638-203 | 2 | 71331764 | 71435061 | + | mRNA | protein_coding |
| 441952 | enst00000454278 | sg00000075292 | znf638-208 | 2 | 71331766 | 71349141 | + | mRNA | protein_coding |
| 441952 | enst00000455226 | sg00000075292 | znf638-209 | 2 | 71331766 | 71349141 | + | mRNA | protein_coding |
| 441968 | enst00000487707 | sg00000075292 | znf638-220 | 2 | 71331782 | 71348838 | + | lnc_RNA | processed_transcript |
| 441968 | enst00000417778 | sg00000075292 | znf638-205 | 2 | 71331782 | 71349042 | + | mRNA | protein_coding |
| 441968 | enst00000454122 | sg00000075292 | znf638-207 | 2 | 71331782 | 71349063 | + | mRNA | protein_coding |
| 441968 | enst00000264447 | sg00000075292 | znf638-201 | 2 | 71331782 | 71435061 | + | mRNA | protein_coding |
| 475615 | enst00000601581 | sg00000075292 | znf638-227 | 2 | 71365429 | 71375335 | + | lnc_RNA | processed_transcript |
| 484124 | enst00000434786 | sg00000281195 | ac007878.1-201 | 2 | 71373938 | 71376320 | + | lnc_RNA | lncrna |
| -485525 | enst00000452525 | sg00000229229 | ac022201.1-201 | 2 | 70402934 | 70422678 | + | lnc_RNA | lncrna |
| 489702 | enst00000486494 | sg00000075292 | znf638-218 | 2 | 71379516 | 71380720 | + | lnc_RNA | retained_intron |
| 490044 | enst00000363909 | sg00000200779 | rnu6-105p-201 | 2 | 71379755 | 71379858 | - | snRNA | snrna |
| 490362 | enst00000491843 | sg00000075292 | znf638-222 | 2 | 71380176 | 71398757 | + | lnc_RNA | retained_intron |
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