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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 |
|---|---|---|---|---|---|---|---|---|
| #154 | 7 | 128915264 | 128916729 | 1465 | 3 | 50 | 1.94847e-15 | 1.25828e-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 |
|---|---|---|---|---|---|---|---|---|---|
| -1201 | enst00000469533 | sg00000224163 | ac025594.1-201 | 7 | 128912732 | 128914063 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -4545 | enst00000610776 | sg00000135253 | kcp-203 | 7 | 128876865 | 128910719 | - | mRNA | protein_coding |
| -4545 | enst00000611280 | sg00000135253 | kcp-204 | 7 | 128876940 | 128910719 | - | mRNA | nonsense_mediated_decay |
| -4545 | enst00000613019 | sg00000135253 | kcp-206 | 7 | 128876940 | 128910719 | - | mRNA | protein_coding |
| -4545 | enst00000612224 | sg00000135253 | kcp-205 | 7 | 128889947 | 128910719 | - | lnc_RNA | processed_transcript |
| -4588 | enst00000620378 | sg00000135253 | kcp-208 | 7 | 128877043 | 128910676 | - | mRNA | protein_coding |
| -11912 | enst00000616669 | sg00000135253 | kcp-207 | 7 | 128889947 | 128903352 | - | lnc_RNA | retained_intron |
| 20728 | enst00000652525 | sg00000128604 | irf5-218 | 7 | 128937457 | 128942224 | + | mRNA | protein_coding |
| 20883 | enst00000489702 | sg00000128604 | irf5-213 | 7 | 128937612 | 128950027 | + | mRNA | protein_coding |
| 21198 | enst00000357234 | sg00000128604 | irf5-202 | 7 | 128937927 | 128950038 | + | mRNA | protein_coding |
| 21208 | enst00000488569 | sg00000128604 | irf5-212 | 7 | 128937937 | 128946942 | + | lnc_RNA | retained_intron |
| 21211 | enst00000477535 | sg00000128604 | irf5-210 | 7 | 128937940 | 128948832 | + | mRNA | protein_coding |
| 21211 | enst00000613821 | sg00000128604 | irf5-214 | 7 | 128937940 | 128947256 | + | mRNA | protein_coding |
| 21233 | enst00000479582 | sg00000128604 | irf5-211 | 7 | 128937962 | 128946540 | + | mRNA | protein_coding |
| 21243 | enst00000464557 | sg00000128604 | irf5-205 | 7 | 128937972 | 128945967 | + | mRNA | protein_coding |
| 21252 | enst00000461416 | sg00000128604 | irf5-204 | 7 | 128937981 | 128947745 | + | lnc_RNA | retained_intron |
| 21260 | enst00000402030 | sg00000128604 | irf5-203 | 7 | 128937989 | 128950035 | + | mRNA | protein_coding |
| 21262 | enst00000473787 | sg00000128604 | irf5-209 | 7 | 128937991 | 128946556 | + | mRNA | nonsense_mediated_decay |
| 21300 | enst00000652142 | sg00000128604 | irf5-217 | 7 | 128938029 | 128947295 | + | lnc_RNA | processed_transcript |
| 21488 | enst00000650798 | sg00000128604 | irf5-216 | 7 | 128938217 | 128947256 | + | lnc_RNA | processed_transcript |
| 21488 | enst00000249375 | sg00000128604 | irf5-201 | 7 | 128938217 | 128950030 | + | mRNA | protein_coding |
| 23477 | enst00000467002 | sg00000128604 | irf5-207 | 7 | 128940206 | 128942259 | + | mRNA | protein_coding |
| 23943 | enst00000473745 | sg00000128604 | irf5-208 | 7 | 128940672 | 128949388 | + | mRNA | protein_coding |
| 24109 | enst00000619830 | sg00000128604 | irf5-215 | 7 | 128940838 | 128948982 | + | mRNA | protein_coding |
| 24109 | enst00000465603 | sg00000128604 | irf5-206 | 7 | 128940838 | 128949388 | + | mRNA | nonsense_mediated_decay |
| -34341 | enst00000492679 | sg00000135253 | kcp-202 | 7 | 128862451 | 128880923 | - | lnc_RNA | retained_intron |
| -35452 | enst00000460528 | sg00000135253 | kcp-201 | 7 | 128873815 | 128879812 | - | lnc_RNA | retained_intron |
| -36542 | enst00000673954 | sg00000135253 | kcp-209 | 7 | 128874292 | 128878722 | - | mRNA | protein_coding |
| 36587 | enst00000613068 | sg00000275106 | ac025594.2-201 | 7 | 128952527 | 128953316 | - | unconfirmed_transcript | tec |
| -48934 | enst00000609480 | sg00000272899 | atp6v1fnb-201 | 7 | 128866330 | 128872047 | + | mRNA | protein_coding |
| -52360 | enst00000492758 | sg00000128524 | atp6v1f-202 | 7 | 128862904 | 128865844 | + | mRNA | protein_coding |
| -52408 | enst00000249289 | sg00000128524 | atp6v1f-201 | 7 | 128862856 | 128865847 | + | mRNA | protein_coding |
| -52638 | enst00000469965 | sg00000242902 | flnc-as1-201 | 7 | 128850162 | 128862626 | - | lnc_RNA | lncrna |
| 54005 | enst00000492941 | sg00000242241 | rn7sl306p-201 | 7 | 128970734 | 128971029 | + | ncRNA | misc_rna |
| -73933 | enst00000388853 | sg00000128591 | flnc-203 | 7 | 128841331 | 128842858 | + | lnc_RNA | retained_intron |
| -84838 | enst00000346177 | sg00000128591 | flnc-202 | 7 | 128830426 | 128859274 | + | mRNA | protein_coding |
| -84887 | enst00000325888 | sg00000128591 | flnc-201 | 7 | 128830377 | 128859272 | + | mRNA | protein_coding |
| -100615 | enst00000471729 | sg00000128596 | ccdc136-207 | 7 | 128814649 | 128821885 | + | lnc_RNA | processed_transcript |
| -106097 | enst00000460941 | sg00000128596 | ccdc136-204 | 7 | 128809167 | 128810196 | + | lnc_RNA | retained_intron |
| -108517 | enst00000485832 | sg00000128596 | ccdc136-210 | 7 | 128806747 | 128807833 | + | lnc_RNA | retained_intron |
| -108889 | enst00000464672 | sg00000128596 | ccdc136-205 | 7 | 128806375 | 128822132 | + | mRNA | protein_coding |
| -109416 | enst00000528772 | sg00000128596 | ccdc136-215 | 7 | 128805848 | 128818268 | + | lnc_RNA | retained_intron |
| 112160 | enst00000459650 | sg00000244556 | odcp-201 | 7 | 129028889 | 129030527 | + | pseudogenic_transcript | processed_pseudogene |
| -114054 | enst00000494552 | sg00000128596 | ccdc136-214 | 7 | 128801210 | 128822125 | + | mRNA | protein_coding |
| -114078 | enst00000480137 | sg00000128596 | ccdc136-209 | 7 | 128801186 | 128822130 | + | lnc_RNA | retained_intron |
| -123246 | enst00000487361 | sg00000128596 | ccdc136-212 | 7 | 128792018 | 128822119 | + | mRNA | protein_coding |
| -123296 | enst00000297788 | sg00000128596 | ccdc136-201 | 7 | 128791968 | 128822130 | + | mRNA | protein_coding |
| -123646 | enst00000488925 | sg00000128596 | ccdc136-213 | 7 | 128791618 | 128794522 | + | mRNA | protein_coding |
| -123806 | enst00000472049 | sg00000128596 | ccdc136-208 | 7 | 128791458 | 128792428 | + | mRNA | protein_coding |
| -123814 | enst00000464832 | sg00000128596 | ccdc136-206 | 7 | 128791450 | 128822128 | + | mRNA | protein_coding |
| -123820 | enst00000378685 | sg00000128596 | ccdc136-202 | 7 | 128791444 | 128822127 | + | mRNA | protein_coding |
| -123854 | enst00000459946 | sg00000128596 | ccdc136-203 | 7 | 128791410 | 128794728 | + | mRNA | protein_coding |
| -124507 | enst00000485998 | sg00000128596 | ccdc136-211 | 7 | 128790757 | 128801250 | + | mRNA | protein_coding |
| 138154 | enst00000471166 | sg00000064419 | tnpo3-202 | 7 | 128957223 | 129054883 | - | mRNA | protein_coding |
| 138185 | enst00000265388 | sg00000064419 | tnpo3-201 | 7 | 128954180 | 129054914 | - | mRNA | protein_coding |
| 138364 | enst00000482320 | sg00000064419 | tnpo3-204 | 7 | 128955088 | 129055093 | - | mRNA | protein_coding |
| 138415 | enst00000471234 | sg00000064419 | tnpo3-203 | 7 | 128955088 | 129055144 | - | mRNA | protein_coding |
| 138444 | enst00000627585 | sg00000064419 | tnpo3-205 | 7 | 128954180 | 129055173 | - | mRNA | protein_coding |
| 138494 | enst00000635637 | sg00000230359 | tpi1p2-202 | 7 | 129055223 | 129057239 | + | lnc_RNA | processed_transcript |
| 139290 | enst00000491343 | sg00000230359 | tpi1p2-201 | 7 | 129056019 | 129056770 | + | pseudogenic_transcript | transcribed_processed_pseudogene |
| -139474 | enst00000249389 | sg00000128617 | opn1sw-201 | 7 | 128772491 | 128775790 | - | mRNA | protein_coding |
| 149733 | enst00000492994 | sg00000242162 | ac018639.1-201 | 7 | 129066021 | 129066462 | - | pseudogenic_transcript | processed_pseudogene |
| -153926 | enst00000493781 | sg00000244218 | rn7sl81p-201 | 7 | 128761338 | 128761598 | + | ncRNA | misc_rna |
| -156302 | enst00000493278 | sg00000128595 | calu-204 | 7 | 128758962 | 128771807 | + | mRNA | protein_coding |
| -175860 | enst00000479257 | sg00000128595 | calu-203 | 7 | 128739404 | 128769936 | + | mRNA | protein_coding |
| -175901 | enst00000449187 | sg00000128595 | calu-202 | 7 | 128739363 | 128770576 | + | mRNA | protein_coding |
| -175905 | enst00000249364 | sg00000128595 | calu-201 | 7 | 128739359 | 128773400 | + | mRNA | protein_coding |
| -175972 | enst00000542996 | sg00000128595 | calu-206 | 7 | 128739292 | 128771477 | + | mRNA | protein_coding |
| -175972 | enst00000535011 | sg00000128595 | calu-205 | 7 | 128739292 | 128771477 | + | mRNA | protein_coding |
| 179082 | enst00000487324 | sg00000241102 | ac011005.2-201 | 7 | 129095301 | 129095811 | - | pseudogenic_transcript | processed_pseudogene |
| 180006 | enst00000491624 | sg00000241573 | ac011005.3-201 | 7 | 129096027 | 129096735 | - | pseudogenic_transcript | processed_pseudogene |
| -196435 | enst00000466842 | sg00000135248 | fam71f1-202 | 7 | 128718829 | 128726854 | + | mRNA | protein_coding |
| -199859 | enst00000483459 | sg00000135248 | fam71f1-205 | 7 | 128715405 | 128719082 | + | lnc_RNA | processed_transcript |
| -199875 | enst00000471558 | sg00000135248 | fam71f1-204 | 7 | 128715389 | 128726868 | + | mRNA | nonsense_mediated_decay |
| -199875 | enst00000315184 | sg00000135248 | fam71f1-201 | 7 | 128715389 | 128731743 | + | mRNA | protein_coding |
| 201098 | enst00000473154 | sg00000240416 | cycsp20-201 | 7 | 129117513 | 129117827 | - | pseudogenic_transcript | processed_pseudogene |
| -201373 | enst00000621392 | sg00000135248 | fam71f1-209 | 7 | 128713891 | 128731743 | + | mRNA | protein_coding |
| -206174 | enst00000469348 | sg00000135248 | fam71f1-203 | 7 | 128709090 | 128724967 | + | lnc_RNA | processed_transcript |
| -206174 | enst00000493738 | sg00000135248 | fam71f1-208 | 7 | 128709090 | 128723426 | + | lnc_RNA | retained_intron |
| -206189 | enst00000484425 | sg00000135248 | fam71f1-206 | 7 | 128709075 | 128731623 | + | mRNA | nonsense_mediated_decay |
| -206203 | enst00000485070 | sg00000135248 | fam71f1-207 | 7 | 128709061 | 128731611 | + | mRNA | protein_coding |
| 209789 | enst00000467614 | sg00000230626 | ac011005.1-201 | 7 | 129126518 | 129130793 | + | mRNA | protein_coding |
| -217554 | enst00000517057 | sg00000252866 | rna5sp243-201 | 7 | 128697710 | 128697744 | + | pseudogenic_transcript | rrna_pseudogene |
| -217825 | enst00000364171 | sg00000201041 | rna5sp242-201 | 7 | 128697439 | 128697556 | + | pseudogenic_transcript | rrna_pseudogene |
| -221814 | enst00000489760 | sg00000239722 | imp3p2-201 | 7 | 128693450 | 128693924 | + | pseudogenic_transcript | processed_pseudogene |
| -224813 | enst00000605007 | sg00000271344 | ac018638.6-201 | 7 | 128690451 | 128691717 | + | lnc_RNA | lncrna |
| 227978 | enst00000486685 | sg00000158457 | tspan33-201 | 7 | 129144707 | 129169699 | + | mRNA | protein_coding |
| -232223 | enst00000641143 | sg00000205085 | fam71f2-203 | 7 | 128683041 | 128686875 | + | lnc_RNA | processed_transcript |
| -242866 | enst00000474069 | sg00000205085 | fam71f2-201 | 7 | 128672398 | 128683159 | + | mRNA | protein_coding |
| -242965 | enst00000477515 | sg00000205085 | fam71f2-202 | 7 | 128672299 | 128683134 | + | mRNA | protein_coding |
| -242971 | enst00000641987 | sg00000205085 | fam71f2-207 | 7 | 128672293 | 128684246 | + | mRNA | nonsense_mediated_decay |
| -242972 | enst00000641605 | sg00000205085 | fam71f2-205 | 7 | 128672292 | 128687872 | + | mRNA | protein_coding |
| -242972 | enst00000641888 | sg00000205085 | fam71f2-206 | 7 | 128672292 | 128684246 | + | mRNA | nonsense_mediated_decay |
| -242976 | enst00000641443 | sg00000205085 | fam71f2-204 | 7 | 128672288 | 128678112 | + | lnc_RNA | processed_transcript |
| -245372 | enst00000461273 | sg00000241493 | ac018638.3-201 | 7 | 128669087 | 128669892 | - | pseudogenic_transcript | processed_pseudogene |
| 245721 | enst00000496963 | sg00000158457 | tspan33-202 | 7 | 129162450 | 129164810 | + | lnc_RNA | retained_intron |
| 248120 | enst00000363759 | sg00000200629 | rny1p11-201 | 7 | 129164849 | 129164961 | + | ncRNA | misc_rna |
| -248221 | enst00000605836 | sg00000271553 | ac018638.7-201 | 7 | 128667043 | 128668156 | + | lnc_RNA | lncrna |
| 249711 | enst00000614309 | sg00000158457 | tspan33-204 | 7 | 129166440 | 129168830 | + | lnc_RNA | retained_intron |
| 251483 | enst00000498745 | sg00000158457 | tspan33-203 | 7 | 129168212 | 129169697 | + | lnc_RNA | processed_transcript |
| -256473 | enst00000629111 | sg00000281490 | cicp14-201 | 7 | 128655962 | 128658791 | - | pseudogenic_transcript | processed_pseudogene |
| -261245 | enst00000414464 | sg00000229413 | ac018638.1-201 | 7 | 128653690 | 128654019 | - | pseudogenic_transcript | processed_pseudogene |
| -261295 | enst00000450885 | sg00000243679 | ac018638.5-201 | 7 | 128653969 | 128654722 | + | pseudogenic_transcript | processed_pseudogene |
| -262423 | enst00000471258 | sg00000230715 | ac018638.2-201 | 7 | 128652841 | 128653243 | + | pseudogenic_transcript | processed_pseudogene |
| -264079 | enst00000465971 | sg00000243302 | ac018638.4-201 | 7 | 128651185 | 128652334 | + | pseudogenic_transcript | processed_pseudogene |
| 271904 | enst00000249373 | sg00000128602 | smo-201 | 7 | 129188633 | 129213545 | + | mRNA | protein_coding |
| 271966 | enst00000655644 | sg00000128602 | smo-205 | 7 | 129188695 | 129213536 | + | mRNA | nonsense_mediated_decay |
| -288092 | enst00000411257 | sg00000223189 | rnu6-177p-201 | 7 | 128627172 | 128627275 | + | snRNA | snrna |
| 289421 | enst00000462420 | sg00000128602 | smo-202 | 7 | 129206150 | 129211128 | + | mRNA | nonsense_mediated_decay |
| 289556 | enst00000495998 | sg00000128602 | smo-204 | 7 | 129206285 | 129209281 | + | lnc_RNA | retained_intron |
| 293779 | enst00000475779 | sg00000128602 | smo-203 | 7 | 129210508 | 129212152 | + | mRNA | nonsense_mediated_decay |
| 296816 | enst00000466717 | sg00000243230 | ac011005.4-201 | 7 | 129209775 | 129213545 | - | lnc_RNA | lncrna |
| -297399 | enst00000588755 | sg00000281896 | ac018638.8-201 | 7 | 128617865 | 128625905 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 308294 | enst00000325006 | sg00000158467 | ahcyl2-201 | 7 | 129225023 | 129430211 | + | mRNA | protein_coding |
| 308321 | enst00000446544 | sg00000158467 | ahcyl2-202 | 7 | 129225050 | 129430211 | + | mRNA | protein_coding |
| -340513 | enst00000605862 | sg00000242588 | ac108010.1-201 | 7 | 128574751 | 128626473 | + | lnc_RNA | lncrna |
| -344576 | enst00000393266 | sg00000213280 | ac090114.1-201 | 7 | 128570241 | 128570688 | - | pseudogenic_transcript | processed_pseudogene |
| -381612 | enst00000479267 | sg00000280828 | ac090114.3-201 | 7 | 128533652 | 128615970 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -384195 | enst00000608477 | sg00000273270 | ac090114.2-201 | 7 | 128524016 | 128531069 | - | lnc_RNA | lncrna |
| -421421 | enst00000481392 | sg00000165055 | mettl2b-205 | 7 | 128493843 | 128502832 | + | mRNA | protein_coding |
| -431106 | enst00000613842 | sg00000276988 | ac010655.5-201 | 7 | 128483907 | 128484158 | - | ncRNA | misc_rna |
| 434774 | enst00000461161 | sg00000158467 | ahcyl2-204 | 7 | 129351503 | 129397269 | + | lnc_RNA | processed_transcript |
| -435775 | enst00000419443 | sg00000165055 | mettl2b-202 | 7 | 128479489 | 128488597 | + | mRNA | protein_coding |
| -435801 | enst00000473488 | sg00000165055 | mettl2b-203 | 7 | 128479463 | 128483390 | + | lnc_RNA | processed_transcript |
| -438510 | enst00000480046 | sg00000165055 | mettl2b-204 | 7 | 128476754 | 128506602 | + | mRNA | protein_coding |
| -438515 | enst00000497665 | sg00000165055 | mettl2b-207 | 7 | 128476749 | 128498142 | + | mRNA | nonsense_mediated_decay |
| -438535 | enst00000262432 | sg00000165055 | mettl2b-201 | 7 | 128476729 | 128502924 | + | mRNA | protein_coding |
| -438535 | enst00000482555 | sg00000165055 | mettl2b-206 | 7 | 128476729 | 128502126 | + | lnc_RNA | retained_intron |
| -448701 | enst00000478818 | sg00000272601 | ac010655.3-201 | 7 | 128466563 | 128469171 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 451394 | enst00000460109 | sg00000158467 | ahcyl2-203 | 7 | 129368123 | 129389113 | + | mRNA | protein_coding |
| 451412 | enst00000474594 | sg00000158467 | ahcyl2-208 | 7 | 129368141 | 129427211 | + | mRNA | protein_coding |
| 457757 | enst00000668770 | sg00000286722 | ac009244.2-201 | 7 | 129366827 | 129374486 | - | lnc_RNA | lncrna |
| -458905 | enst00000466473 | sg00000135245 | hilpda-203 | 7 | 128456359 | 128458415 | + | lnc_RNA | processed_transcript |
| 458914 | enst00000490911 | sg00000158467 | ahcyl2-210 | 7 | 129375643 | 129427175 | + | mRNA | protein_coding |
| 459108 | enst00000466993 | sg00000158467 | ahcyl2-206 | 7 | 129375837 | 129400320 | + | mRNA | protein_coding |
| -459327 | enst00000493710 | sg00000240758 | ac010655.2-201 | 7 | 128455937 | 128469197 | + | lnc_RNA | lncrna |
| -459361 | enst00000481454 | sg00000135245 | hilpda-204 | 7 | 128455903 | 128458418 | + | lnc_RNA | processed_transcript |
| -459386 | enst00000257696 | sg00000135245 | hilpda-201 | 7 | 128455878 | 128458418 | + | mRNA | protein_coding |
| -459415 | enst00000435296 | sg00000135245 | hilpda-202 | 7 | 128455849 | 128457924 | + | mRNA | protein_coding |
| -459424 | enst00000462662 | sg00000273184 | ac010655.4-201 | 7 | 128455840 | 128493859 | + | lnc_RNA | lncrna |
| 460809 | enst00000466924 | sg00000158467 | ahcyl2-205 | 7 | 129377538 | 129427212 | + | mRNA | protein_coding |
| 471364 | enst00000472554 | sg00000158467 | ahcyl2-207 | 7 | 129388093 | 129397319 | + | lnc_RNA | processed_transcript |
| -471754 | enst00000459236 | sg00000238590 | rnu7-54p-201 | 7 | 128443449 | 128443510 | - | snRNA | snrna |
| 472078 | enst00000491079 | sg00000158467 | ahcyl2-211 | 7 | 129388807 | 129400361 | + | lnc_RNA | retained_intron |
| -481551 | enst00000449336 | sg00000228700 | ac010655.1-201 | 7 | 128433422 | 128433713 | - | pseudogenic_transcript | processed_pseudogene |
| 483571 | enst00000492628 | sg00000158467 | ahcyl2-212 | 7 | 129400300 | 129405508 | + | lnc_RNA | retained_intron |
| 493641 | enst00000450566 | sg00000238072 | ac009244.1-201 | 7 | 129410113 | 129410370 | - | 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