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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 |
|---|---|---|---|---|---|---|---|---|
| #95 | 2 | 172080093 | 172081574 | 1481 | 3 | 40 | 1.07668e-17 | 1.12711e-15 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 3166 | enst00000361609 | sg00000144355 | dlx1-202 | 2 | 172084740 | 172086854 | + | mRNA | protein_coding |
| 3175 | enst00000469444 | sg00000144355 | dlx1-205 | 2 | 172084749 | 172088051 | + | mRNA | protein_coding |
| 3933 | enst00000361725 | sg00000144355 | dlx1-203 | 2 | 172085507 | 172089674 | + | mRNA | protein_coding |
| 3962 | enst00000341900 | sg00000144355 | dlx1-201 | 2 | 172085536 | 172089677 | + | mRNA | protein_coding |
| 3983 | enst00000409492 | sg00000144355 | dlx1-204 | 2 | 172085557 | 172087138 | + | lnc_RNA | retained_intron |
| 4693 | enst00000475989 | sg00000144355 | dlx1-206 | 2 | 172086267 | 172089312 | + | lnc_RNA | retained_intron |
| 5793 | enst00000550686 | sg00000144355 | dlx1-207 | 2 | 172087367 | 172088373 | + | lnc_RNA | processed_transcript |
| -9430 | enst00000468537 | sg00000172878 | metap1d-203 | 2 | 172070663 | 172080479 | + | lnc_RNA | processed_transcript |
| -14489 | enst00000392582 | sg00000172878 | metap1d-202 | 2 | 172065604 | 172072454 | + | lnc_RNA | processed_transcript |
| -18520 | enst00000488581 | sg00000172878 | metap1d-204 | 2 | 172061573 | 172080499 | + | lnc_RNA | processed_transcript |
| 21326 | enst00000466293 | sg00000115844 | dlx2-202 | 2 | 172100557 | 172102900 | - | mRNA | protein_coding |
| 21326 | enst00000234198 | sg00000115844 | dlx2-201 | 2 | 172099438 | 172102900 | - | mRNA | protein_coding |
| 21432 | enst00000448117 | sg00000236651 | dlx2-dt-201 | 2 | 172103006 | 172109982 | + | lnc_RNA | lncrna |
| 55771 | enst00000667725 | sg00000232555 | ac104088.1-205 | 2 | 172137345 | 172328595 | + | lnc_RNA | lncrna |
| 55800 | enst00000662340 | sg00000232555 | ac104088.1-202 | 2 | 172137374 | 172323742 | + | lnc_RNA | lncrna |
| -58294 | enst00000491440 | sg00000172878 | metap1d-205 | 2 | 172021799 | 172063750 | + | lnc_RNA | processed_transcript |
| -80138 | enst00000493742 | sg00000172878 | metap1d-207 | 2 | 171999955 | 172061994 | + | lnc_RNA | processed_transcript |
| -80140 | enst00000315796 | sg00000172878 | metap1d-201 | 2 | 171999953 | 172082430 | + | mRNA | protein_coding |
| -80150 | enst00000493035 | sg00000172878 | metap1d-206 | 2 | 171999943 | 172064414 | + | lnc_RNA | processed_transcript |
| -80234 | enst00000464063 | sg00000115840 | slc25a12-204 | 2 | 171855927 | 171999859 | - | lnc_RNA | processed_transcript |
| -80238 | enst00000472748 | sg00000115840 | slc25a12-206 | 2 | 171844369 | 171999855 | - | lnc_RNA | processed_transcript |
| -80301 | enst00000484227 | sg00000115840 | slc25a12-208 | 2 | 171855801 | 171999792 | - | lnc_RNA | processed_transcript |
| -115260 | enst00000392584 | sg00000128708 | hat1-202 | 2 | 171964833 | 171980855 | + | lnc_RNA | retained_intron |
| 152656 | enst00000662764 | sg00000288048 | ac104088.3-201 | 2 | 172234230 | 172237223 | + | lnc_RNA | lncrna |
| -157486 | enst00000494601 | sg00000128708 | hat1-206 | 2 | 171922607 | 171983623 | + | lnc_RNA | retained_intron |
| -157631 | enst00000460481 | sg00000128708 | hat1-205 | 2 | 171922462 | 171923475 | + | lnc_RNA | processed_transcript |
| -157631 | enst00000457761 | sg00000128708 | hat1-204 | 2 | 171922462 | 171979995 | + | mRNA | nonsense_mediated_decay |
| -157632 | enst00000264108 | sg00000128708 | hat1-201 | 2 | 171922461 | 171983686 | + | mRNA | protein_coding |
| -157645 | enst00000412731 | sg00000128708 | hat1-203 | 2 | 171922448 | 171983682 | + | mRNA | nonsense_mediated_decay |
| -185849 | enst00000422440 | sg00000115840 | slc25a12-202 | 2 | 171783405 | 171894244 | - | mRNA | protein_coding |
| -185849 | enst00000426896 | sg00000115840 | slc25a12-203 | 2 | 171834031 | 171894244 | - | mRNA | nonsense_mediated_decay |
| -185870 | enst00000263812 | sg00000115840 | slc25a12-201 | 2 | 171784775 | 171894223 | - | mRNA | nonsense_mediated_decay |
| -186835 | enst00000475360 | sg00000115840 | slc25a12-207 | 2 | 171837149 | 171893258 | - | mRNA | nonsense_mediated_decay |
| 219571 | enst00000657632 | sg00000232555 | ac104088.1-203 | 2 | 172301145 | 172367941 | + | lnc_RNA | lncrna |
| -223423 | enst00000516970 | sg00000252779 | rnu6-182p-201 | 2 | 171856566 | 171856670 | - | snRNA | snrna |
| 224213 | enst00000671082 | sg00000232555 | ac104088.1-204 | 2 | 172305787 | 172370401 | + | lnc_RNA | lncrna |
| 233713 | enst00000445613 | sg00000232555 | ac104088.1-201 | 2 | 172315287 | 172323737 | + | lnc_RNA | lncrna |
| -245758 | enst00000485880 | sg00000115840 | slc25a12-209 | 2 | 171815109 | 171834335 | - | lnc_RNA | retained_intron |
| 249008 | enst00000668498 | sg00000286557 | ac104088.2-201 | 2 | 172323260 | 172330582 | - | lnc_RNA | lncrna |
| -269813 | enst00000494892 | sg00000115840 | slc25a12-210 | 2 | 171809425 | 171810280 | - | lnc_RNA | processed_transcript |
| -291151 | enst00000472070 | sg00000115840 | slc25a12-205 | 2 | 171784832 | 171788942 | - | lnc_RNA | retained_intron |
| 342599 | enst00000623218 | sg00000278924 | ac078883.3-201 | 2 | 172423807 | 172424173 | - | unconfirmed_transcript | tec |
| 345780 | enst00000412899 | sg00000091409 | itga6-204 | 2 | 172427354 | 172474977 | + | mRNA | protein_coding |
| 345844 | enst00000409532 | sg00000091409 | itga6-203 | 2 | 172427418 | 172504534 | + | mRNA | protein_coding |
| 345981 | enst00000264107 | sg00000091409 | itga6-201 | 2 | 172427555 | 172506230 | + | mRNA | protein_coding |
| 346012 | enst00000409080 | sg00000091409 | itga6-202 | 2 | 172427586 | 172506459 | + | mRNA | protein_coding |
| 346215 | enst00000442250 | sg00000091409 | itga6-206 | 2 | 172427789 | 172504252 | + | mRNA | protein_coding |
| 346215 | enst00000458358 | sg00000091409 | itga6-207 | 2 | 172427789 | 172504252 | + | mRNA | protein_coding |
| 347029 | enst00000441212 | sg00000226963 | ac078883.2-201 | 2 | 172427774 | 172428603 | - | lnc_RNA | lncrna |
| -353535 | enst00000479806 | sg00000077380 | dync1i2-223 | 2 | 171726558 | 171748407 | + | lnc_RNA | retained_intron |
| -364703 | enst00000470286 | sg00000077380 | dync1i2-220 | 2 | 171715390 | 171726852 | + | lnc_RNA | retained_intron |
| -367691 | enst00000476551 | sg00000077380 | dync1i2-222 | 2 | 171712402 | 171715376 | + | lnc_RNA | retained_intron |
| -373203 | enst00000482454 | sg00000077380 | dync1i2-224 | 2 | 171706890 | 171748409 | + | lnc_RNA | retained_intron |
| 384438 | enst00000417539 | sg00000232788 | itga6-as1-201 | 2 | 172465147 | 172466012 | - | lnc_RNA | lncrna |
| 384448 | enst00000458314 | sg00000232788 | itga6-as1-202 | 2 | 172464262 | 172466022 | - | lnc_RNA | lncrna |
| 387424 | enst00000497107 | sg00000091409 | itga6-211 | 2 | 172468998 | 172474112 | + | lnc_RNA | retained_intron |
| -389948 | enst00000422646 | sg00000077380 | dync1i2-210 | 2 | 171690145 | 171725677 | + | mRNA | protein_coding |
| -391783 | enst00000430778 | sg00000077380 | dync1i2-213 | 2 | 171688310 | 171712779 | + | mRNA | protein_coding |
| -391790 | enst00000425485 | sg00000077380 | dync1i2-212 | 2 | 171688303 | 171725946 | + | mRNA | protein_coding |
| -391790 | enst00000423910 | sg00000077380 | dync1i2-211 | 2 | 171688303 | 171725650 | + | mRNA | protein_coding |
| -392082 | enst00000412370 | sg00000077380 | dync1i2-209 | 2 | 171688011 | 171715368 | + | mRNA | protein_coding |
| -392087 | enst00000443458 | sg00000077380 | dync1i2-216 | 2 | 171688006 | 171715351 | + | mRNA | protein_coding |
| -392212 | enst00000435234 | sg00000077380 | dync1i2-214 | 2 | 171687881 | 171726913 | + | mRNA | protein_coding |
| -392301 | enst00000445378 | sg00000077380 | dync1i2-217 | 2 | 171687792 | 171725955 | + | mRNA | nonsense_mediated_decay |
| -392317 | enst00000409453 | sg00000077380 | dync1i2-205 | 2 | 171687776 | 171748420 | + | mRNA | protein_coding |
| -392338 | enst00000411953 | sg00000077380 | dync1i2-208 | 2 | 171687755 | 171715350 | + | mRNA | protein_coding |
| -392349 | enst00000409773 | sg00000077380 | dync1i2-206 | 2 | 171687744 | 171748416 | + | mRNA | protein_coding |
| -392385 | enst00000409317 | sg00000077380 | dync1i2-204 | 2 | 171687708 | 171748011 | + | mRNA | protein_coding |
| -392388 | enst00000456808 | sg00000077380 | dync1i2-219 | 2 | 171687705 | 171725693 | + | mRNA | protein_coding |
| -392421 | enst00000409197 | sg00000077380 | dync1i2-203 | 2 | 171687672 | 171748411 | + | mRNA | protein_coding |
| -392592 | enst00000508530 | sg00000077380 | dync1i2-225 | 2 | 171687501 | 171748411 | + | mRNA | protein_coding |
| -392621 | enst00000471482 | sg00000077380 | dync1i2-221 | 2 | 171687472 | 171693084 | + | lnc_RNA | retained_intron |
| -392621 | enst00000438879 | sg00000077380 | dync1i2-215 | 2 | 171687472 | 171725713 | + | mRNA | protein_coding |
| -392622 | enst00000410079 | sg00000077380 | dync1i2-207 | 2 | 171687471 | 171747989 | + | mRNA | protein_coding |
| -392623 | enst00000397119 | sg00000077380 | dync1i2-202 | 2 | 171687470 | 171748409 | + | mRNA | protein_coding |
| -392684 | enst00000340296 | sg00000077380 | dync1i2-201 | 2 | 171687409 | 171748411 | + | mRNA | protein_coding |
| -392684 | enst00000452242 | sg00000077380 | dync1i2-218 | 2 | 171687409 | 171726081 | + | mRNA | protein_coding |
| 406388 | enst00000416789 | sg00000091409 | itga6-205 | 2 | 172487962 | 172504328 | + | mRNA | protein_coding |
| 406431 | enst00000469534 | sg00000091409 | itga6-208 | 2 | 172488005 | 172489928 | + | lnc_RNA | retained_intron |
| 409218 | enst00000470259 | sg00000091409 | itga6-209 | 2 | 172490792 | 172491254 | + | lnc_RNA | retained_intron |
| 409355 | enst00000475302 | sg00000091409 | itga6-210 | 2 | 172490929 | 172501818 | + | lnc_RNA | retained_intron |
| 430936 | enst00000416080 | sg00000225205 | ac078883.1-203 | 2 | 172509029 | 172512510 | - | lnc_RNA | lncrna |
| 473799 | enst00000443353 | sg00000152256 | pdk1-208 | 2 | 172555373 | 172565073 | + | mRNA | protein_coding |
| 474053 | enst00000436490 | sg00000152256 | pdk1-206 | 2 | 172555627 | 172564687 | + | mRNA | nonsense_mediated_decay |
| 474395 | enst00000282077 | sg00000152256 | pdk1-201 | 2 | 172555969 | 172608669 | + | mRNA | protein_coding |
| 474433 | enst00000392571 | sg00000152256 | pdk1-202 | 2 | 172556007 | 172595969 | + | mRNA | protein_coding |
| 474477 | enst00000410055 | sg00000152256 | pdk1-203 | 2 | 172556051 | 172599137 | + | mRNA | protein_coding |
| 474528 | enst00000431718 | sg00000152256 | pdk1-205 | 2 | 172556102 | 172570820 | + | mRNA | nonsense_mediated_decay |
| 474739 | enst00000416991 | sg00000152256 | pdk1-204 | 2 | 172556313 | 172570812 | + | mRNA | protein_coding |
| 474833 | enst00000436922 | sg00000225205 | ac078883.1-205 | 2 | 172555426 | 172556407 | - | lnc_RNA | lncrna |
| 474834 | enst00000444919 | sg00000225205 | ac078883.1-204 | 2 | 172552615 | 172556408 | - | lnc_RNA | lncrna |
| 474955 | enst00000442417 | sg00000225205 | ac078883.1-201 | 2 | 172480840 | 172556529 | - | lnc_RNA | lncrna |
| 474991 | enst00000439519 | sg00000152256 | pdk1-207 | 2 | 172556565 | 172565073 | + | mRNA | protein_coding |
| 475022 | enst00000450443 | sg00000225205 | ac078883.1-202 | 2 | 172503439 | 172556596 | - | lnc_RNA | lncrna |
| 476678 | enst00000362996 | sg00000199866 | ac093818.1-201 | 2 | 172558151 | 172558252 | - | ncRNA | misc_rna |
| 489011 | enst00000466437 | sg00000152256 | pdk1-209 | 2 | 172570585 | 172595962 | + | lnc_RNA | retained_intron |
| -493000 | enst00000418090 | sg00000233934 | rpl21p38-201 | 2 | 171587093 | 171587259 | + | 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