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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 |
|---|---|---|---|---|---|---|---|---|
| #193 | 7 | 5295984 | 5297370 | 1386 | 3 | 40 | 2.8241e-14 | 1.45514e-12 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 1959 | enst00000439491 | sg00000164638 | slc29a4-205 | 7 | 5299329 | 5303680 | + | lnc_RNA | processed_transcript |
| -12955 | enst00000406453 | sg00000164638 | slc29a4-203 | 7 | 5283029 | 5304060 | + | mRNA | protein_coding |
| -13015 | enst00000297195 | sg00000164638 | slc29a4-201 | 7 | 5282969 | 5304060 | + | mRNA | protein_coding |
| -13022 | enst00000444741 | sg00000164638 | slc29a4-206 | 7 | 5282962 | 5291767 | + | mRNA | protein_coding |
| -13054 | enst00000396872 | sg00000164638 | slc29a4-202 | 7 | 5282930 | 5306870 | + | mRNA | protein_coding |
| -21615 | enst00000434816 | sg00000164638 | slc29a4-204 | 7 | 5274369 | 5291766 | + | mRNA | protein_coding |
| 23237 | enst00000328270 | sg00000182095 | tnrc18-201 | 7 | 5313111 | 5320607 | - | mRNA | protein_coding |
| 23292 | enst00000464852 | sg00000182095 | tnrc18-209 | 7 | 5320140 | 5320662 | - | lnc_RNA | retained_intron |
| 28204 | enst00000497663 | sg00000182095 | tnrc18-210 | 7 | 5324247 | 5325574 | - | lnc_RNA | retained_intron |
| 35508 | enst00000455076 | sg00000182095 | tnrc18-208 | 7 | 5324222 | 5332878 | - | mRNA | protein_coding |
| 64657 | enst00000440081 | sg00000182095 | tnrc18-207 | 7 | 5352002 | 5362027 | - | mRNA | protein_coding |
| -66576 | enst00000479690 | sg00000157954 | wipi2-209 | 7 | 5229408 | 5231327 | + | lnc_RNA | retained_intron |
| -70034 | enst00000471851 | sg00000157954 | wipi2-207 | 7 | 5225950 | 5231723 | + | lnc_RNA | retained_intron |
| -79393 | enst00000488359 | sg00000157954 | wipi2-213 | 7 | 5216591 | 5225978 | + | lnc_RNA | processed_transcript |
| -79812 | enst00000480238 | sg00000157954 | wipi2-210 | 7 | 5216172 | 5225854 | + | lnc_RNA | processed_transcript |
| -81423 | enst00000465102 | sg00000157954 | wipi2-205 | 7 | 5214561 | 5222812 | + | lnc_RNA | retained_intron |
| -81715 | enst00000484262 | sg00000157954 | wipi2-211 | 7 | 5214269 | 5231064 | + | mRNA | protein_coding |
| -81798 | enst00000475309 | sg00000157954 | wipi2-208 | 7 | 5214186 | 5219031 | + | lnc_RNA | retained_intron |
| 90659 | enst00000413081 | sg00000182095 | tnrc18-204 | 7 | 5376114 | 5388029 | - | mRNA | protein_coding |
| -105291 | enst00000496867 | sg00000157954 | wipi2-214 | 7 | 5190693 | 5218013 | + | lnc_RNA | processed_transcript |
| -105711 | enst00000382384 | sg00000157954 | wipi2-202 | 7 | 5190273 | 5231470 | + | mRNA | protein_coding |
| -105719 | enst00000485854 | sg00000157954 | wipi2-212 | 7 | 5190265 | 5214702 | + | lnc_RNA | processed_transcript |
| -105725 | enst00000466014 | sg00000157954 | wipi2-206 | 7 | 5190259 | 5230947 | + | lnc_RNA | retained_intron |
| -105738 | enst00000404704 | sg00000157954 | wipi2-204 | 7 | 5190246 | 5231104 | + | mRNA | protein_coding |
| -105751 | enst00000288828 | sg00000157954 | wipi2-201 | 7 | 5190233 | 5233840 | + | mRNA | protein_coding |
| -105788 | enst00000401525 | sg00000157954 | wipi2-203 | 7 | 5190196 | 5231524 | + | mRNA | protein_coding |
| 110024 | enst00000434361 | sg00000182095 | tnrc18-206 | 7 | 5389305 | 5407394 | - | mRNA | protein_coding |
| -115923 | enst00000365169 | sg00000202039 | rnu6-215p-201 | 7 | 5180061 | 5180162 | + | snRNA | snrna |
| 122457 | enst00000342963 | sg00000241269 | ac093620.1-201 | 7 | 5419827 | 5420767 | + | lnc_RNA | lncrna |
| 122476 | enst00000455866 | sg00000188365 | ac092171.1-201 | 7 | 5419846 | 5423122 | + | lnc_RNA | lncrna |
| 126176 | enst00000430969 | sg00000182095 | tnrc18-205 | 7 | 5306800 | 5423546 | - | mRNA | protein_coding |
| 126176 | enst00000399537 | sg00000182095 | tnrc18-203 | 7 | 5306790 | 5423546 | - | mRNA | protein_coding |
| 128044 | enst00000399434 | sg00000182095 | tnrc18-202 | 7 | 5389450 | 5425414 | - | mRNA | protein_coding |
| 128400 | enst00000609130 | sg00000272953 | ac092171.4-201 | 7 | 5425770 | 5426401 | + | lnc_RNA | lncrna |
| 131361 | enst00000608012 | sg00000273084 | ac092171.5-201 | 7 | 5428731 | 5429672 | + | lnc_RNA | lncrna |
| 131557 | enst00000610122 | sg00000234432 | ac092171.3-201 | 7 | 5426277 | 5428927 | - | lnc_RNA | lncrna |
| -151438 | enst00000422060 | sg00000159904 | znf890p-201 | 7 | 5121572 | 5144546 | - | lnc_RNA | processed_transcript |
| -168189 | enst00000530367 | sg00000159904 | znf890p-202 | 7 | 5121239 | 5127795 | - | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 178434 | enst00000444210 | sg00000230733 | ac092171.2-201 | 7 | 5475804 | 5479811 | + | lnc_RNA | lncrna |
| -178849 | enst00000608262 | sg00000272595 | or10ah1p-201 | 7 | 5117135 | 5118087 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -192261 | enst00000641483 | sg00000272595 | or10ah1p-202 | 7 | 5103723 | 5120245 | + | lnc_RNA | processed_transcript |
| -192265 | enst00000641781 | sg00000272595 | or10ah1p-203 | 7 | 5103719 | 5120245 | + | lnc_RNA | processed_transcript |
| 198547 | enst00000385238 | sg00000207973 | mir589-201 | 7 | 5495819 | 5495917 | - | miRNA | mirna |
| 203626 | enst00000620087 | sg00000155034 | fbxl18-205 | 7 | 5480582 | 5500996 | - | mRNA | protein_coding |
| 204549 | enst00000458142 | sg00000155034 | fbxl18-204 | 7 | 5489178 | 5501919 | - | mRNA | protein_coding |
| 216382 | enst00000415009 | sg00000155034 | fbxl18-202 | 7 | 5431335 | 5513752 | - | mRNA | nonsense_mediated_decay |
| 216398 | enst00000453700 | sg00000155034 | fbxl18-203 | 7 | 5480451 | 5513768 | - | mRNA | protein_coding |
| 216439 | enst00000382368 | sg00000155034 | fbxl18-201 | 7 | 5475797 | 5513809 | - | mRNA | protein_coding |
| -223859 | enst00000498308 | sg00000273313 | rbakdn-201 | 7 | 5072125 | 5073223 | + | lnc_RNA | lncrna |
| 230728 | enst00000464611 | sg00000075624 | actb-207 | 7 | 5527151 | 5528098 | - | mRNA | protein_coding |
| 232579 | enst00000642480 | sg00000075624 | actb-213 | 7 | 5528586 | 5529949 | - | mRNA | protein_coding |
| 232612 | enst00000417101 | sg00000075624 | actb-202 | 7 | 5529235 | 5529982 | - | mRNA | protein_coding |
| 233213 | enst00000480301 | sg00000075624 | actb-210 | 7 | 5529067 | 5530583 | - | lnc_RNA | retained_intron |
| 233220 | enst00000477812 | sg00000075624 | actb-209 | 7 | 5528470 | 5530590 | - | lnc_RNA | retained_intron |
| 233225 | enst00000473257 | sg00000075624 | actb-208 | 7 | 5528004 | 5530595 | - | lnc_RNA | processed_transcript |
| 233227 | enst00000645576 | sg00000075624 | actb-215 | 7 | 5528011 | 5530597 | - | mRNA | protein_coding |
| 233230 | enst00000645025 | sg00000075624 | actb-214 | 7 | 5528934 | 5530600 | - | lnc_RNA | retained_intron |
| 233231 | enst00000484841 | sg00000075624 | actb-211 | 7 | 5528717 | 5530601 | - | lnc_RNA | processed_transcript |
| 233231 | enst00000646664 | sg00000075624 | actb-217 | 7 | 5527148 | 5530601 | - | mRNA | protein_coding |
| 233231 | enst00000425660 | sg00000075624 | actb-203 | 7 | 5527156 | 5530601 | - | mRNA | nonsense_mediated_decay |
| 233231 | enst00000462494 | sg00000075624 | actb-206 | 7 | 5527156 | 5530601 | - | lnc_RNA | retained_intron |
| 233232 | enst00000493945 | sg00000075624 | actb-212 | 7 | 5527536 | 5530602 | - | mRNA | protein_coding |
| 233234 | enst00000647275 | sg00000075624 | actb-218 | 7 | 5528150 | 5530604 | - | mRNA | protein_coding |
| -238997 | enst00000476992 | sg00000146587 | rbak-203 | 7 | 5056987 | 5063875 | + | lnc_RNA | retained_intron |
| -250073 | enst00000396904 | sg00000272968 | rbak-rbakdn-201 | 7 | 5045911 | 5073221 | + | mRNA | protein_coding |
| -250124 | enst00000396912 | sg00000146587 | rbak-202 | 7 | 5045860 | 5069487 | + | mRNA | protein_coding |
| -250163 | enst00000353796 | sg00000146587 | rbak-201 | 7 | 5045821 | 5067257 | + | mRNA | protein_coding |
| -258153 | enst00000338590 | sg00000275328 | spdye19p-201 | 7 | 5031608 | 5037831 | - | pseudogenic_transcript | unprocessed_pseudogene |
| 259361 | enst00000609813 | sg00000272719 | ac006483.2-201 | 7 | 5556731 | 5557245 | + | lnc_RNA | lncrna |
| 263373 | enst00000487308 | sg00000228974 | ac006483.1-201 | 7 | 5560743 | 5561055 | + | pseudogenic_transcript | processed_pseudogene |
| 265346 | enst00000646584 | sg00000075624 | actb-216 | 7 | 5561852 | 5562716 | - | lnc_RNA | processed_transcript |
| 265420 | enst00000414620 | sg00000075624 | actb-201 | 7 | 5529282 | 5562790 | - | mRNA | protein_coding |
| 265458 | enst00000443528 | sg00000075624 | actb-205 | 7 | 5529216 | 5562828 | - | mRNA | protein_coding |
| 266414 | enst00000432588 | sg00000075624 | actb-204 | 7 | 5528592 | 5563784 | - | mRNA | protein_coding |
| -286656 | enst00000603090 | sg00000270822 | ac092032.1-201 | 7 | 5009164 | 5009328 | - | pseudogenic_transcript | processed_pseudogene |
| 295446 | enst00000382361 | sg00000075618 | fscn1-201 | 7 | 5592816 | 5606655 | + | mRNA | protein_coding |
| 296478 | enst00000444748 | sg00000075618 | fscn1-203 | 7 | 5593848 | 5603983 | + | mRNA | protein_coding |
| 297177 | enst00000447103 | sg00000075618 | fscn1-204 | 7 | 5594547 | 5603946 | + | mRNA | protein_coding |
| 297316 | enst00000405801 | sg00000075618 | fscn1-202 | 7 | 5594686 | 5603998 | + | mRNA | protein_coding |
| -302475 | enst00000471244 | sg00000196204 | rnf216p1-210 | 7 | 4993509 | 4998167 | + | lnc_RNA | processed_transcript |
| 305502 | enst00000473330 | sg00000075618 | fscn1-205 | 7 | 5602872 | 5606654 | + | lnc_RNA | retained_intron |
| -311076 | enst00000466622 | sg00000196204 | rnf216p1-209 | 7 | 4984908 | 4989368 | + | lnc_RNA | processed_transcript |
| -311268 | enst00000464479 | sg00000196204 | rnf216p1-208 | 7 | 4984716 | 4996774 | + | lnc_RNA | processed_transcript |
| -312266 | enst00000407184 | sg00000272968 | rbak-rbakdn-202 | 7 | 4983718 | 5073221 | + | mRNA | protein_coding |
| -312289 | enst00000405396 | sg00000196204 | rnf216p1-204 | 7 | 4983695 | 4997119 | + | lnc_RNA | processed_transcript |
| -319619 | enst00000406608 | sg00000196204 | rnf216p1-206 | 7 | 4976365 | 4996673 | + | lnc_RNA | processed_transcript |
| -321863 | enst00000429902 | sg00000196204 | rnf216p1-207 | 7 | 4974121 | 4985075 | + | lnc_RNA | processed_transcript |
| -321932 | enst00000494947 | sg00000196204 | rnf216p1-213 | 7 | 4974052 | 5040675 | + | lnc_RNA | processed_transcript |
| -321934 | enst00000403969 | sg00000196204 | rnf216p1-201 | 7 | 4974050 | 4997452 | + | lnc_RNA | processed_transcript |
| -321947 | enst00000404006 | sg00000196204 | rnf216p1-202 | 7 | 4974037 | 4998165 | + | lnc_RNA | processed_transcript |
| -321968 | enst00000477090 | sg00000196204 | rnf216p1-211 | 7 | 4974016 | 4996893 | + | lnc_RNA | processed_transcript |
| -321996 | enst00000404404 | sg00000196204 | rnf216p1-203 | 7 | 4973988 | 4998169 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -321996 | enst00000493407 | sg00000196204 | rnf216p1-212 | 7 | 4973988 | 4986591 | + | lnc_RNA | processed_transcript |
| -321996 | enst00000406089 | sg00000196204 | rnf216p1-205 | 7 | 4973988 | 4995522 | + | lnc_RNA | processed_transcript |
| -336771 | enst00000612910 | sg00000136297 | mmd2-204 | 7 | 4909734 | 4959213 | - | mRNA | protein_coding |
| -336771 | enst00000401401 | sg00000136297 | mmd2-201 | 7 | 4905998 | 4959213 | - | mRNA | protein_coding |
| -336772 | enst00000404774 | sg00000136297 | mmd2-202 | 7 | 4905989 | 4959212 | - | mRNA | protein_coding |
| -336793 | enst00000406755 | sg00000136297 | mmd2-203 | 7 | 4905989 | 4959191 | - | mRNA | protein_coding |
| 352645 | enst00000469375 | sg00000011275 | rnf216-206 | 7 | 5622927 | 5650015 | - | lnc_RNA | processed_transcript |
| 383091 | enst00000443837 | sg00000237738 | rnf216-it1-201 | 7 | 5662432 | 5680461 | - | lnc_RNA | lncrna |
| -412268 | enst00000399583 | sg00000157927 | radil-201 | 7 | 4797055 | 4883716 | - | mRNA | protein_coding |
| -412330 | enst00000445392 | sg00000157927 | radil-202 | 7 | 4797055 | 4883654 | - | mRNA | nonsense_mediated_decay |
| -413775 | enst00000457174 | sg00000157927 | radil-203 | 7 | 4877738 | 4882209 | - | mRNA | protein_coding |
| 414540 | enst00000635894 | sg00000283419 | mir6874-201 | 7 | 5711840 | 5711910 | - | miRNA | mirna |
| 416071 | enst00000484458 | sg00000011275 | rnf216-209 | 7 | 5641348 | 5713441 | - | lnc_RNA | processed_transcript |
| -430180 | enst00000454916 | sg00000213935 | rpl22p16-201 | 7 | 4865432 | 4865804 | - | pseudogenic_transcript | processed_pseudogene |
| -433954 | enst00000404991 | sg00000218823 | papolb-201 | 7 | 4857738 | 4862030 | - | mRNA | protein_coding |
| 442122 | enst00000479541 | sg00000011275 | rnf216-208 | 7 | 5729530 | 5739492 | - | lnc_RNA | retained_intron |
| -463765 | enst00000484211 | sg00000157927 | radil-207 | 7 | 4815278 | 4832219 | - | lnc_RNA | retained_intron |
| 463768 | enst00000389900 | sg00000011275 | rnf216-201 | 7 | 5622695 | 5761138 | - | mRNA | nonsense_mediated_decay |
| -463775 | enst00000473130 | sg00000157927 | radil-206 | 7 | 4799109 | 4832209 | - | lnc_RNA | retained_intron |
| -480651 | enst00000469399 | sg00000157927 | radil-204 | 7 | 4805245 | 4815333 | - | lnc_RNA | retained_intron |
| 482922 | enst00000476345 | sg00000011275 | rnf216-207 | 7 | 5761088 | 5780292 | - | lnc_RNA | processed_transcript |
| 484250 | enst00000416985 | sg00000011275 | rnf216-204 | 7 | 5761011 | 5781620 | - | mRNA | protein_coding |
| 484276 | enst00000411812 | sg00000011275 | rnf216-203 | 7 | 5741579 | 5781646 | - | mRNA | nonsense_mediated_decay |
| 484326 | enst00000425013 | sg00000011275 | rnf216-205 | 7 | 5620047 | 5781696 | - | mRNA | protein_coding |
| 484369 | enst00000389902 | sg00000011275 | rnf216-202 | 7 | 5622607 | 5781739 | - | mRNA | protein_coding |
| -484695 | enst00000384168 | sg00000206895 | ac092610.1-201 | 7 | 4811188 | 4811289 | - | ncRNA | misc_rna |
| -491916 | enst00000472999 | sg00000157927 | radil-205 | 7 | 4799105 | 4804068 | - | 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