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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 |
|---|---|---|---|---|---|---|---|---|
| #59 | 4 | 8866964 | 8868473 | 1509 | 3 | 45 | 1.17736e-20 | 1.98454e-18 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 3149 | enst00000506970 | sg00000215612 | hmx1-202 | 4 | 8846076 | 8871622 | - | mRNA | protein_coding |
| 3366 | enst00000400677 | sg00000215612 | hmx1-201 | 4 | 8867048 | 8871839 | - | mRNA | protein_coding |
| -6137 | enst00000557144 | sg00000258507 | ac116612.1-201 | 4 | 8858715 | 8860827 | - | lnc_RNA | lncrna |
| 81157 | enst00000508957 | sg00000197468 | ac073648.1-201 | 4 | 8949630 | 8950559 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 91155 | enst00000511903 | sg00000249272 | unc93b8-201 | 4 | 8959628 | 8963981 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 112963 | enst00000504939 | sg00000250804 | ac073648.3-201 | 4 | 8981436 | 8982360 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -119237 | enst00000514043 | sg00000250915 | ac209005.1-201 | 4 | 8745391 | 8747727 | - | lnc_RNA | lncrna |
| 121982 | enst00000510116 | sg00000249347 | ac073648.2-201 | 4 | 8990455 | 8990806 | + | pseudogenic_transcript | processed_pseudogene |
| 132368 | enst00000641589 | sg00000284636 | ac073648.6-201 | 4 | 9000841 | 9001058 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 152688 | enst00000603502 | sg00000271057 | ac073648.5-201 | 4 | 9020857 | 9021161 | - | pseudogenic_transcript | processed_pseudogene |
| 161813 | enst00000442655 | sg00000251313 | ac073648.4-201 | 4 | 9030286 | 9031066 | + | pseudogenic_transcript | processed_pseudogene |
| 183578 | enst00000506029 | sg00000250342 | snrpcp16-201 | 4 | 9051842 | 9052051 | - | pseudogenic_transcript | processed_pseudogene |
| 195793 | enst00000662683 | sg00000288075 | ac108519.1-205 | 4 | 9063028 | 9064266 | - | lnc_RNA | lncrna |
| 208476 | enst00000671426 | sg00000287972 | ac073648.7-201 | 4 | 9076949 | 9092530 | + | lnc_RNA | lncrna |
| 210550 | enst00000504828 | sg00000249767 | enpp7p10-201 | 4 | 9079023 | 9141608 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -248872 | enst00000513486 | sg00000109625 | cpz-206 | 4 | 8618092 | 8619487 | + | lnc_RNA | retained_intron |
| -264994 | enst00000513120 | sg00000155269 | gpr78-206 | 4 | 8601970 | 8619761 | + | lnc_RNA | retained_intron |
| -274130 | enst00000514875 | sg00000109625 | cpz-208 | 4 | 8592834 | 8599961 | + | lnc_RNA | retained_intron |
| -274167 | enst00000504070 | sg00000109625 | cpz-204 | 4 | 8592797 | 8601450 | + | lnc_RNA | processed_transcript |
| -274182 | enst00000514602 | sg00000109625 | cpz-207 | 4 | 8592782 | 8601508 | + | lnc_RNA | retained_intron |
| -274199 | enst00000360986 | sg00000109625 | cpz-202 | 4 | 8592765 | 8619752 | + | mRNA | protein_coding |
| -274208 | enst00000315782 | sg00000109625 | cpz-201 | 4 | 8592756 | 8619749 | + | mRNA | protein_coding |
| -274238 | enst00000515606 | sg00000109625 | cpz-209 | 4 | 8592726 | 8619751 | + | mRNA | nonsense_mediated_decay |
| -274256 | enst00000506287 | sg00000109625 | cpz-205 | 4 | 8592708 | 8601498 | + | lnc_RNA | processed_transcript |
| -274304 | enst00000382480 | sg00000109625 | cpz-203 | 4 | 8592660 | 8619759 | + | mRNA | protein_coding |
| 282945 | enst00000659603 | sg00000288075 | ac108519.1-204 | 4 | 9034519 | 9151418 | - | lnc_RNA | lncrna |
| 282968 | enst00000664986 | sg00000288075 | ac108519.1-206 | 4 | 9128119 | 9151441 | - | lnc_RNA | lncrna |
| 283802 | enst00000668176 | sg00000288075 | ac108519.1-207 | 4 | 9129944 | 9152275 | - | lnc_RNA | lncrna |
| -284173 | enst00000504255 | sg00000155269 | gpr78-204 | 4 | 8582791 | 8587750 | + | lnc_RNA | processed_transcript |
| 284823 | enst00000509817 | sg00000163612 | fam86kp-201 | 4 | 9153296 | 9165451 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -286572 | enst00000382487 | sg00000155269 | gpr78-201 | 4 | 8580392 | 8590023 | + | mRNA | protein_coding |
| -286727 | enst00000509216 | sg00000155269 | gpr78-205 | 4 | 8580237 | 8587520 | + | lnc_RNA | processed_transcript |
| -288639 | enst00000514302 | sg00000155269 | gpr78-207 | 4 | 8578325 | 8619749 | + | mRNA | nonsense_mediated_decay |
| 301797 | enst00000514230 | sg00000250268 | alg1l14p-201 | 4 | 9166297 | 9170270 | - | pseudogenic_transcript | unprocessed_pseudogene |
| 301936 | enst00000512047 | sg00000229924 | fam90a26-201 | 4 | 9170409 | 9176730 | + | mRNA | protein_coding |
| -308132 | enst00000503448 | sg00000155269 | gpr78-202 | 4 | 8558832 | 8580711 | + | lnc_RNA | processed_transcript |
| -308239 | enst00000503981 | sg00000155269 | gpr78-203 | 4 | 8558725 | 8580524 | + | lnc_RNA | processed_transcript |
| 342184 | enst00000421288 | sg00000231396 | usp17l10-202 | 4 | 9210657 | 9212608 | + | mRNA | protein_coding |
| 342184 | enst00000417945 | sg00000231396 | usp17l10-201 | 4 | 9210657 | 9212249 | + | mRNA | protein_coding |
| 346932 | enst00000613973 | sg00000233136 | usp17l11-202 | 4 | 9215405 | 9217356 | + | mRNA | protein_coding |
| 346932 | enst00000457736 | sg00000233136 | usp17l11-201 | 4 | 9215405 | 9216997 | + | mRNA | protein_coding |
| 351679 | enst00000415041 | sg00000227551 | usp17l12-201 | 4 | 9220152 | 9221744 | + | mRNA | protein_coding |
| -356052 | enst00000660284 | sg00000205959 | ac105345.1-203 | 4 | 8510912 | 8516759 | + | lnc_RNA | lncrna |
| 356423 | enst00000616303 | sg00000232399 | usp17l13-202 | 4 | 9224896 | 9226847 | + | mRNA | protein_coding |
| 356423 | enst00000429667 | sg00000232399 | usp17l13-201 | 4 | 9224896 | 9226488 | + | mRNA | protein_coding |
| -360136 | enst00000382488 | sg00000205959 | ac105345.1-202 | 4 | 8506828 | 8512610 | + | lnc_RNA | lncrna |
| 361168 | enst00000504838 | sg00000249482 | usp17l14p-201 | 4 | 9229641 | 9231233 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 365912 | enst00000456464 | sg00000223569 | usp17l15-201 | 4 | 9234385 | 9235974 | + | mRNA | protein_coding |
| 365912 | enst00000621432 | sg00000223569 | usp17l15-202 | 4 | 9234385 | 9236334 | + | mRNA | protein_coding |
| 370657 | enst00000507155 | sg00000250231 | usp17l16p-201 | 4 | 9239130 | 9240722 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 375406 | enst00000511568 | sg00000249104 | usp17l17-201 | 4 | 9243879 | 9245471 | + | mRNA | protein_coding |
| 375406 | enst00000614762 | sg00000249104 | usp17l17-202 | 4 | 9243879 | 9245830 | + | mRNA | protein_coding |
| 380157 | enst00000619296 | sg00000250844 | usp17l18-202 | 4 | 9248630 | 9250581 | + | mRNA | protein_coding |
| 380157 | enst00000504209 | sg00000250844 | usp17l18-201 | 4 | 9248630 | 9250222 | + | mRNA | protein_coding |
| -384694 | enst00000528132 | sg00000205959 | ac105345.1-201 | 4 | 8482270 | 8509195 | + | lnc_RNA | lncrna |
| 384905 | enst00000615989 | sg00000248920 | usp17l19-202 | 4 | 9253378 | 9255329 | + | mRNA | protein_coding |
| 384905 | enst00000515566 | sg00000248920 | usp17l19-201 | 4 | 9253378 | 9254970 | + | mRNA | protein_coding |
| 389651 | enst00000613757 | sg00000250745 | usp17l20-202 | 4 | 9258124 | 9260075 | + | mRNA | protein_coding |
| 389651 | enst00000506151 | sg00000250745 | usp17l20-201 | 4 | 9258124 | 9259716 | + | mRNA | protein_coding |
| -393448 | enst00000511366 | sg00000155275 | trmt44-204 | 4 | 8473516 | 8493531 | + | lnc_RNA | processed_transcript |
| -393657 | enst00000511149 | sg00000155275 | trmt44-203 | 4 | 8473307 | 8475965 | + | lnc_RNA | processed_transcript |
| 394399 | enst00000621388 | sg00000249811 | usp17l21-202 | 4 | 9262872 | 9264823 | + | mRNA | protein_coding |
| 394399 | enst00000506414 | sg00000249811 | usp17l21-201 | 4 | 9262872 | 9264464 | + | mRNA | protein_coding |
| -396038 | enst00000531038 | sg00000155275 | trmt44-207 | 4 | 8470926 | 8493531 | + | lnc_RNA | retained_intron |
| 399146 | enst00000622009 | sg00000248933 | usp17l22-202 | 4 | 9267619 | 9269570 | + | mRNA | protein_coding |
| 399146 | enst00000511280 | sg00000248933 | usp17l22-201 | 4 | 9267619 | 9269211 | + | mRNA | protein_coding |
| 403891 | enst00000506619 | sg00000250913 | usp17l23-201 | 4 | 9272364 | 9272914 | + | mRNA | protein_coding |
| -412022 | enst00000515186 | sg00000251186 | ac105345.2-201 | 4 | 8453410 | 8454942 | - | lnc_RNA | lncrna |
| -412548 | enst00000532477 | sg00000155275 | trmt44-208 | 4 | 8454416 | 8476554 | + | lnc_RNA | processed_transcript |
| -426002 | enst00000504134 | sg00000155275 | trmt44-202 | 4 | 8440962 | 8449877 | + | mRNA | protein_coding |
| -426159 | enst00000528167 | sg00000155275 | trmt44-206 | 4 | 8440805 | 8449720 | + | lnc_RNA | processed_transcript |
| -426187 | enst00000389737 | sg00000155275 | trmt44-201 | 4 | 8440777 | 8476555 | + | mRNA | protein_coding |
| -426241 | enst00000356406 | sg00000087008 | acox3-201 | 4 | 8366282 | 8440723 | - | mRNA | protein_coding |
| -426241 | enst00000413009 | sg00000087008 | acox3-202 | 4 | 8366712 | 8440723 | - | mRNA | protein_coding |
| -428095 | enst00000513449 | sg00000155275 | trmt44-205 | 4 | 8438869 | 8468559 | + | mRNA | protein_coding |
| -430824 | enst00000532937 | sg00000155275 | trmt44-209 | 4 | 8436140 | 8439301 | + | lnc_RNA | retained_intron |
| -438478 | enst00000503233 | sg00000087008 | acox3-203 | 4 | 8366961 | 8428486 | - | mRNA | protein_coding |
| -438503 | enst00000514423 | sg00000087008 | acox3-207 | 4 | 8410282 | 8428461 | - | mRNA | protein_coding |
| -451109 | enst00000510365 | sg00000087008 | acox3-205 | 4 | 8374468 | 8415855 | - | lnc_RNA | retained_intron |
| 456692 | enst00000504481 | sg00000232264 | usp17l24-201 | 4 | 9325165 | 9326757 | + | mRNA | protein_coding |
| 456692 | enst00000622713 | sg00000232264 | usp17l24-202 | 4 | 9325165 | 9327116 | + | mRNA | protein_coding |
| 461438 | enst00000509271 | sg00000230430 | usp17l25-201 | 4 | 9329911 | 9331503 | + | mRNA | protein_coding |
| 461438 | enst00000621472 | sg00000230430 | usp17l25-202 | 4 | 9329911 | 9331862 | + | mRNA | protein_coding |
| 466185 | enst00000509660 | sg00000229579 | usp17l26-201 | 4 | 9334658 | 9336250 | + | mRNA | protein_coding |
| 466185 | enst00000610514 | sg00000229579 | usp17l26-202 | 4 | 9334658 | 9336609 | + | mRNA | protein_coding |
| 470930 | enst00000507227 | sg00000227140 | usp17l5-201 | 4 | 9339403 | 9340995 | + | mRNA | protein_coding |
| -472073 | enst00000508302 | sg00000087008 | acox3-204 | 4 | 8381554 | 8394891 | - | lnc_RNA | processed_transcript |
| -473949 | enst00000365184 | sg00000202054 | rna5sp152-201 | 4 | 8393015 | 8393124 | + | pseudogenic_transcript | rrna_pseudogene |
| 475675 | enst00000515574 | sg00000235780 | usp17l27-201 | 4 | 9344148 | 9345740 | + | mRNA | protein_coding |
| 480420 | enst00000504543 | sg00000231051 | usp17l28-201 | 4 | 9348893 | 9350485 | + | mRNA | protein_coding |
| 485165 | enst00000511681 | sg00000231637 | usp17l29-201 | 4 | 9353638 | 9355230 | + | mRNA | protein_coding |
| 489910 | enst00000508843 | sg00000251694 | usp17l9p-201 | 4 | 9358383 | 9359975 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -492797 | enst00000515797 | sg00000087008 | acox3-208 | 4 | 8366712 | 8374167 | - | lnc_RNA | processed_transcript |
| -493149 | enst00000512411 | sg00000087008 | acox3-206 | 4 | 8366712 | 8373815 | - | lnc_RNA | retained_intron |
| 494656 | enst00000504104 | sg00000228856 | usp17l30-201 | 4 | 9363129 | 9364721 | + | mRNA | protein_coding |
| 499401 | enst00000382470 | sg00000205946 | usp17l6p-201 | 4 | 9367874 | 9369070 | + | pseudogenic_transcript | unprocessed_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