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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 |
|---|---|---|---|---|---|---|---|---|
| #159 | 10 | 43395730 | 43397662 | 1932 | 3 | 56 | 2.70495e-15 | 1.69187e-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 |
|---|---|---|---|---|---|---|---|---|---|
| 0 | enst00000443950 | sg00000169813 | hnrnpf-204 | 10 | 43385617 | 43396831 | - | mRNA | protein_coding |
| 0 | enst00000477108 | sg00000169813 | hnrnpf-205 | 10 | 43387589 | 43397278 | - | mRNA | protein_coding |
| 0 | enst00000498176 | sg00000169813 | hnrnpf-206 | 10 | 43387643 | 43396817 | - | lnc_RNA | processed_transcript |
| 0 | enst00000544000 | sg00000169813 | hnrnpf-207 | 10 | 43385617 | 43397346 | - | mRNA | protein_coding |
| 10157 | enst00000357065 | sg00000169813 | hnrnpf-203 | 10 | 43385617 | 43407819 | - | mRNA | protein_coding |
| 11220 | enst00000356053 | sg00000169813 | hnrnpf-202 | 10 | 43385617 | 43408882 | - | mRNA | protein_coding |
| 11504 | enst00000337970 | sg00000169813 | hnrnpf-201 | 10 | 43386022 | 43409166 | - | mRNA | protein_coding |
| 19776 | enst00000408473 | sg00000221400 | snord3j-201 | 10 | 43417249 | 43417438 | - | snoRNA | snorna |
| -21261 | enst00000479189 | sg00000150201 | fxyd4-202 | 10 | 43374469 | 43376335 | + | lnc_RNA | processed_transcript |
| 23076 | enst00000442526 | sg00000230555 | al450326.1-201 | 10 | 43420738 | 43422100 | + | lnc_RNA | lncrna |
| -24077 | enst00000480834 | sg00000150201 | fxyd4-203 | 10 | 43371653 | 43376332 | + | lnc_RNA | processed_transcript |
| -24086 | enst00000616495 | sg00000150201 | fxyd4-204 | 10 | 43371644 | 43376335 | + | mRNA | protein_coding |
| -24094 | enst00000476166 | sg00000150201 | fxyd4-201 | 10 | 43371636 | 43376335 | + | mRNA | protein_coding |
| 39179 | enst00000315429 | sg00000243660 | znf487-201 | 10 | 43436841 | 43481678 | + | mRNA | protein_coding |
| 39186 | enst00000652684 | sg00000243660 | znf487-208 | 10 | 43436848 | 43483181 | + | mRNA | protein_coding |
| 39464 | enst00000456416 | sg00000243660 | znf487-204 | 10 | 43437126 | 43481731 | + | mRNA | protein_coding |
| 39464 | enst00000437590 | sg00000243660 | znf487-202 | 10 | 43437126 | 43483179 | + | mRNA | protein_coding |
| 39486 | enst00000490208 | sg00000243660 | znf487-205 | 10 | 43437148 | 43454532 | + | lnc_RNA | processed_transcript |
| 39496 | enst00000451167 | sg00000243660 | znf487-203 | 10 | 43437158 | 43475830 | + | mRNA | protein_coding |
| -44938 | enst00000650340 | sg00000285712 | ac068707.1-201 | 10 | 43325833 | 43350792 | - | lnc_RNA | lncrna |
| -53944 | enst00000408541 | sg00000221468 | rnu6atac11p-201 | 10 | 43341786 | 43341910 | + | snRNA | snrna |
| 54258 | enst00000596267 | sg00000243660 | znf487-206 | 10 | 43451920 | 43454664 | + | lnc_RNA | processed_transcript |
| 60403 | enst00000516723 | sg00000252532 | rnu7-193p-201 | 10 | 43458065 | 43458129 | + | snRNA | snrna |
| -72065 | enst00000451438 | sg00000224265 | linc02633-201 | 10 | 43323665 | 43327932 | + | lnc_RNA | lncrna |
| 78149 | enst00000651159 | sg00000243660 | znf487-207 | 10 | 43475811 | 43481922 | + | mRNA | protein_coding |
| 125594 | enst00000421913 | sg00000236114 | al450326.2-201 | 10 | 43523256 | 43525217 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -128811 | enst00000395810 | sg00000198915 | rasgef1a-204 | 10 | 43194536 | 43266919 | - | mRNA | protein_coding |
| -165991 | enst00000374459 | sg00000198915 | rasgef1a-202 | 10 | 43194535 | 43229739 | - | mRNA | protein_coding |
| 170797 | enst00000306006 | sg00000196793 | znf239-201 | 10 | 43556344 | 43568459 | - | mRNA | protein_coding |
| 176922 | enst00000374446 | sg00000196793 | znf239-202 | 10 | 43556344 | 43574584 | - | mRNA | protein_coding |
| 176935 | enst00000491188 | sg00000196793 | znf239-204 | 10 | 43557529 | 43574597 | - | lnc_RNA | processed_transcript |
| 176956 | enst00000535642 | sg00000196793 | znf239-205 | 10 | 43556347 | 43574618 | - | mRNA | protein_coding |
| 176956 | enst00000426961 | sg00000196793 | znf239-203 | 10 | 43556347 | 43574618 | - | mRNA | protein_coding |
| -186546 | enst00000395809 | sg00000198915 | rasgef1a-203 | 10 | 43196093 | 43209184 | - | mRNA | protein_coding |
| -191911 | enst00000472864 | sg00000198915 | rasgef1a-205 | 10 | 43200195 | 43203819 | - | lnc_RNA | processed_transcript |
| -193048 | enst00000374455 | sg00000198915 | rasgef1a-201 | 10 | 43199116 | 43202682 | - | mRNA | protein_coding |
| 198963 | enst00000667961 | sg00000287852 | al450326.3-201 | 10 | 43583498 | 43596625 | - | lnc_RNA | lncrna |
| 208589 | enst00000417455 | sg00000232004 | cap1p2-201 | 10 | 43604843 | 43606251 | - | pseudogenic_transcript | processed_pseudogene |
| 208757 | enst00000430885 | sg00000198298 | znf485-203 | 10 | 43606419 | 43616395 | + | mRNA | protein_coding |
| 208757 | enst00000480678 | sg00000198298 | znf485-204 | 10 | 43606419 | 43607400 | + | lnc_RNA | retained_intron |
| 208764 | enst00000374435 | sg00000198298 | znf485-202 | 10 | 43606426 | 43617903 | + | mRNA | protein_coding |
| 208776 | enst00000361807 | sg00000198298 | znf485-201 | 10 | 43606438 | 43617904 | + | mRNA | protein_coding |
| 231155 | enst00000458063 | sg00000223910 | znf32-as3-201 | 10 | 43628817 | 43674703 | + | lnc_RNA | lncrna |
| 233285 | enst00000436649 | sg00000238263 | rpl21p88-201 | 10 | 43630947 | 43631382 | + | pseudogenic_transcript | processed_pseudogene |
| 233902 | enst00000431956 | sg00000237389 | al645634.2-201 | 10 | 43630882 | 43631564 | - | lnc_RNA | lncrna |
| 246210 | enst00000453284 | sg00000226245 | znf32-as1-201 | 10 | 43643872 | 43645047 | + | lnc_RNA | lncrna |
| 248280 | enst00000418966 | sg00000230565 | znf32-as2-201 | 10 | 43645942 | 43648019 | + | lnc_RNA | lncrna |
| 248613 | enst00000485351 | sg00000169740 | znf32-203 | 10 | 43644649 | 43646275 | - | lnc_RNA | processed_transcript |
| 251042 | enst00000395797 | sg00000169740 | znf32-202 | 10 | 43643860 | 43648704 | - | mRNA | protein_coding |
| 251219 | enst00000374433 | sg00000169740 | znf32-201 | 10 | 43643862 | 43648881 | - | mRNA | protein_coding |
| -257285 | enst00000374466 | sg00000169826 | csgalnact2-201 | 10 | 43138445 | 43185302 | + | mRNA | protein_coding |
| -257396 | enst00000609407 | sg00000273008 | ac010864.1-201 | 10 | 43136824 | 43138334 | - | lnc_RNA | lncrna |
| 268006 | enst00000418426 | sg00000228426 | al645634.1-201 | 10 | 43665668 | 43667005 | + | lnc_RNA | lncrna |
| -290998 | enst00000479913 | sg00000165731 | ret-203 | 10 | 43104732 | 43106490 | + | lnc_RNA | retained_intron |
| -295246 | enst00000638465 | sg00000165731 | ret-206 | 10 | 43100484 | 43102835 | + | mRNA | protein_coding |
| -295246 | enst00000640619 | sg00000165731 | ret-207 | 10 | 43100484 | 43102839 | + | mRNA | protein_coding |
| -318656 | enst00000498820 | sg00000165731 | ret-204 | 10 | 43077074 | 43114593 | + | mRNA | protein_coding |
| -318661 | enst00000672389 | sg00000165731 | ret-209 | 10 | 43077069 | 43126775 | + | mRNA | nonsense_mediated_decay |
| -318661 | enst00000340058 | sg00000165731 | ret-201 | 10 | 43077069 | 43127504 | + | mRNA | protein_coding |
| -318661 | enst00000615310 | sg00000165731 | ret-205 | 10 | 43077069 | 43130345 | + | mRNA | protein_coding |
| -318661 | enst00000355710 | sg00000165731 | ret-202 | 10 | 43077069 | 43130351 | + | mRNA | protein_coding |
| -318666 | enst00000671844 | sg00000165731 | ret-208 | 10 | 43077064 | 43127435 | + | mRNA | nonsense_mediated_decay |
| 330555 | enst00000603304 | sg00000271173 | al355989.1-201 | 10 | 43728217 | 43728728 | + | pseudogenic_transcript | processed_pseudogene |
| 334672 | enst00000451503 | sg00000224162 | uqcrhp3-201 | 10 | 43732334 | 43732584 | + | pseudogenic_transcript | processed_pseudogene |
| 344688 | enst00000447108 | sg00000223746 | elocp30-201 | 10 | 43741437 | 43742350 | - | pseudogenic_transcript | processed_pseudogene |
| 380964 | enst00000423349 | sg00000234973 | linc02658-202 | 10 | 43777562 | 43778626 | - | lnc_RNA | lncrna |
| 381163 | enst00000419406 | sg00000234973 | linc02658-201 | 10 | 43777562 | 43778825 | - | lnc_RNA | lncrna |
| 381284 | enst00000659335 | sg00000226808 | linc00840-212 | 10 | 43778946 | 43862005 | + | lnc_RNA | lncrna |
| 381299 | enst00000666323 | sg00000226808 | linc00840-217 | 10 | 43778961 | 43862005 | + | lnc_RNA | lncrna |
| 392725 | enst00000401429 | sg00000226790 | hnrnpa3p1-201 | 10 | 43789249 | 43790387 | - | pseudogenic_transcript | processed_pseudogene |
| -398167 | enst00000579544 | sg00000263795 | mir5100-201 | 10 | 42997563 | 42997681 | + | miRNA | mirna |
| -414223 | enst00000431395 | sg00000229630 | linc01264-201 | 10 | 42979017 | 42981507 | - | lnc_RNA | lncrna |
| 447527 | enst00000666387 | sg00000226808 | linc00840-218 | 10 | 43845189 | 43862005 | + | lnc_RNA | lncrna |
| 447534 | enst00000664505 | sg00000226808 | linc00840-215 | 10 | 43845196 | 43849968 | + | lnc_RNA | lncrna |
| 447540 | enst00000374432 | sg00000226808 | linc00840-201 | 10 | 43845202 | 43850651 | + | lnc_RNA | lncrna |
| 447543 | enst00000661424 | sg00000226808 | linc00840-214 | 10 | 43845205 | 43868209 | + | lnc_RNA | lncrna |
| 447599 | enst00000667243 | sg00000226808 | linc00840-219 | 10 | 43845261 | 43850558 | + | lnc_RNA | lncrna |
| 447599 | enst00000649239 | sg00000226808 | linc00840-203 | 10 | 43845261 | 43875202 | + | lnc_RNA | lncrna |
| 447744 | enst00000669972 | sg00000226808 | linc00840-220 | 10 | 43845406 | 43878967 | + | lnc_RNA | lncrna |
| 447863 | enst00000652937 | sg00000226808 | linc00840-205 | 10 | 43845525 | 43862157 | + | lnc_RNA | lncrna |
| 448711 | enst00000649942 | sg00000226808 | linc00840-204 | 10 | 43846373 | 43850501 | + | lnc_RNA | lncrna |
| 448744 | enst00000658791 | sg00000226808 | linc00840-210 | 10 | 43846406 | 43851017 | + | lnc_RNA | lncrna |
| 448753 | enst00000653073 | sg00000226808 | linc00840-206 | 10 | 43846415 | 43850835 | + | lnc_RNA | lncrna |
| 460147 | enst00000654492 | sg00000226808 | linc00840-207 | 10 | 43857809 | 43895435 | + | lnc_RNA | lncrna |
| 461704 | enst00000659064 | sg00000226808 | linc00840-211 | 10 | 43859366 | 43901004 | + | lnc_RNA | lncrna |
| 461737 | enst00000657037 | sg00000226808 | linc00840-208 | 10 | 43859399 | 43895435 | + | lnc_RNA | lncrna |
| 461745 | enst00000665279 | sg00000226808 | linc00840-216 | 10 | 43859407 | 43895435 | + | lnc_RNA | lncrna |
| 461749 | enst00000431737 | sg00000226808 | linc00840-202 | 10 | 43859411 | 43895433 | + | lnc_RNA | lncrna |
| 461750 | enst00000660203 | sg00000226808 | linc00840-213 | 10 | 43859412 | 43862153 | + | lnc_RNA | lncrna |
| 462150 | enst00000657471 | sg00000226808 | linc00840-209 | 10 | 43859812 | 43895431 | + | lnc_RNA | lncrna |
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