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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 |
|---|---|---|---|---|---|---|---|---|
| #70 | 1 | 3062986 | 3064284 | 1298 | 3 | 44 | 8.94323e-20 | 1.25717e-17 |
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 | enst00000321399 | sg00000177133 | prdm16-dt-202 | 1 | 3059615 | 3063786 | - | lnc_RNA | lncrna |
| 0 | enst00000415573 | sg00000177133 | prdm16-dt-204 | 1 | 3061289 | 3063682 | - | lnc_RNA | lncrna |
| -244 | enst00000670730 | sg00000177133 | prdm16-dt-210 | 1 | 3059638 | 3062742 | - | lnc_RNA | lncrna |
| -455 | enst00000606861 | sg00000177133 | prdm16-dt-208 | 1 | 3059615 | 3062531 | - | lnc_RNA | lncrna |
| -591 | enst00000420957 | sg00000177133 | prdm16-dt-205 | 1 | 3061959 | 3062395 | - | pseudogenic_transcript | pseudogene |
| -954 | enst00000453118 | sg00000177133 | prdm16-dt-207 | 1 | 3059617 | 3062032 | - | lnc_RNA | lncrna |
| -1120 | enst00000667159 | sg00000177133 | prdm16-dt-209 | 1 | 3059624 | 3061866 | - | lnc_RNA | lncrna |
| -1235 | enst00000413472 | sg00000177133 | prdm16-dt-203 | 1 | 3059617 | 3061751 | - | lnc_RNA | lncrna |
| 3485 | enst00000321336 | sg00000177133 | prdm16-dt-201 | 1 | 3064072 | 3067769 | - | lnc_RNA | lncrna |
| 4153 | enst00000445317 | sg00000177133 | prdm16-dt-206 | 1 | 3059617 | 3068437 | - | lnc_RNA | lncrna |
| 4884 | enst00000511072 | sg00000142611 | prdm16-206 | 1 | 3069168 | 3434342 | + | mRNA | protein_coding |
| 4899 | enst00000607632 | sg00000142611 | prdm16-210 | 1 | 3069183 | 3186591 | + | lnc_RNA | retained_intron |
| 4913 | enst00000378391 | sg00000142611 | prdm16-203 | 1 | 3069197 | 3435421 | + | mRNA | protein_coding |
| 4919 | enst00000270722 | sg00000142611 | prdm16-201 | 1 | 3069203 | 3438621 | + | mRNA | protein_coding |
| 4927 | enst00000514189 | sg00000142611 | prdm16-208 | 1 | 3069211 | 3434342 | + | mRNA | protein_coding |
| -41519 | enst00000378404 | sg00000169717 | actrt2-201 | 1 | 3021467 | 3022903 | + | mRNA | protein_coding |
| 63691 | enst00000635819 | sg00000283572 | mir4251-201 | 1 | 3127975 | 3128035 | + | miRNA | mirna |
| 69425 | enst00000440516 | sg00000226286 | al008733.1-201 | 1 | 3132927 | 3133709 | - | lnc_RNA | lncrna |
| -94279 | enst00000642073 | sg00000284745 | al589702.1-202 | 1 | 2961018 | 2968707 | - | lnc_RNA | lncrna |
| -99571 | enst00000641229 | sg00000284745 | al589702.1-201 | 1 | 2960658 | 2963415 | - | lnc_RNA | lncrna |
| 141704 | enst00000624175 | sg00000279839 | al512383.1-201 | 1 | 3205988 | 3208664 | + | unconfirmed_transcript | tec |
| 173647 | enst00000512462 | sg00000142611 | prdm16-207 | 1 | 3237931 | 3433925 | + | lnc_RNA | processed_transcript |
| 179848 | enst00000463591 | sg00000142611 | prdm16-204 | 1 | 3244132 | 3386918 | + | mRNA | protein_coding |
| 245812 | enst00000607061 | sg00000272235 | al590438.1-201 | 1 | 3306636 | 3310096 | - | lnc_RNA | lncrna |
| -247988 | enst00000429389 | sg00000231630 | al592464.1-201 | 1 | 2814432 | 2814998 | - | lnc_RNA | lncrna |
| -248930 | enst00000664694 | sg00000287396 | al592464.3-201 | 1 | 2814056 | 2817767 | + | lnc_RNA | lncrna |
| -250294 | enst00000457440 | sg00000233234 | al592464.2-201 | 1 | 2811850 | 2812692 | - | lnc_RNA | lncrna |
| 258865 | enst00000669140 | sg00000287828 | al354743.2-201 | 1 | 3313052 | 3323149 | - | lnc_RNA | lncrna |
| -261269 | enst00000401095 | sg00000215912 | ttc34-201 | 1 | 2635976 | 2801717 | - | mRNA | protein_coding |
| -273321 | enst00000637179 | sg00000215912 | ttc34-202 | 1 | 2641368 | 2789665 | - | mRNA | protein_coding |
| -289383 | enst00000638002 | sg00000283259 | ac242022.1-201 | 1 | 2773603 | 2776473 | + | lnc_RNA | lncrna |
| -294895 | enst00000648684 | sg00000285945 | ac242022.2-201 | 1 | 2768091 | 2784733 | + | lnc_RNA | lncrna |
| 309644 | enst00000665088 | sg00000286518 | al354743.1-201 | 1 | 3367815 | 3373928 | - | lnc_RNA | lncrna |
| 332207 | enst00000509860 | sg00000142611 | prdm16-205 | 1 | 3396491 | 3434293 | + | mRNA | protein_coding |
| 360635 | enst00000378389 | sg00000142611 | prdm16-202 | 1 | 3424919 | 3434095 | + | lnc_RNA | processed_transcript |
| 360932 | enst00000606170 | sg00000142611 | prdm16-209 | 1 | 3425216 | 3426072 | + | lnc_RNA | retained_intron |
| 390381 | enst00000378378 | sg00000130762 | arhgef16-203 | 1 | 3454665 | 3481113 | + | mRNA | protein_coding |
| 401721 | enst00000378373 | sg00000130762 | arhgef16-202 | 1 | 3466005 | 3481113 | + | mRNA | protein_coding |
| 402687 | enst00000378371 | sg00000130762 | arhgef16-201 | 1 | 3466971 | 3481113 | + | mRNA | protein_coding |
| 404260 | enst00000445297 | sg00000130762 | arhgef16-205 | 1 | 3468544 | 3473521 | + | mRNA | protein_coding |
| 407323 | enst00000464620 | sg00000130762 | arhgef16-206 | 1 | 3471607 | 3474457 | + | lnc_RNA | retained_intron |
| 407340 | enst00000418137 | sg00000130762 | arhgef16-204 | 1 | 3471624 | 3476019 | + | mRNA | protein_coding |
| 408485 | enst00000485984 | sg00000130762 | arhgef16-207 | 1 | 3472769 | 3481113 | + | lnc_RNA | retained_intron |
| 422962 | enst00000606489 | sg00000272088 | al512413.1-201 | 1 | 3487246 | 3487627 | + | lnc_RNA | lncrna |
| 429202 | enst00000494257 | sg00000162591 | megf6-207 | 1 | 3490312 | 3493486 | - | lnc_RNA | retained_intron |
| 429960 | enst00000461795 | sg00000162591 | megf6-203 | 1 | 3492728 | 3494244 | - | lnc_RNA | retained_intron |
| -429970 | enst00000378412 | sg00000142606 | mmel1-201 | 1 | 2590639 | 2633016 | - | mRNA | protein_coding |
| -430007 | enst00000511099 | sg00000142606 | mmel1-209 | 1 | 2629758 | 2632979 | - | lnc_RNA | processed_transcript |
| -430418 | enst00000427302 | sg00000237058 | mmel1-as1-201 | 1 | 2632568 | 2636620 | + | lnc_RNA | lncrna |
| 431730 | enst00000475790 | sg00000162591 | megf6-204 | 1 | 3492639 | 3496014 | - | lnc_RNA | retained_intron |
| 432433 | enst00000491842 | sg00000162591 | megf6-206 | 1 | 3490925 | 3496717 | - | mRNA | protein_coding |
| -433492 | enst00000504800 | sg00000142606 | mmel1-207 | 1 | 2590926 | 2629494 | - | mRNA | nonsense_mediated_decay |
| -433492 | enst00000502556 | sg00000142606 | mmel1-206 | 1 | 2590926 | 2629494 | - | mRNA | protein_coding |
| -451585 | enst00000509374 | sg00000142606 | mmel1-208 | 1 | 2606281 | 2611401 | - | lnc_RNA | retained_intron |
| 467164 | enst00000294599 | sg00000162591 | megf6-201 | 1 | 3489920 | 3531448 | - | mRNA | protein_coding |
| -468913 | enst00000469962 | sg00000142606 | mmel1-203 | 1 | 2592655 | 2594073 | - | lnc_RNA | retained_intron |
| -470107 | enst00000464195 | sg00000142606 | mmel1-202 | 1 | 2591694 | 2592879 | - | lnc_RNA | retained_intron |
| -470118 | enst00000491941 | sg00000142606 | mmel1-205 | 1 | 2591694 | 2592868 | - | lnc_RNA | retained_intron |
| -470308 | enst00000471840 | sg00000142606 | mmel1-204 | 1 | 2590639 | 2592678 | - | mRNA | protein_coding |
| -474392 | enst00000476686 | sg00000157870 | prxl2b-209 | 1 | 2588594 | 2591468 | + | lnc_RNA | retained_intron |
| -475901 | enst00000477045 | sg00000157870 | prxl2b-210 | 1 | 2587085 | 2588745 | + | lnc_RNA | retained_intron |
| -475908 | enst00000484099 | sg00000157870 | prxl2b-212 | 1 | 2587078 | 2591469 | + | lnc_RNA | processed_transcript |
| -475944 | enst00000481683 | sg00000157870 | prxl2b-211 | 1 | 2587042 | 2589513 | + | lnc_RNA | processed_transcript |
| -476109 | enst00000498083 | sg00000157870 | prxl2b-214 | 1 | 2586877 | 2588992 | + | mRNA | protein_coding |
| -476153 | enst00000465233 | sg00000157870 | prxl2b-207 | 1 | 2586833 | 2588977 | + | mRNA | protein_coding |
| -476169 | enst00000464043 | sg00000157870 | prxl2b-206 | 1 | 2586817 | 2589805 | + | lnc_RNA | processed_transcript |
| -476188 | enst00000378427 | sg00000157870 | prxl2b-203 | 1 | 2586798 | 2591463 | + | mRNA | protein_coding |
| -476190 | enst00000537325 | sg00000157870 | prxl2b-215 | 1 | 2586796 | 2589947 | + | mRNA | protein_coding |
| -476206 | enst00000378424 | sg00000157870 | prxl2b-201 | 1 | 2586780 | 2591467 | + | mRNA | protein_coding |
| -476211 | enst00000419916 | sg00000157870 | prxl2b-204 | 1 | 2586775 | 2591468 | + | mRNA | protein_coding |
| -476236 | enst00000444521 | sg00000157870 | prxl2b-205 | 1 | 2586750 | 2591467 | + | mRNA | protein_coding |
| -476236 | enst00000378425 | sg00000157870 | prxl2b-202 | 1 | 2586750 | 2591467 | + | mRNA | protein_coding |
| -476446 | enst00000474659 | sg00000157870 | prxl2b-208 | 1 | 2586540 | 2589658 | + | lnc_RNA | processed_transcript |
| -476495 | enst00000493183 | sg00000157870 | prxl2b-213 | 1 | 2586491 | 2589632 | + | lnc_RNA | processed_transcript |
| -481426 | enst00000424215 | sg00000228037 | al139246.3-201 | 1 | 2581560 | 2584533 | + | lnc_RNA | lncrna |
| 496506 | enst00000385042 | sg00000207776 | mir551a-201 | 1 | 3560695 | 3560790 | - | miRNA | mirna |
| -496576 | enst00000456687 | sg00000225931 | al139246.2-201 | 1 | 2566410 | 2569888 | + | unconfirmed_transcript | tec |
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