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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 |
|---|---|---|---|---|---|---|---|---|
| #119 | 5 | 73230217 | 73231331 | 1114 | 3 | 38 | 1.12205e-16 | 9.4024e-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 |
|---|---|---|---|---|---|---|---|---|---|
| -16235 | enst00000427584 | sg00000249743 | ac116345.1-203 | 5 | 73213982 | 73244820 | + | lnc_RNA | lncrna |
| -16238 | enst00000663515 | sg00000249743 | ac116345.1-209 | 5 | 73213979 | 73287916 | + | lnc_RNA | lncrna |
| -16247 | enst00000661414 | sg00000249743 | ac116345.1-208 | 5 | 73213970 | 73294927 | + | lnc_RNA | lncrna |
| -16263 | enst00000513379 | sg00000249743 | ac116345.1-202 | 5 | 73213954 | 73294930 | + | lnc_RNA | lncrna |
| -16263 | enst00000667953 | sg00000249743 | ac116345.1-207 | 5 | 73213954 | 73294927 | + | lnc_RNA | lncrna |
| -16270 | enst00000515556 | sg00000249743 | ac116345.1-201 | 5 | 73213947 | 73288839 | + | lnc_RNA | lncrna |
| -16287 | enst00000654696 | sg00000249743 | ac116345.1-206 | 5 | 73213930 | 73295258 | + | lnc_RNA | lncrna |
| -28244 | enst00000664281 | sg00000287090 | ac116345.4-201 | 5 | 73195314 | 73201973 | - | lnc_RNA | lncrna |
| -56925 | enst00000511737 | sg00000164325 | tmem174-202 | 5 | 73173292 | 73175058 | + | lnc_RNA | processed_transcript |
| -57024 | enst00000296776 | sg00000164325 | tmem174-201 | 5 | 73173193 | 73175143 | + | mRNA | protein_coding |
| 60259 | enst00000503403 | sg00000249743 | ac116345.1-204 | 5 | 73291590 | 73294934 | + | lnc_RNA | lncrna |
| 60605 | enst00000513280 | sg00000249743 | ac116345.1-205 | 5 | 73291936 | 73294922 | + | lnc_RNA | lncrna |
| -77279 | enst00000512837 | sg00000250747 | ac116345.2-201 | 5 | 73152416 | 73152938 | - | pseudogenic_transcript | processed_pseudogene |
| -79625 | enst00000508255 | sg00000251599 | ac116345.3-201 | 5 | 73132008 | 73150592 | - | lnc_RNA | lncrna |
| 106575 | enst00000511174 | sg00000251543 | linc02230-201 | 5 | 73337906 | 73338533 | + | lnc_RNA | lncrna |
| -109642 | enst00000454765 | sg00000157111 | tmem171-202 | 5 | 73120575 | 73131809 | + | mRNA | protein_coding |
| -109648 | enst00000287773 | sg00000157111 | tmem171-201 | 5 | 73120569 | 73131809 | + | mRNA | protein_coding |
| 151053 | enst00000505955 | sg00000249149 | ac099522.1-201 | 5 | 73382384 | 73410509 | + | lnc_RNA | processed_transcript |
| -171796 | enst00000508431 | sg00000157107 | fcho2-205 | 5 | 73058421 | 73077440 | + | lnc_RNA | retained_intron |
| 178733 | enst00000514718 | sg00000249149 | ac099522.1-202 | 5 | 73410064 | 73410430 | + | pseudogenic_transcript | transcribed_processed_pseudogene |
| -179117 | enst00000503302 | sg00000157107 | fcho2-203 | 5 | 73051100 | 73052856 | + | lnc_RNA | retained_intron |
| -195749 | enst00000511264 | sg00000157107 | fcho2-206 | 5 | 73034468 | 73037192 | + | lnc_RNA | retained_intron |
| -208938 | enst00000502452 | sg00000248930 | ac020893.1-201 | 5 | 73020700 | 73021279 | - | pseudogenic_transcript | processed_pseudogene |
| 215026 | enst00000514661 | sg00000247993 | foxd1-as1-201 | 5 | 73446357 | 73446984 | + | lnc_RNA | lncrna |
| 215657 | enst00000513595 | sg00000251493 | foxd1-201 | 5 | 73444827 | 73446988 | - | lnc_RNA | processed_transcript |
| 217446 | enst00000615637 | sg00000251493 | foxd1-202 | 5 | 73446266 | 73448777 | - | mRNA | protein_coding |
| 220167 | enst00000512310 | sg00000251604 | linc01385-201 | 5 | 73451498 | 73453395 | + | lnc_RNA | lncrna |
| -233297 | enst00000506083 | sg00000251467 | ac020893.2-201 | 5 | 72996920 | 72997642 | + | pseudogenic_transcript | processed_pseudogene |
| 241565 | enst00000506196 | sg00000251324 | linc01386-201 | 5 | 73454187 | 73472896 | - | lnc_RNA | lncrna |
| 266962 | enst00000607001 | sg00000272525 | ac099522.2-201 | 5 | 73497550 | 73498293 | - | lnc_RNA | lncrna |
| 267077 | enst00000335895 | sg00000145741 | btf3-201 | 5 | 73498408 | 73505495 | + | mRNA | protein_coding |
| 267100 | enst00000512257 | sg00000145741 | btf3-207 | 5 | 73498431 | 73499651 | + | lnc_RNA | retained_intron |
| 267105 | enst00000514505 | sg00000145741 | btf3-209 | 5 | 73498436 | 73505435 | + | lnc_RNA | processed_transcript |
| 267111 | enst00000514360 | sg00000145741 | btf3-208 | 5 | 73498442 | 73505495 | + | lnc_RNA | retained_intron |
| 267118 | enst00000380591 | sg00000145741 | btf3-202 | 5 | 73498449 | 73505635 | + | mRNA | protein_coding |
| 267126 | enst00000510787 | sg00000145741 | btf3-206 | 5 | 73498457 | 73502685 | + | lnc_RNA | retained_intron |
| 267142 | enst00000508901 | sg00000145741 | btf3-204 | 5 | 73498473 | 73504829 | + | lnc_RNA | retained_intron |
| 267179 | enst00000507081 | sg00000145741 | btf3-203 | 5 | 73498510 | 73504403 | + | mRNA | protein_coding |
| 271260 | enst00000509708 | sg00000145741 | btf3-205 | 5 | 73502591 | 73505493 | + | mRNA | protein_coding |
| -274146 | enst00000287761 | sg00000157107 | fcho2-201 | 5 | 72956071 | 73038123 | + | mRNA | protein_coding |
| -274148 | enst00000512348 | sg00000157107 | fcho2-207 | 5 | 72956069 | 73088428 | + | mRNA | protein_coding |
| -274151 | enst00000507345 | sg00000157107 | fcho2-204 | 5 | 72956066 | 73017282 | + | mRNA | protein_coding |
| -274176 | enst00000430046 | sg00000157107 | fcho2-202 | 5 | 72956041 | 73090522 | + | mRNA | protein_coding |
| -274518 | enst00000606587 | sg00000272081 | ac008972.2-201 | 5 | 72955206 | 72955699 | - | lnc_RNA | lncrna |
| -275943 | enst00000607027 | sg00000271926 | ac008972.1-201 | 5 | 72953635 | 72954274 | - | lnc_RNA | lncrna |
| 277354 | enst00000327891 | sg00000255883 | fundc2p1-201 | 5 | 73508685 | 73509254 | + | pseudogenic_transcript | processed_pseudogene |
| 323099 | enst00000505301 | sg00000164331 | ankra2-203 | 5 | 73552531 | 73554430 | - | lnc_RNA | retained_intron |
| 323877 | enst00000515249 | sg00000164331 | ankra2-207 | 5 | 73552619 | 73555208 | - | lnc_RNA | retained_intron |
| -329343 | enst00000503084 | sg00000083312 | tnpo1-202 | 5 | 72900874 | 72908913 | + | lnc_RNA | retained_intron |
| 330038 | enst00000514916 | sg00000164331 | ankra2-206 | 5 | 73557434 | 73561369 | - | lnc_RNA | retained_intron |
| 331315 | enst00000506130 | sg00000164331 | ankra2-204 | 5 | 73557431 | 73562646 | - | lnc_RNA | retained_intron |
| 333873 | enst00000509433 | sg00000164331 | ankra2-205 | 5 | 73562486 | 73565204 | - | lnc_RNA | retained_intron |
| 334065 | enst00000504641 | sg00000164331 | ankra2-202 | 5 | 73554907 | 73565396 | - | mRNA | protein_coding |
| 334112 | enst00000513824 | sg00000164338 | utp15-207 | 5 | 73565443 | 73568432 | + | mRNA | protein_coding |
| 334308 | enst00000296785 | sg00000164331 | ankra2-201 | 5 | 73552190 | 73565639 | - | mRNA | protein_coding |
| 334336 | enst00000515804 | sg00000164331 | ankra2-208 | 5 | 73557431 | 73565667 | - | lnc_RNA | retained_intron |
| 334410 | enst00000543251 | sg00000164338 | utp15-208 | 5 | 73565741 | 73583377 | + | mRNA | protein_coding |
| 334412 | enst00000509005 | sg00000164338 | utp15-204 | 5 | 73565743 | 73580514 | + | mRNA | protein_coding |
| 334412 | enst00000510478 | sg00000164338 | utp15-205 | 5 | 73565743 | 73567677 | + | lnc_RNA | retained_intron |
| 334412 | enst00000296792 | sg00000164338 | utp15-201 | 5 | 73565743 | 73583380 | + | mRNA | protein_coding |
| 334423 | enst00000508686 | sg00000164338 | utp15-203 | 5 | 73565754 | 73567366 | + | mRNA | protein_coding |
| 334442 | enst00000508491 | sg00000164338 | utp15-202 | 5 | 73565773 | 73580199 | + | mRNA | protein_coding |
| -336541 | enst00000605210 | sg00000083312 | tnpo1-214 | 5 | 72893676 | 72905580 | + | mRNA | protein_coding |
| 341158 | enst00000512550 | sg00000164338 | utp15-206 | 5 | 73572489 | 73578416 | + | lnc_RNA | retained_intron |
| -351032 | enst00000497334 | sg00000242602 | ac008953.1-201 | 5 | 72878868 | 72879185 | - | pseudogenic_transcript | processed_pseudogene |
| -351626 | enst00000581683 | sg00000263593 | mir4804-201 | 5 | 72878591 | 72878663 | + | miRNA | mirna |
| -357549 | enst00000505082 | sg00000083312 | tnpo1-203 | 5 | 72872668 | 72887210 | + | lnc_RNA | processed_transcript |
| -358470 | enst00000508762 | sg00000083312 | tnpo1-206 | 5 | 72871747 | 72883099 | + | lnc_RNA | processed_transcript |
| -381832 | enst00000509030 | sg00000083312 | tnpo1-207 | 5 | 72848385 | 72862396 | + | lnc_RNA | processed_transcript |
| -381832 | enst00000511754 | sg00000083312 | tnpo1-208 | 5 | 72848385 | 72865731 | + | lnc_RNA | processed_transcript |
| -381832 | enst00000506528 | sg00000083312 | tnpo1-205 | 5 | 72848385 | 72872720 | + | lnc_RNA | processed_transcript |
| -382033 | enst00000506351 | sg00000083312 | tnpo1-204 | 5 | 72848184 | 72908951 | + | mRNA | protein_coding |
| -382047 | enst00000513944 | sg00000083312 | tnpo1-209 | 5 | 72848170 | 72861915 | + | lnc_RNA | processed_transcript |
| 394827 | enst00000545377 | sg00000214944 | arhgef28-214 | 5 | 73626158 | 73941992 | + | mRNA | protein_coding |
| 394827 | enst00000296794 | sg00000214944 | arhgef28-201 | 5 | 73626158 | 73911697 | + | mRNA | protein_coding |
| 394827 | enst00000513042 | sg00000214944 | arhgef28-212 | 5 | 73626158 | 73941992 | + | mRNA | protein_coding |
| 394865 | enst00000509848 | sg00000214944 | arhgef28-208 | 5 | 73626196 | 73752977 | + | mRNA | protein_coding |
| -413424 | enst00000518279 | sg00000083312 | tnpo1-211 | 5 | 72816793 | 72865693 | + | lnc_RNA | processed_transcript |
| -413545 | enst00000523768 | sg00000083312 | tnpo1-213 | 5 | 72816672 | 72905429 | + | mRNA | protein_coding |
| -413568 | enst00000520850 | sg00000083312 | tnpo1-212 | 5 | 72816649 | 72883097 | + | mRNA | nonsense_mediated_decay |
| -413593 | enst00000515483 | sg00000083312 | tnpo1-210 | 5 | 72816624 | 72855916 | + | lnc_RNA | processed_transcript |
| -413652 | enst00000507957 | sg00000249085 | ac035140.1-201 | 5 | 72794405 | 72816565 | - | lnc_RNA | lncrna |
| -413905 | enst00000337273 | sg00000083312 | tnpo1-201 | 5 | 72816312 | 72916733 | + | mRNA | protein_coding |
| 453501 | enst00000426542 | sg00000214944 | arhgef28-203 | 5 | 73684832 | 73941993 | + | mRNA | protein_coding |
| 453501 | enst00000437974 | sg00000214944 | arhgef28-204 | 5 | 73684832 | 73941589 | + | mRNA | protein_coding |
| -458484 | enst00000659888 | sg00000251613 | ac063979.2-205 | 5 | 72761084 | 72771733 | - | lnc_RNA | lncrna |
| -458484 | enst00000663630 | sg00000251613 | ac063979.2-204 | 5 | 72689724 | 72771733 | - | lnc_RNA | lncrna |
| -458484 | enst00000662691 | sg00000251613 | ac063979.2-203 | 5 | 72689724 | 72771733 | - | lnc_RNA | lncrna |
| -461515 | enst00000384043 | sg00000206770 | ac063979.1-201 | 5 | 72768702 | 72768811 | + | ncRNA | misc_rna |
| -467490 | enst00000508217 | sg00000251613 | ac063979.2-202 | 5 | 72690549 | 72762727 | - | lnc_RNA | lncrna |
| -468552 | enst00000513767 | sg00000251613 | ac063979.2-201 | 5 | 72687112 | 72761665 | - | lnc_RNA | lncrna |
| -496384 | enst00000415539 | sg00000223497 | h2bp4-201 | 5 | 72733833 | 72734209 | + | pseudogenic_transcript | unitary_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