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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 |
|---|---|---|---|---|---|---|---|---|
| #77 | 18 | 5890207 | 5891836 | 1629 | 3 | 51 | 2.19393e-19 | 2.83359e-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 |
|---|---|---|---|---|---|---|---|---|---|
| 268 | enst00000383490 | sg00000206432 | tmem200c-201 | 18 | 5890185 | 5892104 | - | mRNA | protein_coding |
| -2589 | enst00000577694 | sg00000264449 | ap001021.1-203 | 18 | 5887618 | 5909122 | + | lnc_RNA | lncrna |
| -2665 | enst00000580845 | sg00000264449 | ap001021.1-202 | 18 | 5887542 | 5889518 | + | lnc_RNA | lncrna |
| -2720 | enst00000582939 | sg00000264449 | ap001021.1-201 | 18 | 5887487 | 5889463 | + | lnc_RNA | lncrna |
| 3909 | enst00000659442 | sg00000266846 | ap001021.3-202 | 18 | 5895745 | 6108382 | + | lnc_RNA | lncrna |
| 3920 | enst00000664630 | sg00000264449 | ap001021.1-204 | 18 | 5895756 | 5989369 | + | lnc_RNA | lncrna |
| 4040 | enst00000659662 | sg00000264449 | ap001021.1-205 | 18 | 5895876 | 5989335 | + | lnc_RNA | lncrna |
| 4119 | enst00000581347 | sg00000206432 | tmem200c-202 | 18 | 5882072 | 5895955 | - | mRNA | protein_coding |
| -49512 | enst00000606807 | sg00000272380 | mir3976-201 | 18 | 5840695 | 5840833 | + | miRNA | mirna |
| -50889 | enst00000659973 | sg00000261738 | mir3976hg-220 | 18 | 5839318 | 5852033 | + | lnc_RNA | lncrna |
| 64265 | enst00000577704 | sg00000265487 | ap001021.2-201 | 18 | 5956101 | 5960785 | + | lnc_RNA | lncrna |
| 126003 | enst00000363767 | sg00000200637 | rnu5f-3p-201 | 18 | 6017723 | 6017839 | - | snRNA | snrna |
| 133255 | enst00000577935 | sg00000266846 | ap001021.3-201 | 18 | 6025091 | 6082455 | + | lnc_RNA | lncrna |
| -141388 | enst00000664262 | sg00000261738 | mir3976hg-224 | 18 | 5748819 | 5843187 | + | lnc_RNA | lncrna |
| -141388 | enst00000656844 | sg00000261738 | mir3976hg-217 | 18 | 5748819 | 5823265 | + | lnc_RNA | lncrna |
| -141388 | enst00000653609 | sg00000261738 | mir3976hg-208 | 18 | 5748819 | 5811299 | + | lnc_RNA | lncrna |
| -141388 | enst00000671001 | sg00000261738 | mir3976hg-237 | 18 | 5748819 | 5793798 | + | lnc_RNA | lncrna |
| -141388 | enst00000666692 | sg00000261738 | mir3976hg-228 | 18 | 5748819 | 5851648 | + | lnc_RNA | lncrna |
| -141388 | enst00000562452 | sg00000261738 | mir3976hg-201 | 18 | 5748819 | 5876328 | + | lnc_RNA | lncrna |
| -141389 | enst00000667098 | sg00000261738 | mir3976hg-229 | 18 | 5748818 | 5843183 | + | lnc_RNA | lncrna |
| -141392 | enst00000661027 | sg00000261738 | mir3976hg-221 | 18 | 5748815 | 5795837 | + | lnc_RNA | lncrna |
| -141392 | enst00000580378 | sg00000261738 | mir3976hg-203 | 18 | 5748815 | 5793874 | + | lnc_RNA | lncrna |
| -141392 | enst00000668423 | sg00000261738 | mir3976hg-232 | 18 | 5748815 | 5793872 | + | lnc_RNA | lncrna |
| -141392 | enst00000653236 | sg00000261738 | mir3976hg-207 | 18 | 5748815 | 5795901 | + | lnc_RNA | lncrna |
| -141397 | enst00000668925 | sg00000261738 | mir3976hg-234 | 18 | 5748810 | 5843187 | + | lnc_RNA | lncrna |
| -141397 | enst00000566533 | sg00000261738 | mir3976hg-202 | 18 | 5748810 | 5795901 | + | lnc_RNA | lncrna |
| -141398 | enst00000654796 | sg00000261738 | mir3976hg-211 | 18 | 5748809 | 5750372 | + | lnc_RNA | lncrna |
| -141398 | enst00000668692 | sg00000261738 | mir3976hg-233 | 18 | 5748809 | 5795846 | + | lnc_RNA | lncrna |
| -141398 | enst00000658289 | sg00000261738 | mir3976hg-218 | 18 | 5748809 | 5793794 | + | lnc_RNA | lncrna |
| -141398 | enst00000653157 | sg00000261738 | mir3976hg-205 | 18 | 5748809 | 5795663 | + | lnc_RNA | lncrna |
| -141400 | enst00000652835 | sg00000261738 | mir3976hg-204 | 18 | 5748807 | 5793874 | + | lnc_RNA | lncrna |
| -141400 | enst00000666521 | sg00000261738 | mir3976hg-227 | 18 | 5748807 | 5793874 | + | lnc_RNA | lncrna |
| -141400 | enst00000654963 | sg00000261738 | mir3976hg-213 | 18 | 5748807 | 5793883 | + | lnc_RNA | lncrna |
| -141400 | enst00000654509 | sg00000261738 | mir3976hg-210 | 18 | 5748807 | 5843187 | + | lnc_RNA | lncrna |
| -141402 | enst00000665407 | sg00000261738 | mir3976hg-225 | 18 | 5748805 | 5851648 | + | lnc_RNA | lncrna |
| -141408 | enst00000655587 | sg00000261738 | mir3976hg-214 | 18 | 5748799 | 5843187 | + | lnc_RNA | lncrna |
| -141411 | enst00000668422 | sg00000261738 | mir3976hg-231 | 18 | 5748796 | 5852121 | + | lnc_RNA | lncrna |
| -141417 | enst00000662782 | sg00000261738 | mir3976hg-223 | 18 | 5748790 | 5795901 | + | lnc_RNA | lncrna |
| -141421 | enst00000654839 | sg00000261738 | mir3976hg-212 | 18 | 5748786 | 5843187 | + | lnc_RNA | lncrna |
| -141448 | enst00000653194 | sg00000261738 | mir3976hg-206 | 18 | 5748759 | 5793874 | + | lnc_RNA | lncrna |
| -141450 | enst00000655616 | sg00000261738 | mir3976hg-215 | 18 | 5748757 | 5851846 | + | lnc_RNA | lncrna |
| -141452 | enst00000658316 | sg00000261738 | mir3976hg-219 | 18 | 5748755 | 5793949 | + | lnc_RNA | lncrna |
| -141469 | enst00000665768 | sg00000261738 | mir3976hg-226 | 18 | 5748738 | 5794288 | + | lnc_RNA | lncrna |
| -141469 | enst00000667177 | sg00000261738 | mir3976hg-230 | 18 | 5748738 | 5843187 | + | lnc_RNA | lncrna |
| -147023 | enst00000670176 | sg00000261738 | mir3976hg-235 | 18 | 5743184 | 5750932 | + | lnc_RNA | lncrna |
| -168246 | enst00000670689 | sg00000261738 | mir3976hg-236 | 18 | 5721961 | 5743344 | + | lnc_RNA | lncrna |
| -168339 | enst00000656406 | sg00000261738 | mir3976hg-216 | 18 | 5721868 | 5745399 | + | lnc_RNA | lncrna |
| -168353 | enst00000661123 | sg00000261738 | mir3976hg-222 | 18 | 5721854 | 5750252 | + | lnc_RNA | lncrna |
| -168395 | enst00000654302 | sg00000261738 | mir3976hg-209 | 18 | 5721812 | 5795873 | + | lnc_RNA | lncrna |
| -259507 | enst00000578431 | sg00000082397 | epb41l3-210 | 18 | 5478354 | 5630700 | - | lnc_RNA | processed_transcript |
| -259544 | enst00000637651 | sg00000082397 | epb41l3-236 | 18 | 5392445 | 5630663 | - | mRNA | nonsense_mediated_decay |
| -261216 | enst00000545076 | sg00000082397 | epb41l3-207 | 18 | 5393103 | 5628991 | - | mRNA | protein_coding |
| -312559 | enst00000582592 | sg00000082397 | epb41l3-228 | 18 | 5478399 | 5577648 | - | mRNA | protein_coding |
| -323077 | enst00000578391 | sg00000264000 | ap005059.1-201 | 18 | 5567130 | 5570942 | + | lnc_RNA | lncrna |
| -345897 | enst00000342933 | sg00000082397 | epb41l3-202 | 18 | 5392381 | 5544310 | - | mRNA | protein_coding |
| -345926 | enst00000540638 | sg00000082397 | epb41l3-204 | 18 | 5393093 | 5544281 | - | mRNA | protein_coding |
| -345965 | enst00000341928 | sg00000082397 | epb41l3-201 | 18 | 5392384 | 5544242 | - | mRNA | protein_coding |
| -346240 | enst00000400111 | sg00000082397 | epb41l3-203 | 18 | 5392433 | 5543967 | - | mRNA | protein_coding |
| -346787 | enst00000584015 | sg00000082397 | epb41l3-231 | 18 | 5478241 | 5543420 | - | mRNA | protein_coding |
| -349651 | enst00000544123 | sg00000082397 | epb41l3-206 | 18 | 5392381 | 5540556 | - | mRNA | protein_coding |
| -349651 | enst00000585142 | sg00000082397 | epb41l3-235 | 18 | 5478283 | 5540556 | - | mRNA | protein_coding |
| -349735 | enst00000581833 | sg00000082397 | epb41l3-227 | 18 | 5478272 | 5540472 | - | mRNA | protein_coding |
| -349783 | enst00000580179 | sg00000082397 | epb41l3-217 | 18 | 5478383 | 5540424 | - | mRNA | protein_coding |
| -349792 | enst00000582703 | sg00000082397 | epb41l3-229 | 18 | 5478350 | 5540415 | - | mRNA | protein_coding |
| -349811 | enst00000584670 | sg00000082397 | epb41l3-234 | 18 | 5419799 | 5540396 | - | mRNA | protein_coding |
| -361208 | enst00000584651 | sg00000082397 | epb41l3-233 | 18 | 5445140 | 5528999 | - | mRNA | protein_coding |
| 364911 | enst00000578427 | sg00000264707 | l3mbtl4-as1-201 | 18 | 6256747 | 6260934 | + | lnc_RNA | lncrna |
| -368784 | enst00000580989 | sg00000082397 | epb41l3-222 | 18 | 5478247 | 5521423 | - | mRNA | protein_coding |
| -400837 | enst00000580308 | sg00000082397 | epb41l3-218 | 18 | 5478241 | 5489370 | - | mRNA | protein_coding |
| -400957 | enst00000578503 | sg00000082397 | epb41l3-212 | 18 | 5445140 | 5489250 | - | mRNA | protein_coding |
| -401160 | enst00000580866 | sg00000082397 | epb41l3-221 | 18 | 5445140 | 5489047 | - | mRNA | nonsense_mediated_decay |
| -401268 | enst00000581454 | sg00000082397 | epb41l3-225 | 18 | 5445140 | 5488939 | - | lnc_RNA | processed_transcript |
| -423844 | enst00000542652 | sg00000082397 | epb41l3-205 | 18 | 5392386 | 5466363 | - | lnc_RNA | processed_transcript |
| -426580 | enst00000577527 | sg00000265316 | ap005059.2-201 | 18 | 5463627 | 5480975 | + | lnc_RNA | lncrna |
| 434885 | enst00000583054 | sg00000154655 | l3mbtl4-207 | 18 | 6239799 | 6326721 | - | mRNA | protein_coding |
| -456086 | enst00000581757 | sg00000082397 | epb41l3-226 | 18 | 5431212 | 5434121 | - | lnc_RNA | processed_transcript |
| -456651 | enst00000578432 | sg00000082397 | epb41l3-211 | 18 | 5429248 | 5433556 | - | lnc_RNA | processed_transcript |
| -466800 | enst00000580316 | sg00000082397 | epb41l3-219 | 18 | 5398113 | 5423407 | - | mRNA | protein_coding |
| -470001 | enst00000578395 | sg00000082397 | epb41l3-209 | 18 | 5406848 | 5420206 | - | lnc_RNA | processed_transcript |
| -470369 | enst00000578196 | sg00000082397 | epb41l3-208 | 18 | 5400869 | 5419838 | - | lnc_RNA | retained_intron |
| -470392 | enst00000581387 | sg00000082397 | epb41l3-224 | 18 | 5397393 | 5419815 | - | mRNA | protein_coding |
| -470394 | enst00000578524 | sg00000082397 | epb41l3-213 | 18 | 5396201 | 5419813 | - | mRNA | protein_coding |
| -470406 | enst00000579271 | sg00000082397 | epb41l3-215 | 18 | 5397395 | 5419801 | - | mRNA | protein_coding |
| -470407 | enst00000581292 | sg00000082397 | epb41l3-223 | 18 | 5397158 | 5419800 | - | mRNA | protein_coding |
| -470413 | enst00000580647 | sg00000082397 | epb41l3-220 | 18 | 5397398 | 5419794 | - | mRNA | protein_coding |
| -474056 | enst00000582729 | sg00000082397 | epb41l3-230 | 18 | 5400997 | 5416151 | - | lnc_RNA | processed_transcript |
| 475840 | enst00000578677 | sg00000154655 | l3mbtl4-204 | 18 | 6356709 | 6367676 | - | lnc_RNA | processed_transcript |
| 475847 | enst00000400105 | sg00000154655 | l3mbtl4-203 | 18 | 5954706 | 6367683 | - | mRNA | protein_coding |
| 482589 | enst00000637586 | sg00000283532 | mir4317-201 | 18 | 6374361 | 6374425 | - | miRNA | mirna |
| -482879 | enst00000584055 | sg00000082397 | epb41l3-232 | 18 | 5397248 | 5407328 | - | lnc_RNA | retained_intron |
| -490641 | enst00000578618 | sg00000082397 | epb41l3-214 | 18 | 5392386 | 5399566 | - | lnc_RNA | retained_intron |
| -493875 | enst00000579951 | sg00000082397 | epb41l3-216 | 18 | 5394783 | 5396332 | - | mRNA | protein_coding |
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