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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 |
|---|---|---|---|---|---|---|---|---|
| #2 | 5 | 171313349 | 171317243 | 3894 | 3 | 110 | 1.67786e-48 | 8.34314e-45 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| -3572 | enst00000619056 | sg00000275038 | ac091980.2-201 | 5 | 171305980 | 171309777 | - | lnc_RNA | lncrna |
| -4101 | enst00000296921 | sg00000164438 | tlx3-201 | 5 | 171309248 | 171312139 | + | mRNA | protein_coding |
| 28387 | enst00000524262 | sg00000213393 | ac091980.1-201 | 5 | 171345343 | 171345630 | - | pseudogenic_transcript | processed_pseudogene |
| 41874 | enst00000580597 | sg00000265740 | rn7sl339p-201 | 5 | 171359117 | 171359412 | + | ncRNA | misc_rna |
| 48352 | enst00000522496 | sg00000254256 | rpsap71-201 | 5 | 171365595 | 171367693 | + | pseudogenic_transcript | processed_pseudogene |
| 48875 | enst00000384182 | sg00000206909 | snora70j-201 | 5 | 171366118 | 171366252 | + | snoRNA | snorna |
| 49056 | enst00000522888 | sg00000254012 | rpl10p8-201 | 5 | 171366299 | 171366611 | + | pseudogenic_transcript | processed_pseudogene |
| -61483 | enst00000523223 | sg00000253213 | ac010306.1-201 | 5 | 171251866 | 171252982 | + | pseudogenic_transcript | processed_pseudogene |
| 69517 | enst00000577566 | sg00000264249 | mir3912-201 | 5 | 171386656 | 171386760 | - | miRNA | mirna |
| 69873 | enst00000517671 | sg00000181163 | npm1-204 | 5 | 171387116 | 171410883 | + | mRNA | protein_coding |
| 70405 | enst00000296930 | sg00000181163 | npm1-201 | 5 | 171387648 | 171411137 | + | mRNA | protein_coding |
| 70556 | enst00000521672 | sg00000181163 | npm1-208 | 5 | 171387799 | 171400155 | + | mRNA | protein_coding |
| 70586 | enst00000351986 | sg00000181163 | npm1-202 | 5 | 171387829 | 171410884 | + | mRNA | protein_coding |
| 70608 | enst00000393820 | sg00000181163 | npm1-203 | 5 | 171387851 | 171407125 | + | mRNA | protein_coding |
| 70609 | enst00000523339 | sg00000181163 | npm1-210 | 5 | 171387852 | 171390163 | + | lnc_RNA | retained_intron |
| 70638 | enst00000523622 | sg00000181163 | npm1-211 | 5 | 171387881 | 171391369 | + | mRNA | protein_coding |
| 70642 | enst00000518587 | sg00000181163 | npm1-205 | 5 | 171387885 | 171392963 | + | lnc_RNA | retained_intron |
| -72316 | enst00000521834 | sg00000204764 | ranbp17-214 | 5 | 171241033 | 171271619 | + | lnc_RNA | processed_transcript |
| 72851 | enst00000521260 | sg00000181163 | npm1-207 | 5 | 171390094 | 171391777 | + | lnc_RNA | retained_intron |
| 73840 | enst00000521710 | sg00000181163 | npm1-209 | 5 | 171391083 | 171391749 | + | lnc_RNA | retained_intron |
| 83543 | enst00000519955 | sg00000181163 | npm1-206 | 5 | 171400786 | 171405732 | + | lnc_RNA | retained_intron |
| 90250 | enst00000524204 | sg00000181163 | npm1-212 | 5 | 171407493 | 171410884 | + | lnc_RNA | retained_intron |
| 102404 | enst00000274625 | sg00000156427 | fgf18-201 | 5 | 171419647 | 171457626 | + | mRNA | protein_coding |
| -170028 | enst00000524364 | sg00000204764 | ranbp17-222 | 5 | 171143321 | 171213682 | + | lnc_RNA | processed_transcript |
| -170037 | enst00000523665 | sg00000204764 | ranbp17-220 | 5 | 171143312 | 171205579 | + | lnc_RNA | processed_transcript |
| -170077 | enst00000520586 | sg00000204764 | ranbp17-209 | 5 | 171143272 | 171205607 | + | lnc_RNA | processed_transcript |
| -170082 | enst00000521759 | sg00000204764 | ranbp17-213 | 5 | 171143267 | 171299177 | + | lnc_RNA | processed_transcript |
| -345093 | enst00000518492 | sg00000204764 | ranbp17-204 | 5 | 170968256 | 171029200 | + | mRNA | nonsense_mediated_decay |
| -359728 | enst00000521165 | sg00000204764 | ranbp17-212 | 5 | 170953621 | 170968506 | + | lnc_RNA | retained_intron |
| -388993 | enst00000517629 | sg00000204764 | ranbp17-203 | 5 | 170924356 | 170924918 | + | lnc_RNA | processed_transcript |
| -393898 | enst00000522380 | sg00000204764 | ranbp17-216 | 5 | 170919451 | 170970658 | + | lnc_RNA | processed_transcript |
| -395178 | enst00000520879 | sg00000204764 | ranbp17-211 | 5 | 170918171 | 170953668 | + | lnc_RNA | processed_transcript |
| -402321 | enst00000522734 | sg00000204764 | ranbp17-218 | 5 | 170911028 | 170924407 | + | mRNA | protein_coding |
| -416420 | enst00000522096 | sg00000253966 | ac008514.2-201 | 5 | 170896929 | 170904461 | + | pseudogenic_transcript | processed_pseudogene |
| 420276 | enst00000650062 | sg00000285914 | ac022440.1-201 | 5 | 171724575 | 171737519 | - | lnc_RNA | lncrna |
| -431510 | enst00000523727 | sg00000204764 | ranbp17-221 | 5 | 170881839 | 170896238 | + | lnc_RNA | retained_intron |
| -446514 | enst00000494330 | sg00000244501 | rn7sl623p-201 | 5 | 170866835 | 170867144 | + | ncRNA | misc_rna |
| -449863 | enst00000519944 | sg00000204764 | ranbp17-207 | 5 | 170863486 | 170892490 | + | mRNA | protein_coding |
| -451314 | enst00000520864 | sg00000204764 | ranbp17-210 | 5 | 170862035 | 171207903 | + | mRNA | nonsense_mediated_decay |
| -451326 | enst00000519130 | sg00000204764 | ranbp17-205 | 5 | 170862023 | 170911342 | + | lnc_RNA | retained_intron |
| -451331 | enst00000523189 | sg00000204764 | ranbp17-219 | 5 | 170862018 | 171300015 | + | mRNA | protein_coding |
| -451331 | enst00000522533 | sg00000204764 | ranbp17-217 | 5 | 170862018 | 171300015 | + | mRNA | nonsense_mediated_decay |
| -451331 | enst00000522066 | sg00000204764 | ranbp17-215 | 5 | 170862018 | 171300015 | + | mRNA | nonsense_mediated_decay |
| -451331 | enst00000519949 | sg00000204764 | ranbp17-208 | 5 | 170862018 | 171300015 | + | mRNA | nonsense_mediated_decay |
| -451331 | enst00000519256 | sg00000204764 | ranbp17-206 | 5 | 170862018 | 171243064 | + | mRNA | nonsense_mediated_decay |
| -451417 | enst00000389118 | sg00000204764 | ranbp17-201 | 5 | 170861932 | 171298858 | + | mRNA | nonsense_mediated_decay |
| -451479 | enst00000443155 | sg00000204764 | ranbp17-202 | 5 | 170861870 | 170911409 | + | lnc_RNA | retained_intron |
| 456409 | enst00000524175 | sg00000253110 | ac011410.1-201 | 5 | 171773652 | 171774739 | + | lnc_RNA | lncrna |
| 465189 | enst00000640082 | sg00000185662 | smim23-204 | 5 | 171782432 | 171791136 | + | lnc_RNA | processed_transcript |
| 468623 | enst00000523047 | sg00000185662 | smim23-202 | 5 | 171785866 | 171791136 | + | mRNA | protein_coding |
| 468623 | enst00000639838 | sg00000185662 | smim23-203 | 5 | 171785866 | 171796126 | + | mRNA | nonsense_mediated_decay |
| 468629 | enst00000330910 | sg00000185662 | smim23-201 | 5 | 171785872 | 171794598 | + | 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