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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 |
|---|---|---|---|---|---|---|---|---|
| #200 | 7 | 25852165 | 25853174 | 1009 | 3 | 31 | 4.43381e-14 | 2.20471e-12 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| -20256 | enst00000666265 | sg00000286725 | ac018706.1-201 | 7 | 25831335 | 25831909 | - | lnc_RNA | lncrna |
| 96229 | enst00000602992 | sg00000270933 | ac010719.1-201 | 7 | 25948657 | 25949403 | - | lnc_RNA | lncrna |
| 96812 | enst00000362215 | sg00000199085 | mir148a-201 | 7 | 25949919 | 25949986 | - | miRNA | mirna |
| -101133 | enst00000659634 | sg00000223561 | ac005165.1-222 | 7 | 25655206 | 25751032 | - | lnc_RNA | lncrna |
| -101133 | enst00000456777 | sg00000223561 | ac005165.1-202 | 7 | 25593305 | 25751032 | - | lnc_RNA | lncrna |
| -101256 | enst00000671106 | sg00000223561 | ac005165.1-225 | 7 | 25659965 | 25750909 | - | lnc_RNA | lncrna |
| -101275 | enst00000659273 | sg00000287096 | ac005165.3-201 | 7 | 25750890 | 25756256 | + | lnc_RNA | lncrna |
| -162206 | enst00000466070 | sg00000239622 | ac005165.2-201 | 7 | 25689580 | 25689959 | - | pseudogenic_transcript | processed_pseudogene |
| -188819 | enst00000665149 | sg00000223561 | ac005165.1-219 | 7 | 25655205 | 25663346 | - | lnc_RNA | lncrna |
| -188883 | enst00000661813 | sg00000223561 | ac005165.1-221 | 7 | 25655206 | 25663282 | - | lnc_RNA | lncrna |
| -188979 | enst00000660499 | sg00000223561 | ac005165.1-210 | 7 | 25655206 | 25663186 | - | lnc_RNA | lncrna |
| -188993 | enst00000423689 | sg00000223561 | ac005165.1-203 | 7 | 25655472 | 25663172 | - | lnc_RNA | lncrna |
| -189017 | enst00000653559 | sg00000223561 | ac005165.1-215 | 7 | 25655206 | 25663148 | - | lnc_RNA | lncrna |
| -189025 | enst00000652885 | sg00000223561 | ac005165.1-206 | 7 | 25655206 | 25663140 | - | lnc_RNA | lncrna |
| -189025 | enst00000656897 | sg00000223561 | ac005165.1-207 | 7 | 25655206 | 25663140 | - | lnc_RNA | lncrna |
| -189025 | enst00000661881 | sg00000223561 | ac005165.1-220 | 7 | 25660603 | 25663140 | - | lnc_RNA | lncrna |
| -189033 | enst00000658568 | sg00000223561 | ac005165.1-216 | 7 | 25655206 | 25663132 | - | lnc_RNA | lncrna |
| -189041 | enst00000656871 | sg00000223561 | ac005165.1-201 | 7 | 25593304 | 25663124 | - | lnc_RNA | lncrna |
| -189059 | enst00000654115 | sg00000223561 | ac005165.1-224 | 7 | 25655206 | 25663106 | - | lnc_RNA | lncrna |
| -189126 | enst00000446840 | sg00000223561 | ac005165.1-205 | 7 | 25593338 | 25663039 | - | lnc_RNA | lncrna |
| -189126 | enst00000665954 | sg00000223561 | ac005165.1-213 | 7 | 25655219 | 25663039 | - | lnc_RNA | lncrna |
| -189132 | enst00000668233 | sg00000223561 | ac005165.1-214 | 7 | 25655206 | 25663033 | - | lnc_RNA | lncrna |
| -189132 | enst00000669861 | sg00000223561 | ac005165.1-204 | 7 | 25655213 | 25663033 | - | lnc_RNA | lncrna |
| -189185 | enst00000653704 | sg00000223561 | ac005165.1-211 | 7 | 25627745 | 25662980 | - | lnc_RNA | lncrna |
| -189215 | enst00000662377 | sg00000223561 | ac005165.1-208 | 7 | 25655472 | 25662950 | - | lnc_RNA | lncrna |
| -189216 | enst00000652906 | sg00000223561 | ac005165.1-209 | 7 | 25655206 | 25662949 | - | lnc_RNA | lncrna |
| -189233 | enst00000664945 | sg00000223561 | ac005165.1-212 | 7 | 25655472 | 25662932 | - | lnc_RNA | lncrna |
| -189260 | enst00000670917 | sg00000223561 | ac005165.1-223 | 7 | 25655209 | 25662905 | - | lnc_RNA | lncrna |
| -194107 | enst00000659238 | sg00000223561 | ac005165.1-218 | 7 | 25655472 | 25658058 | - | lnc_RNA | lncrna |
| -231724 | enst00000659793 | sg00000223561 | ac005165.1-217 | 7 | 25593338 | 25620441 | - | lnc_RNA | lncrna |
| 299024 | enst00000056233 | sg00000050344 | nfe2l3-201 | 7 | 26152198 | 26187137 | + | mRNA | protein_coding |
| -301103 | enst00000412197 | sg00000227386 | ac091705.1-201 | 7 | 25547762 | 25551062 | - | lnc_RNA | lncrna |
| 324829 | enst00000607375 | sg00000050344 | nfe2l3-203 | 7 | 26178003 | 26183874 | + | mRNA | protein_coding |
| 330886 | enst00000606261 | sg00000050344 | nfe2l3-202 | 7 | 26184060 | 26186317 | + | lnc_RNA | retained_intron |
| 338504 | enst00000476233 | sg00000122566 | hnrnpa2b1-205 | 7 | 26189927 | 26191678 | - | lnc_RNA | processed_transcript |
| 343733 | enst00000495810 | sg00000122566 | hnrnpa2b1-207 | 7 | 26195712 | 26196907 | - | lnc_RNA | retained_intron |
| 347572 | enst00000354667 | sg00000122566 | hnrnpa2b1-201 | 7 | 26189927 | 26200746 | - | mRNA | protein_coding |
| 347572 | enst00000360787 | sg00000122566 | hnrnpa2b1-203 | 7 | 26190125 | 26200746 | - | mRNA | nonsense_mediated_decay |
| 347572 | enst00000356674 | sg00000122566 | hnrnpa2b1-202 | 7 | 26191844 | 26200746 | - | mRNA | protein_coding |
| 347610 | enst00000463181 | sg00000122566 | hnrnpa2b1-204 | 7 | 26190304 | 26200784 | - | lnc_RNA | retained_intron |
| 347619 | enst00000618183 | sg00000122566 | hnrnpa2b1-209 | 7 | 26189936 | 26200793 | - | mRNA | protein_coding |
| 347988 | enst00000337620 | sg00000122565 | cbx3-201 | 7 | 26201162 | 26213356 | + | mRNA | protein_coding |
| 348127 | enst00000608362 | sg00000122566 | hnrnpa2b1-208 | 7 | 26173057 | 26201301 | - | mRNA | protein_coding |
| 348355 | enst00000490912 | sg00000122566 | hnrnpa2b1-206 | 7 | 26191849 | 26201529 | - | lnc_RNA | retained_intron |
| 348571 | enst00000396386 | sg00000122565 | cbx3-202 | 7 | 26201745 | 26213607 | + | mRNA | protein_coding |
| 348583 | enst00000456948 | sg00000122565 | cbx3-204 | 7 | 26201757 | 26208412 | + | mRNA | protein_coding |
| 348591 | enst00000409747 | sg00000122565 | cbx3-203 | 7 | 26201765 | 26213356 | + | mRNA | protein_coding |
| 349289 | enst00000497498 | sg00000122565 | cbx3-208 | 7 | 26202463 | 26211717 | + | lnc_RNA | processed_transcript |
| 352862 | enst00000481300 | sg00000122565 | cbx3-207 | 7 | 26206036 | 26208476 | + | lnc_RNA | retained_intron |
| 353194 | enst00000462165 | sg00000122565 | cbx3-205 | 7 | 26206368 | 26210582 | + | mRNA | protein_coding |
| 354959 | enst00000481057 | sg00000122565 | cbx3-206 | 7 | 26208133 | 26212423 | + | lnc_RNA | retained_intron |
| 401535 | enst00000650328 | sg00000285860 | ac010677.2-201 | 7 | 26226413 | 26254709 | - | lnc_RNA | lncrna |
| -419963 | enst00000668357 | sg00000260951 | ac005100.1-204 | 7 | 25385478 | 25432202 | - | lnc_RNA | lncrna |
| -419977 | enst00000669800 | sg00000260951 | ac005100.1-203 | 7 | 25358292 | 25432188 | - | lnc_RNA | lncrna |
| -420185 | enst00000650415 | sg00000285960 | ac005100.2-201 | 7 | 25431980 | 25500443 | + | lnc_RNA | lncrna |
| 423021 | enst00000441690 | sg00000232383 | ac010677.1-201 | 7 | 26276195 | 26276606 | + | pseudogenic_transcript | processed_pseudogene |
| 438721 | enst00000446848 | sg00000086300 | snx10-207 | 7 | 26291895 | 26374317 | + | mRNA | protein_coding |
| 438747 | enst00000416246 | sg00000086300 | snx10-206 | 7 | 26291921 | 26372022 | + | mRNA | protein_coding |
| 438749 | enst00000338523 | sg00000086300 | snx10-201 | 7 | 26291923 | 26374325 | + | mRNA | protein_coding |
| 438837 | enst00000412416 | sg00000086300 | snx10-205 | 7 | 26292011 | 26361031 | + | mRNA | protein_coding |
| 439880 | enst00000396376 | sg00000086300 | snx10-202 | 7 | 26293054 | 26374329 | + | mRNA | protein_coding |
| -483583 | enst00000662242 | sg00000260951 | ac005100.1-202 | 7 | 25358235 | 25368582 | - | lnc_RNA | lncrna |
| -492257 | enst00000562268 | sg00000260951 | ac005100.1-201 | 7 | 25358240 | 25359908 | - | 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