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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 |
|---|---|---|---|---|---|---|---|---|
| #21 | 1 | 180234214 | 180236317 | 2103 | 3 | 60 | 8.75957e-27 | 4.24449e-24 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| -3916 | enst00000558139 | sg00000121454 | lhx4-202 | 1 | 180230298 | 180248697 | + | lnc_RNA | retained_intron |
| -3950 | enst00000263726 | sg00000121454 | lhx4-201 | 1 | 180230264 | 180278984 | + | mRNA | protein_coding |
| 11968 | enst00000561113 | sg00000121454 | lhx4-203 | 1 | 180248285 | 180271894 | + | mRNA | nonsense_mediated_decay |
| -37532 | enst00000443059 | sg00000116260 | qsox1-204 | 1 | 180196682 | 180198016 | + | mRNA | protein_coding |
| 38364 | enst00000415414 | sg00000230124 | acbd6-202 | 1 | 180269653 | 180274681 | - | lnc_RNA | processed_transcript |
| 38396 | enst00000622400 | sg00000230124 | acbd6-206 | 1 | 180273614 | 180274713 | - | lnc_RNA | processed_transcript |
| 39907 | enst00000440959 | sg00000230124 | acbd6-203 | 1 | 180272602 | 180276224 | - | lnc_RNA | processed_transcript |
| -79317 | enst00000367600 | sg00000116260 | qsox1-201 | 1 | 180154897 | 180198034 | + | mRNA | protein_coding |
| -79344 | enst00000392029 | sg00000116260 | qsox1-203 | 1 | 180154870 | 180189674 | + | mRNA | nonsense_mediated_decay |
| -79345 | enst00000367602 | sg00000116260 | qsox1-202 | 1 | 180154869 | 180204030 | + | mRNA | protein_coding |
| -110324 | enst00000566904 | sg00000261817 | al390718.1-201 | 1 | 180117140 | 180123890 | - | lnc_RNA | lncrna |
| -139067 | enst00000496440 | sg00000135837 | cep350-211 | 1 | 180095147 | 180111031 | + | lnc_RNA | processed_transcript |
| -140500 | enst00000417046 | sg00000135837 | cep350-203 | 1 | 180093714 | 180113380 | + | mRNA | protein_coding |
| -148610 | enst00000490141 | sg00000135837 | cep350-209 | 1 | 180085604 | 180111192 | + | lnc_RNA | processed_transcript |
| -148634 | enst00000484356 | sg00000135837 | cep350-207 | 1 | 180085580 | 180090748 | + | lnc_RNA | processed_transcript |
| -153697 | enst00000437245 | sg00000135837 | cep350-206 | 1 | 180080517 | 180084280 | + | mRNA | protein_coding |
| -160395 | enst00000429851 | sg00000135837 | cep350-205 | 1 | 180073819 | 180113380 | + | mRNA | protein_coding |
| 177071 | enst00000475338 | sg00000230124 | acbd6-204 | 1 | 180286983 | 180413388 | - | lnc_RNA | processed_transcript |
| -192552 | enst00000490047 | sg00000135837 | cep350-208 | 1 | 180041662 | 180048705 | + | mRNA | nonsense_mediated_decay |
| -193011 | enst00000418229 | sg00000135837 | cep350-204 | 1 | 180041203 | 180053834 | + | mRNA | protein_coding |
| 193945 | enst00000496993 | sg00000230124 | acbd6-205 | 1 | 180275380 | 180430262 | - | lnc_RNA | processed_transcript |
| 198483 | enst00000450197 | sg00000235060 | vdac1p4-201 | 1 | 180434800 | 180435936 | + | pseudogenic_transcript | processed_pseudogene |
| 202073 | enst00000579680 | sg00000265435 | mir3121-201 | 1 | 180438314 | 180438390 | - | miRNA | mirna |
| -233406 | enst00000424289 | sg00000223450 | al590632.1-201 | 1 | 180000438 | 180000808 | - | pseudogenic_transcript | processed_pseudogene |
| -248032 | enst00000357434 | sg00000135837 | cep350-201 | 1 | 179986182 | 179992221 | + | mRNA | protein_coding |
| -265528 | enst00000447583 | sg00000235145 | rpsap16-201 | 1 | 179968686 | 179969506 | + | pseudogenic_transcript | processed_pseudogene |
| 266260 | enst00000367595 | sg00000230124 | acbd6-201 | 1 | 180288230 | 180502577 | - | mRNA | protein_coding |
| 266637 | enst00000645415 | sg00000230124 | acbd6-208 | 1 | 180269653 | 180502954 | - | mRNA | nonsense_mediated_decay |
| 266637 | enst00000642319 | sg00000230124 | acbd6-207 | 1 | 180269653 | 180502954 | - | mRNA | protein_coding |
| 273063 | enst00000673955 | sg00000236719 | ovaal-206 | 1 | 180509380 | 180566523 | + | lnc_RNA | lncrna |
| -279404 | enst00000367607 | sg00000135837 | cep350-202 | 1 | 179954810 | 180114875 | + | mRNA | protein_coding |
| -279441 | enst00000491495 | sg00000135837 | cep350-210 | 1 | 179954773 | 179996963 | + | mRNA | protein_coding |
| -279774 | enst00000567904 | sg00000260360 | al353708.1-201 | 1 | 179953184 | 179954440 | - | lnc_RNA | lncrna |
| 282802 | enst00000384178 | sg00000206905 | al358354.1-201 | 1 | 180519016 | 180519119 | - | ncRNA | misc_rna |
| -292418 | enst00000567486 | sg00000261831 | al353708.2-201 | 1 | 179926641 | 179941796 | - | lnc_RNA | lncrna |
| 311119 | enst00000662859 | sg00000236719 | ovaal-204 | 1 | 180547436 | 180566517 | + | lnc_RNA | lncrna |
| 316432 | enst00000648175 | sg00000236719 | ovaal-202 | 1 | 180552749 | 180566520 | + | lnc_RNA | lncrna |
| 322659 | enst00000442621 | sg00000236719 | ovaal-201 | 1 | 180558976 | 180566518 | + | lnc_RNA | lncrna |
| 325201 | enst00000668742 | sg00000236719 | ovaal-205 | 1 | 180561518 | 180566518 | + | lnc_RNA | lncrna |
| 325274 | enst00000660699 | sg00000236719 | ovaal-203 | 1 | 180561591 | 180566516 | + | lnc_RNA | lncrna |
| -330248 | enst00000447964 | sg00000143337 | tor1aip1-203 | 1 | 179903966 | 179918171 | + | mRNA | protein_coding |
| -333952 | enst00000580835 | sg00000264916 | rn7sl230p-201 | 1 | 179900262 | 179900564 | + | ncRNA | misc_rna |
| -350229 | enst00000524653 | sg00000143337 | tor1aip1-205 | 1 | 179883985 | 179908625 | + | lnc_RNA | processed_transcript |
| -350246 | enst00000531726 | sg00000143337 | tor1aip1-211 | 1 | 179883968 | 179904741 | + | lnc_RNA | processed_transcript |
| -350252 | enst00000474875 | sg00000143337 | tor1aip1-204 | 1 | 179883962 | 179917725 | + | lnc_RNA | processed_transcript |
| -350277 | enst00000527867 | sg00000143337 | tor1aip1-207 | 1 | 179883937 | 179901387 | + | lnc_RNA | processed_transcript |
| -351248 | enst00000529091 | sg00000143337 | tor1aip1-209 | 1 | 179882966 | 179904022 | + | mRNA | nonsense_mediated_decay |
| -351325 | enst00000527391 | sg00000143337 | tor1aip1-206 | 1 | 179882889 | 179914054 | + | mRNA | protein_coding |
| -351420 | enst00000531630 | sg00000143337 | tor1aip1-210 | 1 | 179882794 | 179914002 | + | mRNA | protein_coding |
| -351518 | enst00000435319 | sg00000143337 | tor1aip1-202 | 1 | 179882696 | 179920077 | + | mRNA | protein_coding |
| -351619 | enst00000610272 | sg00000272906 | al353708.3-201 | 1 | 179881607 | 179882595 | - | lnc_RNA | lncrna |
| -351902 | enst00000606911 | sg00000143337 | tor1aip1-212 | 1 | 179882312 | 179925000 | + | mRNA | protein_coding |
| -351917 | enst00000271583 | sg00000143337 | tor1aip1-201 | 1 | 179882297 | 179919277 | + | mRNA | protein_coding |
| -352172 | enst00000528443 | sg00000143337 | tor1aip1-208 | 1 | 179882042 | 179919708 | + | mRNA | protein_coding |
| -356411 | enst00000609928 | sg00000169905 | tor1aip2-206 | 1 | 179843931 | 179877803 | - | mRNA | protein_coding |
| -356415 | enst00000367612 | sg00000169905 | tor1aip2-201 | 1 | 179839967 | 179877799 | - | mRNA | protein_coding |
| -356415 | enst00000482587 | sg00000169905 | tor1aip2-203 | 1 | 179859030 | 179877799 | - | mRNA | protein_coding |
| -356424 | enst00000495650 | sg00000169905 | tor1aip2-205 | 1 | 179865065 | 179877790 | - | mRNA | protein_coding |
| -356432 | enst00000474318 | sg00000169905 | tor1aip2-202 | 1 | 179867527 | 179877782 | - | lnc_RNA | processed_transcript |
| -356442 | enst00000483123 | sg00000169905 | tor1aip2-204 | 1 | 179873706 | 179877772 | - | lnc_RNA | processed_transcript |
| 395705 | enst00000367590 | sg00000143324 | xpr1-202 | 1 | 180632022 | 180890279 | + | mRNA | protein_coding |
| 395715 | enst00000367589 | sg00000143324 | xpr1-201 | 1 | 180632032 | 180886126 | + | mRNA | protein_coding |
| -398090 | enst00000442108 | sg00000231966 | linc02818-201 | 1 | 179829609 | 179836124 | - | lnc_RNA | lncrna |
| -416023 | enst00000415218 | sg00000229407 | al359853.1-202 | 1 | 179816184 | 179818191 | - | lnc_RNA | lncrna |
| -416790 | enst00000453051 | sg00000229407 | al359853.1-201 | 1 | 179816184 | 179817424 | - | lnc_RNA | lncrna |
| -491051 | enst00000341785 | sg00000143340 | fam163a-201 | 1 | 179743163 | 179816198 | + | mRNA | protein_coding |
| -492205 | enst00000451471 | sg00000243062 | al359853.2-202 | 1 | 179742009 | 179742697 | + | 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