PycoMeth
Documentation
GitHub
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 |
|---|---|---|---|---|---|---|---|---|
| #29 | X | 21655641 | 21659118 | 3477 | 3 | 105 | 8.09421e-25 | 2.77576e-22 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 0 | enst00000379499 | sg00000185915 | klhl34-201 | X | 21654690 | 21658330 | - | mRNA | protein_coding |
| -10262 | enst00000645238 | sg00000149970 | cnksr2-229 | X | 21645379 | 21654243 | + | lnc_RNA | processed_transcript |
| -12245 | enst00000643484 | sg00000149970 | cnksr2-218 | X | 21643396 | 21652890 | + | lnc_RNA | processed_transcript |
| -49110 | enst00000646690 | sg00000149970 | cnksr2-235 | X | 21606531 | 21654257 | + | lnc_RNA | processed_transcript |
| -60418 | enst00000645539 | sg00000149970 | cnksr2-231 | X | 21595223 | 21652744 | + | lnc_RNA | retained_intron |
| -60770 | enst00000647058 | sg00000149970 | cnksr2-237 | X | 21594871 | 21642357 | + | lnc_RNA | retained_intron |
| 98904 | enst00000494525 | sg00000091482 | smpx-202 | X | 21706338 | 21758022 | - | mRNA | nonsense_mediated_decay |
| 98960 | enst00000646008 | sg00000091482 | smpx-203 | X | 21727291 | 21758078 | - | mRNA | protein_coding |
| 98998 | enst00000379494 | sg00000091482 | smpx-201 | X | 21705978 | 21758116 | - | mRNA | protein_coding |
| -117773 | enst00000642853 | sg00000149970 | cnksr2-212 | X | 21537868 | 21654108 | + | lnc_RNA | processed_transcript |
| -123782 | enst00000643156 | sg00000149970 | cnksr2-213 | X | 21531859 | 21654258 | + | mRNA | nonsense_mediated_decay |
| -154166 | enst00000647349 | sg00000149970 | cnksr2-238 | X | 21501475 | 21609569 | + | lnc_RNA | retained_intron |
| 180499 | enst00000379484 | sg00000012174 | mbtps2-202 | X | 21839617 | 21885423 | + | mRNA | protein_coding |
| 180518 | enst00000465888 | sg00000012174 | mbtps2-203 | X | 21839636 | 21857593 | + | lnc_RNA | processed_transcript |
| 180536 | enst00000365779 | sg00000012174 | mbtps2-201 | X | 21839654 | 21873084 | + | mRNA | protein_coding |
| 182843 | enst00000618062 | sg00000275681 | u73479.1-201 | X | 21841794 | 21841961 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -184907 | enst00000644075 | sg00000149970 | cnksr2-220 | X | 21470734 | 21652822 | + | lnc_RNA | retained_intron |
| 196869 | enst00000429584 | sg00000230797 | yy2-201 | X | 21855987 | 21858740 | + | mRNA | protein_coding |
| 213589 | enst00000383912 | sg00000206639 | u72788.1-201 | X | 21872707 | 21872808 | + | ncRNA | misc_rna |
| -214911 | enst00000643313 | sg00000149970 | cnksr2-217 | X | 21440730 | 21641628 | + | mRNA | protein_coding |
| -229029 | enst00000480138 | sg00000149970 | cnksr2-205 | X | 21426612 | 21470878 | + | lnc_RNA | retained_intron |
| -229061 | enst00000479158 | sg00000149970 | cnksr2-204 | X | 21426580 | 21531968 | + | lnc_RNA | processed_transcript |
| -229144 | enst00000646697 | sg00000149970 | cnksr2-236 | X | 21426497 | 21643600 | + | mRNA | nonsense_mediated_decay |
| -232346 | enst00000644789 | sg00000149970 | cnksr2-224 | X | 21423295 | 21532004 | + | lnc_RNA | retained_intron |
| -233347 | enst00000457739 | sg00000231913 | rarres2p3-201 | X | 21421822 | 21422294 | - | pseudogenic_transcript | processed_pseudogene |
| 280343 | enst00000603134 | sg00000271286 | u73023.1-201 | X | 21939461 | 21940160 | + | pseudogenic_transcript | processed_pseudogene |
| -280808 | enst00000647423 | sg00000149970 | cnksr2-239 | X | 21374833 | 21591467 | + | lnc_RNA | retained_intron |
| -280813 | enst00000647532 | sg00000149970 | cnksr2-240 | X | 21374828 | 21654030 | + | lnc_RNA | retained_intron |
| -280841 | enst00000485012 | sg00000149970 | cnksr2-206 | X | 21374800 | 21591485 | + | lnc_RNA | retained_intron |
| -280847 | enst00000643220 | sg00000149970 | cnksr2-215 | X | 21374794 | 21642657 | + | mRNA | protein_coding |
| -280872 | enst00000643309 | sg00000149970 | cnksr2-216 | X | 21374769 | 21429776 | + | lnc_RNA | retained_intron |
| -280888 | enst00000642460 | sg00000149970 | cnksr2-209 | X | 21374753 | 21532195 | + | lnc_RNA | retained_intron |
| -280898 | enst00000644095 | sg00000149970 | cnksr2-221 | X | 21374743 | 21642799 | + | mRNA | nonsense_mediated_decay |
| -280912 | enst00000642565 | sg00000149970 | cnksr2-211 | X | 21374729 | 21495691 | + | lnc_RNA | retained_intron |
| -280970 | enst00000645791 | sg00000149970 | cnksr2-233 | X | 21374671 | 21645440 | + | mRNA | protein_coding |
| -281031 | enst00000645074 | sg00000149970 | cnksr2-228 | X | 21374610 | 21642657 | + | mRNA | protein_coding |
| -281033 | enst00000644295 | sg00000149970 | cnksr2-222 | X | 21374608 | 21654245 | + | mRNA | protein_coding |
| -281130 | enst00000644585 | sg00000149970 | cnksr2-223 | X | 21374511 | 21654550 | + | mRNA | protein_coding |
| -281173 | enst00000645245 | sg00000149970 | cnksr2-230 | X | 21374468 | 21654263 | + | mRNA | protein_coding |
| -281173 | enst00000646175 | sg00000149970 | cnksr2-234 | X | 21374468 | 21441405 | + | lnc_RNA | retained_intron |
| -281185 | enst00000279451 | sg00000149970 | cnksr2-201 | X | 21374456 | 21642732 | + | mRNA | protein_coding |
| -281193 | enst00000643171 | sg00000149970 | cnksr2-214 | X | 21374448 | 21609568 | + | mRNA | nonsense_mediated_decay |
| -281219 | enst00000644832 | sg00000149970 | cnksr2-226 | X | 21374422 | 21493229 | + | lnc_RNA | retained_intron |
| -281220 | enst00000645679 | sg00000149970 | cnksr2-232 | X | 21374421 | 21426583 | + | lnc_RNA | processed_transcript |
| -281220 | enst00000543067 | sg00000149970 | cnksr2-207 | X | 21374421 | 21642730 | + | mRNA | protein_coding |
| -281220 | enst00000644798 | sg00000149970 | cnksr2-225 | X | 21374421 | 21506814 | + | mRNA | protein_coding |
| -281223 | enst00000425654 | sg00000149970 | cnksr2-203 | X | 21374418 | 21654695 | + | mRNA | protein_coding |
| -281223 | enst00000379510 | sg00000149970 | cnksr2-202 | X | 21374418 | 21654689 | + | mRNA | protein_coding |
| -281257 | enst00000645038 | sg00000149970 | cnksr2-227 | X | 21374384 | 21594454 | + | lnc_RNA | processed_transcript |
| -281284 | enst00000643841 | sg00000149970 | cnksr2-219 | X | 21374357 | 21506742 | + | mRNA | protein_coding |
| -281343 | enst00000642359 | sg00000149970 | cnksr2-208 | X | 21374298 | 21643600 | + | mRNA | protein_coding |
| -281376 | enst00000636450 | sg00000283380 | al807742.1-204 | X | 21081644 | 21374265 | - | lnc_RNA | lncrna |
| -281522 | enst00000637843 | sg00000283380 | al807742.1-205 | X | 21257884 | 21374119 | - | lnc_RNA | lncrna |
| -281575 | enst00000636317 | sg00000283380 | al807742.1-202 | X | 20874168 | 21374066 | - | lnc_RNA | lncrna |
| 281591 | enst00000404933 | sg00000102172 | sms-202 | X | 21940709 | 21994837 | + | mRNA | protein_coding |
| 281597 | enst00000379404 | sg00000102172 | sms-201 | X | 21940715 | 21994473 | + | mRNA | protein_coding |
| 281660 | enst00000478094 | sg00000102172 | sms-204 | X | 21940778 | 21977989 | + | lnc_RNA | processed_transcript |
| 281927 | enst00000457085 | sg00000102172 | sms-203 | X | 21941045 | 21978111 | + | mRNA | protein_coding |
| -282840 | enst00000642501 | sg00000149970 | cnksr2-210 | X | 21372801 | 21645440 | + | mRNA | protein_coding |
| 373207 | enst00000379374 | sg00000102174 | phex-201 | X | 22032325 | 22251310 | + | mRNA | protein_coding |
| 431375 | enst00000475778 | sg00000102174 | phex-202 | X | 22090493 | 22099363 | + | lnc_RNA | processed_transcript |
| -441004 | enst00000383989 | sg00000206716 | rnu6-133p-201 | X | 21214637 | 21214743 | + | snRNA | snrna |
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