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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 |
|---|---|---|---|---|---|---|---|---|
| #53 | 9 | 124014988 | 124016512 | 1524 | 3 | 47 | 4.39029e-21 | 8.23801e-19 |
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 | enst00000488674 | sg00000106689 | lhx2-203 | 9 | 124015397 | 124033301 | + | mRNA | protein_coding |
| -2631 | enst00000446480 | sg00000106689 | lhx2-202 | 9 | 124012357 | 124032884 | + | mRNA | protein_coding |
| -3220 | enst00000373615 | sg00000106689 | lhx2-201 | 9 | 124011768 | 124033301 | + | mRNA | protein_coding |
| -4458 | enst00000421041 | sg00000231227 | ac006450.1-201 | 9 | 124010530 | 124011114 | + | lnc_RNA | lncrna |
| -5592 | enst00000453529 | sg00000236668 | ac006450.3-201 | 9 | 124006277 | 124009396 | - | lnc_RNA | lncrna |
| -13318 | enst00000560961 | sg00000106689 | lhx2-204 | 9 | 124001670 | 124015361 | + | mRNA | protein_coding |
| 16012 | enst00000429482 | sg00000234921 | ac006450.2-201 | 9 | 124031624 | 124032524 | - | lnc_RNA | lncrna |
| -84836 | enst00000373618 | sg00000119522 | dennd1a-201 | 9 | 123413271 | 123930152 | - | mRNA | protein_coding |
| -84862 | enst00000373620 | sg00000119522 | dennd1a-202 | 9 | 123400099 | 123930126 | - | mRNA | protein_coding |
| -84881 | enst00000373624 | sg00000119522 | dennd1a-203 | 9 | 123379654 | 123930107 | - | mRNA | protein_coding |
| -171952 | enst00000421400 | sg00000234881 | pigfp2-201 | 9 | 123843036 | 123843686 | + | pseudogenic_transcript | processed_pseudogene |
| -216473 | enst00000473039 | sg00000119522 | dennd1a-206 | 9 | 123379654 | 123798515 | - | lnc_RNA | processed_transcript |
| 241094 | enst00000540326 | sg00000119408 | nek6-213 | 9 | 124257606 | 124352438 | + | mRNA | protein_coding |
| 241094 | enst00000373603 | sg00000119408 | nek6-204 | 9 | 124257606 | 124353307 | + | mRNA | protein_coding |
| 241451 | enst00000373600 | sg00000119408 | nek6-203 | 9 | 124257963 | 124353307 | + | mRNA | protein_coding |
| 241458 | enst00000320246 | sg00000119408 | nek6-201 | 9 | 124257970 | 124353307 | + | mRNA | protein_coding |
| 241739 | enst00000545174 | sg00000119408 | nek6-214 | 9 | 124258251 | 124352438 | + | mRNA | protein_coding |
| 241748 | enst00000444973 | sg00000119408 | nek6-209 | 9 | 124258260 | 124339607 | + | mRNA | protein_coding |
| 241749 | enst00000454453 | sg00000119408 | nek6-211 | 9 | 124258261 | 124347797 | + | mRNA | protein_coding |
| 244644 | enst00000426157 | sg00000235204 | al162724.2-201 | 9 | 124259250 | 124261156 | - | lnc_RNA | lncrna |
| 244961 | enst00000425237 | sg00000119408 | nek6-208 | 9 | 124261473 | 124339614 | + | mRNA | protein_coding |
| 244961 | enst00000373596 | sg00000119408 | nek6-202 | 9 | 124261473 | 124327445 | + | mRNA | protein_coding |
| 246364 | enst00000437461 | sg00000227200 | al162724.1-201 | 9 | 124262876 | 124265809 | + | lnc_RNA | lncrna |
| -255768 | enst00000411924 | sg00000229115 | al390774.1-201 | 9 | 123759220 | 123759775 | + | pseudogenic_transcript | processed_pseudogene |
| -257229 | enst00000474676 | sg00000119522 | dennd1a-207 | 9 | 123569545 | 123757759 | - | lnc_RNA | processed_transcript |
| 269928 | enst00000423785 | sg00000119408 | nek6-207 | 9 | 124286440 | 124326405 | + | mRNA | protein_coding |
| 275459 | enst00000546191 | sg00000119408 | nek6-215 | 9 | 124291971 | 124352438 | + | mRNA | protein_coding |
| 275467 | enst00000422297 | sg00000119408 | nek6-206 | 9 | 124291979 | 124339608 | + | mRNA | protein_coding |
| 275908 | enst00000539416 | sg00000119408 | nek6-212 | 9 | 124292420 | 124352438 | + | mRNA | protein_coding |
| 276429 | enst00000394199 | sg00000119408 | nek6-205 | 9 | 124292941 | 124352438 | + | mRNA | protein_coding |
| -278551 | enst00000423942 | sg00000230826 | al390774.2-201 | 9 | 123736437 | 123751941 | + | lnc_RNA | lncrna |
| 283473 | enst00000447379 | sg00000119408 | nek6-210 | 9 | 124299985 | 124326438 | + | mRNA | protein_coding |
| -338197 | enst00000394215 | sg00000119522 | dennd1a-204 | 9 | 123401810 | 123676791 | - | mRNA | protein_coding |
| -362697 | enst00000475615 | sg00000119522 | dennd1a-209 | 9 | 123630396 | 123652291 | - | lnc_RNA | processed_transcript |
| 368144 | enst00000478817 | sg00000136930 | psmb7-205 | 9 | 124383622 | 124384656 | - | lnc_RNA | processed_transcript |
| 368144 | enst00000474081 | sg00000136930 | psmb7-204 | 9 | 124383596 | 124384656 | - | lnc_RNA | processed_transcript |
| 398779 | enst00000498485 | sg00000136930 | psmb7-206 | 9 | 124353466 | 124415291 | - | lnc_RNA | processed_transcript |
| 398795 | enst00000466951 | sg00000136930 | psmb7-203 | 9 | 124412400 | 124415307 | - | lnc_RNA | processed_transcript |
| 398930 | enst00000259457 | sg00000136930 | psmb7-201 | 9 | 124353465 | 124415442 | - | mRNA | protein_coding |
| 398932 | enst00000441097 | sg00000136930 | psmb7-202 | 9 | 124396760 | 124415444 | - | mRNA | protein_coding |
| -405535 | enst00000491650 | sg00000119522 | dennd1a-211 | 9 | 123403475 | 123609453 | - | lnc_RNA | processed_transcript |
| -431771 | enst00000497135 | sg00000119522 | dennd1a-212 | 9 | 123411293 | 123583217 | - | lnc_RNA | processed_transcript |
| 434913 | enst00000618308 | sg00000180264 | adgrd2-203 | 9 | 124451425 | 124452579 | + | lnc_RNA | processed_transcript |
| 435179 | enst00000638707 | sg00000180264 | adgrd2-206 | 9 | 124451691 | 124457484 | + | lnc_RNA | processed_transcript |
| 435579 | enst00000334810 | sg00000180264 | adgrd2-201 | 9 | 124452091 | 124478589 | + | mRNA | protein_coding |
| 436999 | enst00000639026 | sg00000180264 | adgrd2-207 | 9 | 124453511 | 124469515 | + | mRNA | nonsense_mediated_decay |
| 448698 | enst00000622546 | sg00000180264 | adgrd2-204 | 9 | 124465210 | 124467340 | + | lnc_RNA | retained_intron |
| 449768 | enst00000638310 | sg00000180264 | adgrd2-205 | 9 | 124466280 | 124475615 | + | mRNA | nonsense_mediated_decay |
| 452046 | enst00000610875 | sg00000180264 | adgrd2-202 | 9 | 124468558 | 124478589 | + | mRNA | nonsense_mediated_decay |
| 484474 | enst00000373587 | sg00000136931 | nr5a1-201 | 9 | 124482728 | 124500986 | - | mRNA | protein_coding |
| 490723 | enst00000455734 | sg00000136931 | nr5a1-203 | 9 | 124500427 | 124507235 | - | mRNA | protein_coding |
| 490887 | enst00000373588 | sg00000136931 | nr5a1-202 | 9 | 124481236 | 124507399 | - | mRNA | protein_coding |
| 490908 | enst00000620110 | sg00000136931 | nr5a1-204 | 9 | 124481236 | 124507420 | - | mRNA | protein_coding |
| 499544 | enst00000369027 | sg00000231149 | al354979.1-201 | 9 | 124514938 | 124516056 | - | 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