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 |
|---|---|---|---|---|---|---|---|---|
| #25 | 18 | 57439921 | 57441962 | 2041 | 3 | 64 | 1.16951e-25 | 4.65229e-23 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 2414 | enst00000481727 | sg00000119547 | onecut2-201 | 18 | 57444376 | 57476760 | + | lnc_RNA | processed_transcript |
| -4547 | enst00000491143 | sg00000119547 | onecut2-202 | 18 | 57435374 | 57491298 | + | mRNA | protein_coding |
| -12788 | enst00000620778 | sg00000277837 | ac090340.1-201 | 18 | 57427133 | 57432112 | + | lnc_RNA | lncrna |
| -76408 | enst00000590600 | sg00000177511 | st8sia3-203 | 18 | 57363513 | 57368933 | + | lnc_RNA | processed_transcript |
| -82769 | enst00000586360 | sg00000177511 | st8sia3-202 | 18 | 57357152 | 57371731 | + | mRNA | protein_coding |
| -87364 | enst00000324000 | sg00000177511 | st8sia3-201 | 18 | 57352557 | 57368931 | + | mRNA | protein_coding |
| 117253 | enst00000591977 | sg00000066926 | fech-207 | 18 | 57551175 | 57559215 | - | mRNA | protein_coding |
| 117583 | enst00000651812 | sg00000066926 | fech-211 | 18 | 57554260 | 57559545 | - | lnc_RNA | retained_intron |
| 144429 | enst00000651787 | sg00000066926 | fech-210 | 18 | 57549569 | 57586391 | - | lnc_RNA | processed_transcript |
| 144659 | enst00000592111 | sg00000066926 | fech-208 | 18 | 57573005 | 57586621 | - | lnc_RNA | retained_intron |
| 144692 | enst00000585878 | sg00000066926 | fech-206 | 18 | 57572990 | 57586654 | - | lnc_RNA | retained_intron |
| 144727 | enst00000585747 | sg00000066926 | fech-205 | 18 | 57567845 | 57586689 | - | lnc_RNA | processed_transcript |
| 144728 | enst00000592699 | sg00000066926 | fech-209 | 18 | 57554259 | 57586690 | - | mRNA | protein_coding |
| 144731 | enst00000382873 | sg00000066926 | fech-202 | 18 | 57549584 | 57586693 | - | mRNA | protein_coding |
| 144737 | enst00000585699 | sg00000066926 | fech-204 | 18 | 57566548 | 57586699 | - | lnc_RNA | processed_transcript |
| 144739 | enst00000585494 | sg00000066926 | fech-203 | 18 | 57550254 | 57586701 | - | mRNA | nonsense_mediated_decay |
| 144740 | enst00000262093 | sg00000066926 | fech-201 | 18 | 57544389 | 57586702 | - | mRNA | protein_coding |
| 144740 | enst00000652755 | sg00000066926 | fech-212 | 18 | 57544389 | 57586702 | - | mRNA | protein_coding |
| 147129 | enst00000611316 | sg00000278703 | ac100847.1-201 | 18 | 57588611 | 57589091 | - | lnc_RNA | lncrna |
| -155213 | enst00000365370 | sg00000202240 | rnu6-737p-201 | 18 | 57284602 | 57284708 | - | snRNA | snrna |
| 163900 | enst00000589314 | sg00000134440 | nars1-210 | 18 | 57601343 | 57605862 | - | lnc_RNA | retained_intron |
| 165228 | enst00000589001 | sg00000134440 | nars1-209 | 18 | 57605934 | 57607190 | - | lnc_RNA | retained_intron |
| 179775 | enst00000590123 | sg00000134440 | nars1-211 | 18 | 57613624 | 57621737 | - | mRNA | nonsense_mediated_decay |
| 179814 | enst00000587366 | sg00000134440 | nars1-206 | 18 | 57613653 | 57621776 | - | lnc_RNA | retained_intron |
| 179823 | enst00000586807 | sg00000134440 | nars1-204 | 18 | 57601350 | 57621785 | - | mRNA | nonsense_mediated_decay |
| 179830 | enst00000587194 | sg00000134440 | nars1-205 | 18 | 57609378 | 57621792 | - | mRNA | protein_coding |
| 179830 | enst00000540592 | sg00000134440 | nars1-203 | 18 | 57607202 | 57621792 | - | mRNA | nonsense_mediated_decay |
| 179838 | enst00000591599 | sg00000134440 | nars1-212 | 18 | 57607654 | 57621800 | - | mRNA | protein_coding |
| 179846 | enst00000411676 | sg00000134440 | nars1-202 | 18 | 57607156 | 57621808 | - | lnc_RNA | retained_intron |
| 179862 | enst00000588661 | sg00000134440 | nars1-208 | 18 | 57607656 | 57621824 | - | mRNA | protein_coding |
| 179874 | enst00000256854 | sg00000134440 | nars1-201 | 18 | 57600656 | 57621836 | - | mRNA | protein_coding |
| 180251 | enst00000587675 | sg00000134440 | nars1-207 | 18 | 57607656 | 57622213 | - | mRNA | protein_coding |
| 188340 | enst00000591854 | sg00000267040 | ac027097.1-201 | 18 | 57630302 | 57667636 | + | lnc_RNA | lncrna |
| 188388 | enst00000592201 | sg00000267040 | ac027097.1-202 | 18 | 57630350 | 57669296 | + | lnc_RNA | lncrna |
| 197493 | enst00000588925 | sg00000267787 | ac027097.2-201 | 18 | 57639455 | 57738044 | + | lnc_RNA | lncrna |
| 199952 | enst00000619899 | sg00000267040 | ac027097.1-203 | 18 | 57641914 | 57668175 | + | lnc_RNA | lncrna |
| 246706 | enst00000588255 | sg00000081923 | atp8b1-202 | 18 | 57684118 | 57688668 | - | lnc_RNA | retained_intron |
| 252291 | enst00000660188 | sg00000267787 | ac027097.2-204 | 18 | 57694253 | 57731754 | + | lnc_RNA | lncrna |
| 253996 | enst00000649476 | sg00000267787 | ac027097.2-202 | 18 | 57695958 | 57738603 | + | lnc_RNA | lncrna |
| 266596 | enst00000589147 | sg00000081923 | atp8b1-203 | 18 | 57697670 | 57708558 | - | lnc_RNA | processed_transcript |
| -268727 | enst00000592678 | sg00000267726 | linc02565-201 | 18 | 57169615 | 57171194 | - | lnc_RNA | lncrna |
| 287575 | enst00000652880 | sg00000267787 | ac027097.2-205 | 18 | 57729537 | 57731754 | + | lnc_RNA | lncrna |
| 289792 | enst00000648467 | sg00000081923 | atp8b1-207 | 18 | 57669423 | 57731754 | - | mRNA | nonsense_mediated_decay |
| -292834 | enst00000585477 | sg00000228075 | bod1l2-201 | 18 | 57147087 | 57150410 | + | mRNA | protein_coding |
| -292923 | enst00000590942 | sg00000267789 | ac100775.1-201 | 18 | 57136322 | 57146998 | - | lnc_RNA | lncrna |
| 293438 | enst00000586729 | sg00000267787 | ac027097.2-203 | 18 | 57735400 | 57738044 | + | lnc_RNA | lncrna |
| 299003 | enst00000585322 | sg00000081923 | atp8b1-201 | 18 | 57731775 | 57740965 | - | mRNA | protein_coding |
| 313432 | enst00000365289 | sg00000202159 | rnu6-742p-201 | 18 | 57755394 | 57755500 | + | snRNA | snrna |
| 360026 | enst00000642462 | sg00000081923 | atp8b1-205 | 18 | 57646443 | 57801988 | - | mRNA | nonsense_mediated_decay |
| 361105 | enst00000648039 | sg00000081923 | atp8b1-206 | 18 | 57646493 | 57803067 | - | mRNA | nonsense_mediated_decay |
| 361139 | enst00000591728 | sg00000081923 | atp8b1-204 | 18 | 57701089 | 57803101 | - | mRNA | nonsense_mediated_decay |
| 361353 | enst00000648908 | sg00000081923 | atp8b1-208 | 18 | 57646426 | 57803315 | - | mRNA | protein_coding |
| -367802 | enst00000553704 | sg00000258609 | linc-ror-201 | 18 | 57054558 | 57072119 | - | lnc_RNA | lncrna |
| -367802 | enst00000643706 | sg00000258609 | linc-ror-203 | 18 | 57063555 | 57072119 | - | lnc_RNA | lncrna |
| -367862 | enst00000645956 | sg00000258609 | linc-ror-207 | 18 | 57054591 | 57072059 | - | lnc_RNA | lncrna |
| -367862 | enst00000646314 | sg00000258609 | linc-ror-208 | 18 | 57054591 | 57072059 | - | lnc_RNA | lncrna |
| -367871 | enst00000644575 | sg00000258609 | linc-ror-205 | 18 | 57057888 | 57072050 | - | lnc_RNA | lncrna |
| -369918 | enst00000644805 | sg00000258609 | linc-ror-206 | 18 | 57057888 | 57070003 | - | lnc_RNA | lncrna |
| -369918 | enst00000644118 | sg00000258609 | linc-ror-204 | 18 | 57057888 | 57070003 | - | lnc_RNA | lncrna |
| -369918 | enst00000642403 | sg00000258609 | linc-ror-202 | 18 | 57057888 | 57070003 | - | lnc_RNA | lncrna |
| -393515 | enst00000668805 | sg00000286777 | ac012301.3-201 | 18 | 57046406 | 57047692 | + | lnc_RNA | lncrna |
| 396514 | enst00000591045 | sg00000231544 | rsl24d1p11-201 | 18 | 57838476 | 57838966 | + | pseudogenic_transcript | processed_pseudogene |
| -412089 | enst00000592032 | sg00000267225 | wdr7-ot1-201 | 18 | 57027832 | 57038845 | + | lnc_RNA | lncrna |
| -477486 | enst00000585669 | sg00000091157 | wdr7-203 | 18 | 56962435 | 57010314 | + | mRNA | protein_coding |
| -482651 | enst00000391237 | sg00000212539 | ac012301.1-201 | 18 | 56957270 | 56957469 | + | snoRNA | snorna |
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