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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 |
|---|---|---|---|---|---|---|---|---|
| #104 | 2 | 156319615 | 156320997 | 1382 | 3 | 45 | 2.19112e-17 | 2.08995e-15 |
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 | enst00000634100 | sg00000282440 | ac074099.1-201 | 2 | 156305108 | 156320255 | - | lnc_RNA | lncrna |
| 9124 | enst00000406048 | sg00000153234 | nr4a2-202 | 2 | 156327904 | 156330121 | - | mRNA | protein_coding |
| 9710 | enst00000409108 | sg00000153234 | nr4a2-203 | 2 | 156325744 | 156330707 | - | mRNA | protein_coding |
| 9724 | enst00000429376 | sg00000153234 | nr4a2-210 | 2 | 156325744 | 156330721 | - | mRNA | protein_coding |
| 9791 | enst00000417764 | sg00000153234 | nr4a2-205 | 2 | 156325100 | 156330788 | - | mRNA | nonsense_mediated_decay |
| 10968 | enst00000417972 | sg00000153234 | nr4a2-206 | 2 | 156325100 | 156331965 | - | mRNA | nonsense_mediated_decay |
| 11716 | enst00000424077 | sg00000153234 | nr4a2-208 | 2 | 156329413 | 156332713 | - | mRNA | protein_coding |
| 11717 | enst00000426264 | sg00000153234 | nr4a2-209 | 2 | 156325082 | 156332714 | - | mRNA | protein_coding |
| 11723 | enst00000421709 | sg00000153234 | nr4a2-207 | 2 | 156329678 | 156332720 | - | mRNA | protein_coding |
| 11724 | enst00000339562 | sg00000153234 | nr4a2-201 | 2 | 156324437 | 156332721 | - | mRNA | protein_coding |
| 21351 | enst00000409572 | sg00000153234 | nr4a2-204 | 2 | 156325098 | 156342348 | - | mRNA | protein_coding |
| -64665 | enst00000637554 | sg00000226383 | linc01876-207 | 2 | 156021751 | 156254950 | - | lnc_RNA | lncrna |
| -64665 | enst00000636956 | sg00000226383 | linc01876-204 | 2 | 156021751 | 156254950 | - | lnc_RNA | lncrna |
| -64673 | enst00000659502 | sg00000226383 | linc01876-211 | 2 | 156020540 | 156254942 | - | lnc_RNA | lncrna |
| -64679 | enst00000428651 | sg00000226383 | linc01876-201 | 2 | 156020540 | 156254936 | - | lnc_RNA | lncrna |
| -64680 | enst00000661513 | sg00000226383 | linc01876-212 | 2 | 156020540 | 156254935 | - | lnc_RNA | lncrna |
| -64681 | enst00000657334 | sg00000226383 | linc01876-210 | 2 | 156020540 | 156254934 | - | lnc_RNA | lncrna |
| -64684 | enst00000637324 | sg00000226383 | linc01876-205 | 2 | 156022781 | 156254931 | - | lnc_RNA | lncrna |
| -64686 | enst00000635799 | sg00000226383 | linc01876-203 | 2 | 156011530 | 156254929 | - | lnc_RNA | lncrna |
| -64697 | enst00000638047 | sg00000226383 | linc01876-209 | 2 | 156020540 | 156254918 | - | lnc_RNA | lncrna |
| -64697 | enst00000662073 | sg00000226383 | linc01876-213 | 2 | 156020535 | 156254918 | - | lnc_RNA | lncrna |
| -64700 | enst00000637665 | sg00000226383 | linc01876-208 | 2 | 156021761 | 156254915 | - | lnc_RNA | lncrna |
| -64710 | enst00000637476 | sg00000226383 | linc01876-206 | 2 | 156022686 | 156254905 | - | lnc_RNA | lncrna |
| 114293 | enst00000415049 | sg00000115159 | gpd2-205 | 2 | 156435290 | 156510849 | + | mRNA | protein_coding |
| 114444 | enst00000310454 | sg00000115159 | gpd2-201 | 2 | 156435441 | 156586403 | + | mRNA | protein_coding |
| 115382 | enst00000438166 | sg00000115159 | gpd2-208 | 2 | 156436379 | 156586403 | + | mRNA | protein_coding |
| 115430 | enst00000495851 | sg00000115159 | gpd2-211 | 2 | 156436427 | 156501881 | + | lnc_RNA | processed_transcript |
| 115488 | enst00000540309 | sg00000115159 | gpd2-213 | 2 | 156436485 | 156583404 | + | mRNA | protein_coding |
| 152575 | enst00000409861 | sg00000115159 | gpd2-204 | 2 | 156473572 | 156613735 | + | mRNA | nonsense_mediated_decay |
| 152575 | enst00000409125 | sg00000115159 | gpd2-202 | 2 | 156473572 | 156583228 | + | mRNA | protein_coding |
| 152575 | enst00000409674 | sg00000115159 | gpd2-203 | 2 | 156473572 | 156583058 | + | mRNA | protein_coding |
| 152575 | enst00000416888 | sg00000115159 | gpd2-206 | 2 | 156473572 | 156501844 | + | mRNA | nonsense_mediated_decay |
| 152595 | enst00000430992 | sg00000115159 | gpd2-207 | 2 | 156473592 | 156510834 | + | mRNA | nonsense_mediated_decay |
| 250175 | enst00000464846 | sg00000115159 | gpd2-209 | 2 | 156571172 | 156583009 | + | lnc_RNA | retained_intron |
| 258086 | enst00000492005 | sg00000115159 | gpd2-210 | 2 | 156579083 | 156583048 | + | lnc_RNA | processed_transcript |
| 258689 | enst00000496190 | sg00000115159 | gpd2-212 | 2 | 156579686 | 156583273 | + | lnc_RNA | processed_transcript |
| -285535 | enst00000450741 | sg00000235548 | ac073551.1-201 | 2 | 156033247 | 156034080 | - | pseudogenic_transcript | processed_pseudogene |
| -295002 | enst00000448255 | sg00000226383 | linc01876-202 | 2 | 156011617 | 156024613 | - | lnc_RNA | lncrna |
| 334227 | enst00000637749 | sg00000283436 | linc01958-201 | 2 | 156655224 | 156695659 | + | lnc_RNA | lncrna |
| 457375 | enst00000416050 | sg00000238069 | rplp0p7-201 | 2 | 156777706 | 156778372 | - | pseudogenic_transcript | processed_pseudogene |
| 467734 | enst00000665531 | sg00000287048 | ac096589.2-201 | 2 | 156788731 | 156865701 | + | lnc_RNA | lncrna |
| 482342 | enst00000670545 | sg00000286889 | ac096589.1-201 | 2 | 156803339 | 156891160 | + | 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