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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 |
|---|---|---|---|---|---|---|---|---|
| #121 | 7 | 102494140 | 102495276 | 1136 | 3 | 37 | 1.24815e-16 | 1.02585e-14 |
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 | enst00000488284 | sg00000170667 | rasa4b-205 | 7 | 102483144 | 102494868 | - | lnc_RNA | retained_intron |
| 0 | enst00000495352 | sg00000170667 | rasa4b-206 | 7 | 102483171 | 102494822 | - | lnc_RNA | retained_intron |
| -829 | enst00000477184 | sg00000170667 | rasa4b-204 | 7 | 102482445 | 102493311 | - | lnc_RNA | retained_intron |
| -829 | enst00000467351 | sg00000170667 | rasa4b-203 | 7 | 102483484 | 102493311 | - | lnc_RNA | retained_intron |
| -15233 | enst00000292614 | sg00000005075 | polr2j-201 | 7 | 102473118 | 102478907 | - | mRNA | protein_coding |
| -15234 | enst00000393794 | sg00000005075 | polr2j-202 | 7 | 102473938 | 102478906 | - | mRNA | protein_coding |
| 22479 | enst00000306682 | sg00000170667 | rasa4b-201 | 7 | 102483562 | 102517755 | - | mRNA | protein_coding |
| 22501 | enst00000541662 | sg00000170667 | rasa4b-207 | 7 | 102483139 | 102517777 | - | mRNA | protein_coding |
| 22505 | enst00000465829 | sg00000170667 | rasa4b-202 | 7 | 102483144 | 102517781 | - | mRNA | protein_coding |
| -22671 | enst00000578629 | sg00000284596 | mir4467-201 | 7 | 102471469 | 102471531 | + | miRNA | mirna |
| -24551 | enst00000468175 | sg00000161036 | lrwd1-204 | 7 | 102469589 | 102473168 | + | mRNA | protein_coding |
| -26798 | enst00000485417 | sg00000161036 | lrwd1-207 | 7 | 102467342 | 102468445 | + | lnc_RNA | retained_intron |
| -28398 | enst00000582533 | sg00000284176 | mir5090-201 | 7 | 102465742 | 102465826 | + | miRNA | mirna |
| -28988 | enst00000485808 | sg00000161036 | lrwd1-208 | 7 | 102465152 | 102468559 | + | mRNA | nonsense_mediated_decay |
| -29045 | enst00000476270 | sg00000161036 | lrwd1-206 | 7 | 102465095 | 102466270 | + | mRNA | nonsense_mediated_decay |
| -29059 | enst00000626402 | sg00000161036 | lrwd1-209 | 7 | 102465081 | 102465589 | + | mRNA | protein_coding |
| -29117 | enst00000473880 | sg00000161036 | lrwd1-205 | 7 | 102465023 | 102473166 | + | lnc_RNA | retained_intron |
| -29139 | enst00000464107 | sg00000161036 | lrwd1-203 | 7 | 102465001 | 102467376 | + | mRNA | nonsense_mediated_decay |
| -29156 | enst00000292616 | sg00000161036 | lrwd1-201 | 7 | 102464984 | 102473168 | + | mRNA | protein_coding |
| -29184 | enst00000463739 | sg00000161036 | lrwd1-202 | 7 | 102464956 | 102468377 | + | mRNA | protein_coding |
| -29277 | enst00000490528 | sg00000160993 | alkbh4-202 | 7 | 102456834 | 102464863 | - | mRNA | nonsense_mediated_decay |
| -29277 | enst00000292566 | sg00000160993 | alkbh4-201 | 7 | 102456238 | 102464863 | - | mRNA | protein_coding |
| -29283 | enst00000498283 | sg00000160993 | alkbh4-203 | 7 | 102459397 | 102464857 | - | lnc_RNA | retained_intron |
| 48573 | enst00000644544 | sg00000284981 | upk3bl2-201 | 7 | 102538417 | 102543849 | - | mRNA | protein_coding |
| 55956 | enst00000507918 | sg00000205238 | spdye2-203 | 7 | 102551232 | 102562069 | + | mRNA | protein_coding |
| -57841 | enst00000473939 | sg00000160991 | orai2-204 | 7 | 102436299 | 102448732 | + | mRNA | protein_coding |
| -57980 | enst00000498661 | sg00000160991 | orai2-209 | 7 | 102436160 | 102446579 | + | mRNA | protein_coding |
| 57980 | enst00000432940 | sg00000205238 | spdye2-202 | 7 | 102553256 | 102561175 | + | mRNA | protein_coding |
| -59360 | enst00000468165 | sg00000239480 | ac073517.1-201 | 7 | 102426818 | 102434780 | - | lnc_RNA | lncrna |
| 60533 | enst00000341656 | sg00000205238 | spdye2-201 | 7 | 102555809 | 102562308 | + | mRNA | protein_coding |
| -60564 | enst00000403646 | sg00000160991 | orai2-202 | 7 | 102433576 | 102448716 | + | mRNA | protein_coding |
| -60564 | enst00000468241 | sg00000160991 | orai2-203 | 7 | 102433576 | 102446924 | + | mRNA | protein_coding |
| -60565 | enst00000495936 | sg00000160991 | orai2-208 | 7 | 102433575 | 102456825 | + | mRNA | protein_coding |
| -60570 | enst00000478730 | sg00000160991 | orai2-205 | 7 | 102433570 | 102451609 | + | mRNA | protein_coding |
| -60591 | enst00000488996 | sg00000160991 | orai2-207 | 7 | 102433549 | 102447048 | + | lnc_RNA | processed_transcript |
| -60610 | enst00000356387 | sg00000160991 | orai2-201 | 7 | 102433530 | 102456821 | + | mRNA | protein_coding |
| -60610 | enst00000611770 | sg00000160991 | orai2-210 | 7 | 102433530 | 102456821 | + | mRNA | protein_coding |
| -61034 | enst00000482237 | sg00000160991 | orai2-206 | 7 | 102433106 | 102439047 | + | mRNA | protein_coding |
| 71353 | enst00000503564 | sg00000168255 | polr2j3-206 | 7 | 102538341 | 102566629 | - | lnc_RNA | processed_transcript |
| 71382 | enst00000504677 | sg00000168255 | polr2j3-207 | 7 | 102540059 | 102566658 | - | lnc_RNA | processed_transcript |
| 71794 | enst00000511773 | sg00000168255 | polr2j3-211 | 7 | 102539676 | 102567070 | - | lnc_RNA | processed_transcript |
| 77194 | enst00000502415 | sg00000168255 | polr2j3-205 | 7 | 102541151 | 102572470 | - | lnc_RNA | processed_transcript |
| 77245 | enst00000621093 | sg00000285437 | polr2j3-221 | 7 | 102567051 | 102572521 | - | mRNA | protein_coding |
| 77245 | enst00000506060 | sg00000168255 | polr2j3-208 | 7 | 102541104 | 102572521 | - | lnc_RNA | processed_transcript |
| 77263 | enst00000379340 | sg00000168255 | polr2j3-201 | 7 | 102537919 | 102572539 | - | mRNA | nonsense_mediated_decay |
| 77277 | enst00000508848 | sg00000168255 | polr2j3-210 | 7 | 102540024 | 102572553 | - | mRNA | nonsense_mediated_decay |
| 77279 | enst00000508910 | sg00000285437 | polr2j3-216 | 7 | 102566627 | 102572555 | - | lnc_RNA | processed_transcript |
| 77284 | enst00000504157 | sg00000285437 | polr2j3-215 | 7 | 102565976 | 102572560 | - | lnc_RNA | processed_transcript |
| 77284 | enst00000464525 | sg00000168255 | polr2j3-202 | 7 | 102537918 | 102572560 | - | mRNA | nonsense_mediated_decay |
| 77291 | enst00000489144 | sg00000168255 | polr2j3-204 | 7 | 102537918 | 102572567 | - | mRNA | nonsense_mediated_decay |
| 77304 | enst00000504101 | sg00000285437 | polr2j3-214 | 7 | 102569305 | 102572580 | - | lnc_RNA | retained_intron |
| 77304 | enst00000613744 | sg00000285437 | polr2j3-220 | 7 | 102566288 | 102572580 | - | mRNA | protein_coding |
| 77307 | enst00000513438 | sg00000285437 | polr2j3-218 | 7 | 102569200 | 102572583 | - | mRNA | protein_coding |
| 77307 | enst00000443430 | sg00000285437 | polr2j3-213 | 7 | 102567484 | 102572583 | - | lnc_RNA | processed_transcript |
| 77307 | enst00000511313 | sg00000285437 | polr2j3-217 | 7 | 102562656 | 102572583 | - | mRNA | protein_coding |
| 77307 | enst00000608621 | sg00000285437 | polr2j3-219 | 7 | 102562133 | 102572583 | - | mRNA | nonsense_mediated_decay |
| 77307 | enst00000507355 | sg00000168255 | polr2j3-209 | 7 | 102543568 | 102572583 | - | mRNA | nonsense_mediated_decay |
| 77373 | enst00000486319 | sg00000168255 | polr2j3-203 | 7 | 102537920 | 102572649 | - | mRNA | nonsense_mediated_decay |
| 77377 | enst00000513506 | sg00000168255 | polr2j3-212 | 7 | 102540024 | 102572653 | - | mRNA | protein_coding |
| 84520 | enst00000538869 | sg00000105808 | rasa4-217 | 7 | 102573807 | 102579796 | - | mRNA | protein_coding |
| -88285 | enst00000408583 | sg00000221510 | mir548o-201 | 7 | 102405742 | 102405855 | - | miRNA | mirna |
| -89783 | enst00000468316 | sg00000128563 | prkrip1-203 | 7 | 102404357 | 102426666 | + | lnc_RNA | retained_intron |
| 97047 | enst00000521822 | sg00000105808 | rasa4-211 | 7 | 102587447 | 102592323 | - | lnc_RNA | processed_transcript |
| 97168 | enst00000514917 | sg00000270249 | ac093668.1-201 | 7 | 102541501 | 102592444 | - | mRNA | protein_coding |
| -97777 | enst00000397912 | sg00000128563 | prkrip1-201 | 7 | 102396363 | 102426666 | + | mRNA | protein_coding |
| 98715 | enst00000522223 | sg00000105808 | rasa4-213 | 7 | 102582350 | 102593991 | - | lnc_RNA | retained_intron |
| 99184 | enst00000520577 | sg00000105808 | rasa4-208 | 7 | 102593714 | 102594460 | - | lnc_RNA | retained_intron |
| 100461 | enst00000521397 | sg00000105808 | rasa4-210 | 7 | 102592351 | 102595737 | - | mRNA | protein_coding |
| 107120 | enst00000519539 | sg00000105808 | rasa4-205 | 7 | 102595302 | 102602396 | - | mRNA | nonsense_mediated_decay |
| 110901 | enst00000519878 | sg00000105808 | rasa4-206 | 7 | 102599860 | 102606177 | - | lnc_RNA | retained_intron |
| -111403 | enst00000426478 | sg00000239486 | ac091390.4-201 | 7 | 102380465 | 102382737 | - | pseudogenic_transcript | unprocessed_pseudogene |
| 116315 | enst00000461209 | sg00000105808 | rasa4-203 | 7 | 102582323 | 102611591 | - | mRNA | protein_coding |
| 116866 | enst00000520042 | sg00000105808 | rasa4-207 | 7 | 102602324 | 102612142 | - | mRNA | protein_coding |
| -117921 | enst00000462601 | sg00000128563 | prkrip1-202 | 7 | 102376219 | 102425541 | + | mRNA | protein_coding |
| 121416 | enst00000521076 | sg00000105808 | rasa4-209 | 7 | 102602324 | 102616692 | - | mRNA | protein_coding |
| 121453 | enst00000462172 | sg00000105808 | rasa4-204 | 7 | 102582691 | 102616729 | - | mRNA | protein_coding |
| 121462 | enst00000522801 | sg00000105808 | rasa4-215 | 7 | 102595665 | 102616738 | - | mRNA | protein_coding |
| 121470 | enst00000522443 | sg00000105808 | rasa4-214 | 7 | 102608558 | 102616746 | - | lnc_RNA | retained_intron |
| 121480 | enst00000449970 | sg00000105808 | rasa4-202 | 7 | 102582325 | 102616756 | - | mRNA | protein_coding |
| 121480 | enst00000521892 | sg00000105808 | rasa4-212 | 7 | 102609075 | 102616756 | - | lnc_RNA | retained_intron |
| 121480 | enst00000523568 | sg00000105808 | rasa4-216 | 7 | 102587342 | 102616756 | - | lnc_RNA | retained_intron |
| 121481 | enst00000262940 | sg00000105808 | rasa4-201 | 7 | 102579646 | 102616757 | - | mRNA | protein_coding |
| -128098 | enst00000482465 | sg00000128563 | prkrip1-206 | 7 | 102366042 | 102426666 | + | lnc_RNA | processed_transcript |
| -129842 | enst00000492837 | sg00000239969 | ac091390.5-203 | 7 | 102364298 | 102380631 | + | lnc_RNA | processed_transcript |
| -129972 | enst00000476426 | sg00000239969 | ac091390.5-202 | 7 | 102364168 | 102376318 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -129978 | enst00000484974 | sg00000239969 | ac091390.5-201 | 7 | 102364162 | 102380633 | + | lnc_RNA | processed_transcript |
| -130243 | enst00000496391 | sg00000128563 | prkrip1-208 | 7 | 102363897 | 102426676 | + | mRNA | protein_coding |
| -130245 | enst00000482549 | sg00000128563 | prkrip1-207 | 7 | 102363895 | 102425449 | + | lnc_RNA | processed_transcript |
| -130246 | enst00000469763 | sg00000128563 | prkrip1-204 | 7 | 102363894 | 102425446 | + | lnc_RNA | processed_transcript |
| -130268 | enst00000477886 | sg00000128563 | prkrip1-205 | 7 | 102363872 | 102404625 | + | lnc_RNA | processed_transcript |
| -137696 | enst00000563237 | sg00000260097 | spdye6-201 | 7 | 102345746 | 102356444 | - | mRNA | protein_coding |
| 147515 | enst00000340457 | sg00000267368 | upk3bl1-201 | 7 | 102637025 | 102642791 | - | mRNA | protein_coding |
| 147593 | enst00000519541 | sg00000205236 | ac105052.1-201 | 7 | 102582523 | 102642869 | - | mRNA | nonsense_mediated_decay |
| 155049 | enst00000507450 | sg00000173678 | spdye2b-203 | 7 | 102650325 | 102661159 | + | mRNA | protein_coding |
| -156824 | enst00000432573 | sg00000228546 | ac091390.3-201 | 7 | 102337316 | 102339115 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 157073 | enst00000436228 | sg00000173678 | spdye2b-201 | 7 | 102652349 | 102660265 | + | mRNA | protein_coding |
| -157271 | enst00000363682 | sg00000200552 | ac091390.2-201 | 7 | 102336869 | 102336970 | + | ncRNA | misc_rna |
| 159617 | enst00000455020 | sg00000173678 | spdye2b-202 | 7 | 102654893 | 102661398 | + | mRNA | protein_coding |
| -164610 | enst00000433904 | sg00000170409 | ac091390.1-201 | 7 | 102327256 | 102329530 | - | pseudogenic_transcript | unprocessed_pseudogene |
| 176325 | enst00000333432 | sg00000228049 | polr2j2-201 | 7 | 102666131 | 102671601 | - | mRNA | protein_coding |
| 176353 | enst00000358438 | sg00000228049 | polr2j2-202 | 7 | 102665368 | 102671629 | - | mRNA | protein_coding |
| 176365 | enst00000476151 | sg00000267645 | ac105052.3-201 | 7 | 102637049 | 102671641 | - | mRNA | nonsense_mediated_decay |
| 183580 | enst00000624140 | sg00000279168 | ac105052.4-202 | 7 | 102672879 | 102678856 | - | lnc_RNA | lncrna |
| 184019 | enst00000639209 | sg00000279168 | ac105052.4-201 | 7 | 102579104 | 102679295 | - | lnc_RNA | lncrna |
| 195193 | enst00000460726 | sg00000233297 | rasa4dp-201 | 7 | 102681836 | 102690469 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -201037 | enst00000581001 | sg00000264675 | mir4285-201 | 7 | 102293103 | 102293187 | + | miRNA | mirna |
| -207252 | enst00000444095 | sg00000160999 | sh2b2-201 | 7 | 102286888 | 102301279 | + | mRNA | protein_coding |
| -208985 | enst00000536178 | sg00000160999 | sh2b2-202 | 7 | 102285155 | 102321711 | + | mRNA | protein_coding |
| -209049 | enst00000617975 | sg00000160999 | sh2b2-203 | 7 | 102285091 | 102314547 | + | mRNA | nonsense_mediated_decay |
| -219966 | enst00000487284 | sg00000257923 | cux1-209 | 7 | 102274174 | 102283932 | + | lnc_RNA | retained_intron |
| -229161 | enst00000621922 | sg00000278586 | ac005088.1-201 | 7 | 102264706 | 102264979 | - | pseudogenic_transcript | processed_pseudogene |
| 253419 | enst00000664535 | sg00000286830 | ac105052.5-201 | 7 | 102699228 | 102748695 | - | lnc_RNA | lncrna |
| 253695 | enst00000442873 | sg00000222011 | fam185a-205 | 7 | 102748971 | 102809225 | + | mRNA | nonsense_mediated_decay |
| 253695 | enst00000481697 | sg00000222011 | fam185a-206 | 7 | 102748971 | 102779810 | + | lnc_RNA | processed_transcript |
| 253702 | enst00000487807 | sg00000222011 | fam185a-207 | 7 | 102748978 | 102787370 | + | lnc_RNA | processed_transcript |
| 253723 | enst00000413034 | sg00000222011 | fam185a-202 | 7 | 102748999 | 102809225 | + | mRNA | protein_coding |
| 253734 | enst00000420217 | sg00000222011 | fam185a-204 | 7 | 102749010 | 102809224 | + | mRNA | nonsense_mediated_decay |
| 253752 | enst00000409231 | sg00000222011 | fam185a-201 | 7 | 102749028 | 102808840 | + | mRNA | protein_coding |
| 253761 | enst00000418198 | sg00000222011 | fam185a-203 | 7 | 102749037 | 102757876 | + | mRNA | protein_coding |
| 254166 | enst00000496790 | sg00000222011 | fam185a-208 | 7 | 102749442 | 102755399 | + | lnc_RNA | processed_transcript |
| 259870 | enst00000434317 | sg00000213385 | ac105052.2-201 | 7 | 102755146 | 102755939 | + | pseudogenic_transcript | processed_pseudogene |
| -299976 | enst00000517015 | sg00000252824 | ac005086.1-201 | 7 | 102194076 | 102194164 | - | snoRNA | snorna |
| -305312 | enst00000624939 | sg00000279724 | ac005086.3-201 | 7 | 102188599 | 102188828 | - | pseudogenic_transcript | pseudogene |
| -307101 | enst00000624984 | sg00000280004 | ac005086.4-201 | 7 | 102186819 | 102187039 | - | pseudogenic_transcript | pseudogene |
| 320995 | enst00000480422 | sg00000161040 | fbxl13-212 | 7 | 102813238 | 102816271 | - | lnc_RNA | processed_transcript |
| -332803 | enst00000623065 | sg00000280404 | ac005086.5-201 | 7 | 102161120 | 102161337 | - | pseudogenic_transcript | pseudogene |
| 339329 | enst00000516834 | sg00000252643 | rnu6-1136p-201 | 7 | 102834605 | 102834708 | + | snRNA | snrna |
| -339677 | enst00000566572 | sg00000261535 | ac005086.2-201 | 7 | 102153355 | 102154463 | - | lnc_RNA | lncrna |
| 362174 | enst00000459286 | sg00000238324 | rn7skp198-201 | 7 | 102857450 | 102857755 | + | ncRNA | misc_rna |
| -389703 | enst00000485792 | sg00000257923 | cux1-208 | 7 | 102104437 | 102115670 | + | lnc_RNA | retained_intron |
| -396662 | enst00000465461 | sg00000257923 | cux1-207 | 7 | 102097478 | 102125778 | + | mRNA | protein_coding |
| 417724 | enst00000498487 | sg00000128606 | lrrc17-205 | 7 | 102913000 | 102933450 | + | lnc_RNA | processed_transcript |
| 417724 | enst00000339431 | sg00000128606 | lrrc17-202 | 7 | 102913000 | 102945111 | + | mRNA | protein_coding |
| 417729 | enst00000249377 | sg00000128606 | lrrc17-201 | 7 | 102913005 | 102944949 | + | mRNA | protein_coding |
| 437954 | enst00000455453 | sg00000128606 | lrrc17-203 | 7 | 102933230 | 102934226 | + | mRNA | protein_coding |
| 438459 | enst00000468216 | sg00000161040 | fbxl13-209 | 7 | 102926283 | 102933735 | - | lnc_RNA | processed_transcript |
| 440908 | enst00000485478 | sg00000128606 | lrrc17-204 | 7 | 102936184 | 102944670 | + | lnc_RNA | processed_transcript |
| 477943 | enst00000477915 | sg00000161040 | fbxl13-211 | 7 | 102883572 | 102973219 | - | lnc_RNA | processed_transcript |
| 478246 | enst00000420058 | sg00000230257 | nfe4-201 | 7 | 102973522 | 102988856 | + | lnc_RNA | processed_transcript |
| 478281 | enst00000652215 | sg00000230257 | nfe4-202 | 7 | 102973557 | 102976215 | + | mRNA | protein_coding |
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