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
#143 7 102593401 102594445 1044 3 35 6.26155e-16 4.35463e-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 enst00000522223 sg00000105808 rasa4-213 7 102582350 102593991 - lnc_RNA retained_intron
15 enst00000520577 sg00000105808 rasa4-208 7 102593714 102594460 - lnc_RNA retained_intron
-957 enst00000514917 sg00000270249 ac093668.1-201 7 102541501 102592444 - mRNA protein_coding
-1078 enst00000521822 sg00000105808 rasa4-211 7 102587447 102592323 - lnc_RNA processed_transcript
1292 enst00000521397 sg00000105808 rasa4-210 7 102592351 102595737 - mRNA protein_coding
7951 enst00000519539 sg00000105808 rasa4-205 7 102595302 102602396 - mRNA nonsense_mediated_decay
11732 enst00000519878 sg00000105808 rasa4-206 7 102599860 102606177 - lnc_RNA retained_intron
-13605 enst00000538869 sg00000105808 rasa4-217 7 102573807 102579796 - mRNA protein_coding
17146 enst00000461209 sg00000105808 rasa4-203 7 102582323 102611591 - mRNA protein_coding
17697 enst00000520042 sg00000105808 rasa4-207 7 102602324 102612142 - mRNA protein_coding
-20748 enst00000513506 sg00000168255 polr2j3-212 7 102540024 102572653 - mRNA protein_coding
-20752 enst00000486319 sg00000168255 polr2j3-203 7 102537920 102572649 - mRNA nonsense_mediated_decay
-20818 enst00000513438 sg00000285437 polr2j3-218 7 102569200 102572583 - mRNA protein_coding
-20818 enst00000608621 sg00000285437 polr2j3-219 7 102562133 102572583 - mRNA nonsense_mediated_decay
-20818 enst00000507355 sg00000168255 polr2j3-209 7 102543568 102572583 - mRNA nonsense_mediated_decay
-20818 enst00000511313 sg00000285437 polr2j3-217 7 102562656 102572583 - mRNA protein_coding
-20818 enst00000443430 sg00000285437 polr2j3-213 7 102567484 102572583 - lnc_RNA processed_transcript
-20821 enst00000613744 sg00000285437 polr2j3-220 7 102566288 102572580 - mRNA protein_coding
-20821 enst00000504101 sg00000285437 polr2j3-214 7 102569305 102572580 - lnc_RNA retained_intron
-20834 enst00000489144 sg00000168255 polr2j3-204 7 102537918 102572567 - mRNA nonsense_mediated_decay
-20841 enst00000504157 sg00000285437 polr2j3-215 7 102565976 102572560 - lnc_RNA processed_transcript
-20841 enst00000464525 sg00000168255 polr2j3-202 7 102537918 102572560 - mRNA nonsense_mediated_decay
-20846 enst00000508910 sg00000285437 polr2j3-216 7 102566627 102572555 - lnc_RNA processed_transcript
-20848 enst00000508848 sg00000168255 polr2j3-210 7 102540024 102572553 - mRNA nonsense_mediated_decay
-20862 enst00000379340 sg00000168255 polr2j3-201 7 102537919 102572539 - mRNA nonsense_mediated_decay
-20880 enst00000621093 sg00000285437 polr2j3-221 7 102567051 102572521 - mRNA protein_coding
-20880 enst00000506060 sg00000168255 polr2j3-208 7 102541104 102572521 - lnc_RNA processed_transcript
-20931 enst00000502415 sg00000168255 polr2j3-205 7 102541151 102572470 - lnc_RNA processed_transcript
22247 enst00000521076 sg00000105808 rasa4-209 7 102602324 102616692 - mRNA protein_coding
22284 enst00000462172 sg00000105808 rasa4-204 7 102582691 102616729 - mRNA protein_coding
22293 enst00000522801 sg00000105808 rasa4-215 7 102595665 102616738 - mRNA protein_coding
22301 enst00000522443 sg00000105808 rasa4-214 7 102608558 102616746 - lnc_RNA retained_intron
22311 enst00000449970 sg00000105808 rasa4-202 7 102582325 102616756 - mRNA protein_coding
22311 enst00000521892 sg00000105808 rasa4-212 7 102609075 102616756 - lnc_RNA retained_intron
22311 enst00000523568 sg00000105808 rasa4-216 7 102587342 102616756 - lnc_RNA retained_intron
22312 enst00000262940 sg00000105808 rasa4-201 7 102579646 102616757 - mRNA protein_coding
-26331 enst00000511773 sg00000168255 polr2j3-211 7 102539676 102567070 - lnc_RNA processed_transcript
-26743 enst00000504677 sg00000168255 polr2j3-207 7 102540059 102566658 - lnc_RNA processed_transcript
-26772 enst00000503564 sg00000168255 polr2j3-206 7 102538341 102566629 - lnc_RNA processed_transcript
-37592 enst00000341656 sg00000205238 spdye2-201 7 102555809 102562308 + mRNA protein_coding
-40145 enst00000432940 sg00000205238 spdye2-202 7 102553256 102561175 + mRNA protein_coding
-42169 enst00000507918 sg00000205238 spdye2-203 7 102551232 102562069 + mRNA protein_coding
48346 enst00000340457 sg00000267368 upk3bl1-201 7 102637025 102642791 - mRNA protein_coding
48424 enst00000519541 sg00000205236 ac105052.1-201 7 102582523 102642869 - mRNA nonsense_mediated_decay
-49552 enst00000644544 sg00000284981 upk3bl2-201 7 102538417 102543849 - mRNA protein_coding
55880 enst00000507450 sg00000173678 spdye2b-203 7 102650325 102661159 + mRNA protein_coding
57904 enst00000436228 sg00000173678 spdye2b-201 7 102652349 102660265 + mRNA protein_coding
60448 enst00000455020 sg00000173678 spdye2b-202 7 102654893 102661398 + mRNA protein_coding
-75620 enst00000465829 sg00000170667 rasa4b-202 7 102483144 102517781 - mRNA protein_coding
-75624 enst00000541662 sg00000170667 rasa4b-207 7 102483139 102517777 - mRNA protein_coding
-75646 enst00000306682 sg00000170667 rasa4b-201 7 102483562 102517755 - mRNA protein_coding
77156 enst00000333432 sg00000228049 polr2j2-201 7 102666131 102671601 - mRNA protein_coding
77184 enst00000358438 sg00000228049 polr2j2-202 7 102665368 102671629 - mRNA protein_coding
77196 enst00000476151 sg00000267645 ac105052.3-201 7 102637049 102671641 - mRNA nonsense_mediated_decay
84411 enst00000624140 sg00000279168 ac105052.4-202 7 102672879 102678856 - lnc_RNA lncrna
84850 enst00000639209 sg00000279168 ac105052.4-201 7 102579104 102679295 - lnc_RNA lncrna
96024 enst00000460726 sg00000233297 rasa4dp-201 7 102681836 102690469 - pseudogenic_transcript unprocessed_pseudogene
-98533 enst00000488284 sg00000170667 rasa4b-205 7 102483144 102494868 - lnc_RNA retained_intron
-98579 enst00000495352 sg00000170667 rasa4b-206 7 102483171 102494822 - lnc_RNA retained_intron
-100090 enst00000477184 sg00000170667 rasa4b-204 7 102482445 102493311 - lnc_RNA retained_intron
-100090 enst00000467351 sg00000170667 rasa4b-203 7 102483484 102493311 - lnc_RNA retained_intron
-114494 enst00000292614 sg00000005075 polr2j-201 7 102473118 102478907 - mRNA protein_coding
-114495 enst00000393794 sg00000005075 polr2j-202 7 102473938 102478906 - mRNA protein_coding
-121932 enst00000578629 sg00000284596 mir4467-201 7 102471469 102471531 + miRNA mirna
-123812 enst00000468175 sg00000161036 lrwd1-204 7 102469589 102473168 + mRNA protein_coding
-126059 enst00000485417 sg00000161036 lrwd1-207 7 102467342 102468445 + lnc_RNA retained_intron
-127659 enst00000582533 sg00000284176 mir5090-201 7 102465742 102465826 + miRNA mirna
-128249 enst00000485808 sg00000161036 lrwd1-208 7 102465152 102468559 + mRNA nonsense_mediated_decay
-128306 enst00000476270 sg00000161036 lrwd1-206 7 102465095 102466270 + mRNA nonsense_mediated_decay
-128320 enst00000626402 sg00000161036 lrwd1-209 7 102465081 102465589 + mRNA protein_coding
-128378 enst00000473880 sg00000161036 lrwd1-205 7 102465023 102473166 + lnc_RNA retained_intron
-128400 enst00000464107 sg00000161036 lrwd1-203 7 102465001 102467376 + mRNA nonsense_mediated_decay
-128417 enst00000292616 sg00000161036 lrwd1-201 7 102464984 102473168 + mRNA protein_coding
-128445 enst00000463739 sg00000161036 lrwd1-202 7 102464956 102468377 + mRNA protein_coding
-128538 enst00000490528 sg00000160993 alkbh4-202 7 102456834 102464863 - mRNA nonsense_mediated_decay
-128538 enst00000292566 sg00000160993 alkbh4-201 7 102456238 102464863 - mRNA protein_coding
-128544 enst00000498283 sg00000160993 alkbh4-203 7 102459397 102464857 - lnc_RNA retained_intron
154250 enst00000664535 sg00000286830 ac105052.5-201 7 102699228 102748695 - lnc_RNA lncrna
154526 enst00000442873 sg00000222011 fam185a-205 7 102748971 102809225 + mRNA nonsense_mediated_decay
154526 enst00000481697 sg00000222011 fam185a-206 7 102748971 102779810 + lnc_RNA processed_transcript
154533 enst00000487807 sg00000222011 fam185a-207 7 102748978 102787370 + lnc_RNA processed_transcript
154554 enst00000413034 sg00000222011 fam185a-202 7 102748999 102809225 + mRNA protein_coding
154565 enst00000420217 sg00000222011 fam185a-204 7 102749010 102809224 + mRNA nonsense_mediated_decay
154583 enst00000409231 sg00000222011 fam185a-201 7 102749028 102808840 + mRNA protein_coding
154592 enst00000418198 sg00000222011 fam185a-203 7 102749037 102757876 + mRNA protein_coding
154997 enst00000496790 sg00000222011 fam185a-208 7 102749442 102755399 + lnc_RNA processed_transcript
-157102 enst00000473939 sg00000160991 orai2-204 7 102436299 102448732 + mRNA protein_coding
-157241 enst00000498661 sg00000160991 orai2-209 7 102436160 102446579 + mRNA protein_coding
-158621 enst00000468165 sg00000239480 ac073517.1-201 7 102426818 102434780 - lnc_RNA lncrna
-159825 enst00000403646 sg00000160991 orai2-202 7 102433576 102448716 + mRNA protein_coding
-159825 enst00000468241 sg00000160991 orai2-203 7 102433576 102446924 + mRNA protein_coding
-159826 enst00000495936 sg00000160991 orai2-208 7 102433575 102456825 + mRNA protein_coding
-159831 enst00000478730 sg00000160991 orai2-205 7 102433570 102451609 + mRNA protein_coding
-159852 enst00000488996 sg00000160991 orai2-207 7 102433549 102447048 + lnc_RNA processed_transcript
-159871 enst00000611770 sg00000160991 orai2-210 7 102433530 102456821 + mRNA protein_coding
-159871 enst00000356387 sg00000160991 orai2-201 7 102433530 102456821 + mRNA protein_coding
-160295 enst00000482237 sg00000160991 orai2-206 7 102433106 102439047 + mRNA protein_coding
160701 enst00000434317 sg00000213385 ac105052.2-201 7 102755146 102755939 + pseudogenic_transcript processed_pseudogene
-187546 enst00000408583 sg00000221510 mir548o-201 7 102405742 102405855 - miRNA mirna
-189044 enst00000468316 sg00000128563 prkrip1-203 7 102404357 102426666 + lnc_RNA retained_intron
-197038 enst00000397912 sg00000128563 prkrip1-201 7 102396363 102426666 + mRNA protein_coding
-210664 enst00000426478 sg00000239486 ac091390.4-201 7 102380465 102382737 - pseudogenic_transcript unprocessed_pseudogene
-217182 enst00000462601 sg00000128563 prkrip1-202 7 102376219 102425541 + mRNA protein_coding
221826 enst00000480422 sg00000161040 fbxl13-212 7 102813238 102816271 - lnc_RNA processed_transcript
-227359 enst00000482465 sg00000128563 prkrip1-206 7 102366042 102426666 + lnc_RNA processed_transcript
-229103 enst00000492837 sg00000239969 ac091390.5-203 7 102364298 102380631 + lnc_RNA processed_transcript
-229233 enst00000476426 sg00000239969 ac091390.5-202 7 102364168 102376318 + pseudogenic_transcript transcribed_unprocessed_pseudogene
-229239 enst00000484974 sg00000239969 ac091390.5-201 7 102364162 102380633 + lnc_RNA processed_transcript
-229504 enst00000496391 sg00000128563 prkrip1-208 7 102363897 102426676 + mRNA protein_coding
-229506 enst00000482549 sg00000128563 prkrip1-207 7 102363895 102425449 + lnc_RNA processed_transcript
-229507 enst00000469763 sg00000128563 prkrip1-204 7 102363894 102425446 + lnc_RNA processed_transcript
-229529 enst00000477886 sg00000128563 prkrip1-205 7 102363872 102404625 + lnc_RNA processed_transcript
-236957 enst00000563237 sg00000260097 spdye6-201 7 102345746 102356444 - mRNA protein_coding
240160 enst00000516834 sg00000252643 rnu6-1136p-201 7 102834605 102834708 + snRNA snrna
-256085 enst00000432573 sg00000228546 ac091390.3-201 7 102337316 102339115 + pseudogenic_transcript unprocessed_pseudogene
-256532 enst00000363682 sg00000200552 ac091390.2-201 7 102336869 102336970 + ncRNA misc_rna
263005 enst00000459286 sg00000238324 rn7skp198-201 7 102857450 102857755 + ncRNA misc_rna
-263871 enst00000433904 sg00000170409 ac091390.1-201 7 102327256 102329530 - pseudogenic_transcript unprocessed_pseudogene
-300298 enst00000581001 sg00000264675 mir4285-201 7 102293103 102293187 + miRNA mirna
-306513 enst00000444095 sg00000160999 sh2b2-201 7 102286888 102301279 + mRNA protein_coding
-308246 enst00000536178 sg00000160999 sh2b2-202 7 102285155 102321711 + mRNA protein_coding
-308310 enst00000617975 sg00000160999 sh2b2-203 7 102285091 102314547 + mRNA nonsense_mediated_decay
318555 enst00000498487 sg00000128606 lrrc17-205 7 102913000 102933450 + lnc_RNA processed_transcript
318555 enst00000339431 sg00000128606 lrrc17-202 7 102913000 102945111 + mRNA protein_coding
318560 enst00000249377 sg00000128606 lrrc17-201 7 102913005 102944949 + mRNA protein_coding
-319227 enst00000487284 sg00000257923 cux1-209 7 102274174 102283932 + lnc_RNA retained_intron
-328422 enst00000621922 sg00000278586 ac005088.1-201 7 102264706 102264979 - pseudogenic_transcript processed_pseudogene
338785 enst00000455453 sg00000128606 lrrc17-203 7 102933230 102934226 + mRNA protein_coding
339290 enst00000468216 sg00000161040 fbxl13-209 7 102926283 102933735 - lnc_RNA processed_transcript
341739 enst00000485478 sg00000128606 lrrc17-204 7 102936184 102944670 + lnc_RNA processed_transcript
378774 enst00000477915 sg00000161040 fbxl13-211 7 102883572 102973219 - lnc_RNA processed_transcript
379077 enst00000420058 sg00000230257 nfe4-201 7 102973522 102988856 + lnc_RNA processed_transcript
379112 enst00000652215 sg00000230257 nfe4-202 7 102973557 102976215 + mRNA protein_coding
-399237 enst00000517015 sg00000252824 ac005086.1-201 7 102194076 102194164 - snoRNA snorna
-404573 enst00000624939 sg00000279724 ac005086.3-201 7 102188599 102188828 - pseudogenic_transcript pseudogene
-406362 enst00000624984 sg00000280004 ac005086.4-201 7 102186819 102187039 - pseudogenic_transcript pseudogene
-432064 enst00000623065 sg00000280404 ac005086.5-201 7 102161120 102161337 - pseudogenic_transcript pseudogene
435659 enst00000447336 sg00000236226 ac073127.1-201 7 103030104 103031354 + lnc_RNA lncrna
-438938 enst00000566572 sg00000261535 ac005086.2-201 7 102153355 102154463 - lnc_RNA lncrna
455614 enst00000436908 sg00000161040 fbxl13-204 7 102813233 103050059 - mRNA protein_coding
480123 enst00000313221 sg00000161040 fbxl13-201 7 102813233 103074568 - mRNA protein_coding
480280 enst00000455112 sg00000161040 fbxl13-207 7 102813275 103074725 - mRNA protein_coding
480280 enst00000456695 sg00000161040 fbxl13-208 7 102813233 103074725 - mRNA protein_coding
480351 enst00000471074 sg00000161040 fbxl13-210 7 102963538 103074796 - lnc_RNA processed_transcript
480366 enst00000440067 sg00000161040 fbxl13-205 7 103025197 103074811 - mRNA protein_coding
480388 enst00000379305 sg00000161040 fbxl13-202 7 102813230 103074833 - mRNA protein_coding
480394 enst00000448002 sg00000161040 fbxl13-206 7 102813230 103074839 - mRNA nonsense_mediated_decay
480398 enst00000379308 sg00000161040 fbxl13-203 7 102813236 103074843 - mRNA protein_coding
480436 enst00000454559 sg00000170632 armc10-209 7 103074881 103099758 + mRNA protein_coding
480436 enst00000425331 sg00000170632 armc10-204 7 103074881 103099749 + mRNA protein_coding
480436 enst00000541300 sg00000170632 armc10-211 7 103074881 103099749 + mRNA protein_coding
480436 enst00000428183 sg00000170632 armc10-205 7 103074881 103099751 + mRNA protein_coding
480436 enst00000441711 sg00000170632 armc10-208 7 103074881 103099758 + mRNA protein_coding
480481 enst00000323735 sg00000170632 armc10-203 7 103074926 103098863 + mRNA nonsense_mediated_decay
480505 enst00000306450 sg00000170632 armc10-201 7 103074950 103098645 + mRNA nonsense_mediated_decay
480695 enst00000323716 sg00000170632 armc10-202 7 103075140 103099759 + mRNA protein_coding
480723 enst00000434153 sg00000170632 armc10-207 7 103075168 103098437 + mRNA protein_coding
-488964 enst00000485792 sg00000257923 cux1-208 7 102104437 102115670 + lnc_RNA retained_intron
492194 enst00000431642 sg00000170632 armc10-206 7 103086639 103098683 + mRNA protein_coding
495165 enst00000428923 sg00000233025 cryzp1-201 7 103088664 103089610 - pseudogenic_transcript processed_pseudogene
-495923 enst00000465461 sg00000257923 cux1-207 7 102097478 102125778 + 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