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
#130 17 74356576 74357824 1248 3 39 2.1207e-16 1.62234e-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
4044 enst00000375366 sg00000204347 btbd17-201 17 74356416 74361868 - mRNA protein_coding
-7986 enst00000549637 sg00000196169 kif19-204 17 74348590 74350481 + lnc_RNA retained_intron
9583 enst00000582579 sg00000257008 gpr142-202 17 74367407 74372622 + mRNA nonsense_mediated_decay
9634 enst00000585308 sg00000257008 gpr142-203 17 74367458 74371840 + mRNA nonsense_mediated_decay
9634 enst00000335666 sg00000257008 gpr142-201 17 74367458 74372600 + mRNA protein_coding
-30319 enst00000547389 sg00000196169 kif19-203 17 74326257 74351319 + lnc_RNA retained_intron
-30345 enst00000359939 sg00000196169 kif19-201 17 74326231 74351345 + lnc_RNA retained_intron
-30350 enst00000551017 sg00000196169 kif19-205 17 74326226 74329466 + lnc_RNA retained_intron
-30350 enst00000389916 sg00000196169 kif19-202 17 74326226 74355820 + mRNA protein_coding
-30366 enst00000551294 sg00000196169 kif19-206 17 74326210 74352326 + mRNA protein_coding
-42732 enst00000579312 sg00000171595 dnai2-204 17 74313844 74314880 + lnc_RNA retained_intron
-46786 enst00000585167 sg00000266106 ac103809.1-201 17 74307210 74309790 - lnc_RNA lncrna
59880 enst00000363151 sg00000200021 rna5sp448-201 17 74417594 74417704 - pseudogenic_transcript rrna_pseudogene
67027 enst00000582444 sg00000170412 gprc5c-209 17 74424851 74440212 + mRNA protein_coding
73560 enst00000342648 sg00000170412 gprc5c-201 17 74431384 74447429 + mRNA protein_coding
73704 enst00000652232 sg00000170412 gprc5c-212 17 74431528 74447427 + mRNA protein_coding
73704 enst00000481232 sg00000170412 gprc5c-205 17 74431528 74447429 + mRNA protein_coding
74264 enst00000392627 sg00000170412 gprc5c-202 17 74432088 74447429 + mRNA protein_coding
74292 enst00000392628 sg00000170412 gprc5c-203 17 74432116 74449509 + mRNA protein_coding
74309 enst00000582473 sg00000170412 gprc5c-210 17 74432133 74439937 + mRNA protein_coding
-75064 enst00000446837 sg00000171595 dnai2-202 17 74281512 74314883 + mRNA protein_coding
-75064 enst00000579490 sg00000171595 dnai2-205 17 74281512 74314884 + mRNA protein_coding
75873 enst00000392629 sg00000170412 gprc5c-204 17 74433697 74447028 + mRNA protein_coding
75873 enst00000652294 sg00000170412 gprc5c-213 17 74433697 74447427 + mRNA protein_coding
82072 enst00000581590 sg00000170412 gprc5c-208 17 74439896 74451653 + mRNA protein_coding
-82320 enst00000579055 sg00000171595 dnai2-203 17 74274256 74314884 + mRNA nonsense_mediated_decay
-82329 enst00000582036 sg00000171595 dnai2-206 17 74274247 74314884 + mRNA protein_coding
-82342 enst00000311014 sg00000171595 dnai2-201 17 74274234 74314884 + mRNA protein_coding
85253 enst00000582873 sg00000170412 gprc5c-211 17 74443077 74447088 + lnc_RNA processed_transcript
85261 enst00000482723 sg00000170412 gprc5c-206 17 74443085 74450580 + lnc_RNA retained_intron
87380 enst00000577663 sg00000170412 gprc5c-207 17 74445204 74447427 + lnc_RNA retained_intron
-94556 enst00000583018 sg00000264272 ac100786.2-201 17 74256896 74262020 - lnc_RNA lncrna
-106619 enst00000526858 sg00000141540 ttyh2-203 17 74249957 74260206 + mRNA nonsense_mediated_decay
-107211 enst00000534039 sg00000141540 ttyh2-207 17 74249365 74250730 + lnc_RNA retained_intron
-107252 enst00000528152 sg00000141540 ttyh2-205 17 74249324 74253246 + lnc_RNA retained_intron
108575 enst00000648095 sg00000167851 cd300a-207 17 74466399 74484794 + mRNA protein_coding
-108618 enst00000441391 sg00000141540 ttyh2-202 17 74247958 74262016 + mRNA protein_coding
108810 enst00000360141 sg00000167851 cd300a-202 17 74466634 74484794 + mRNA protein_coding
108834 enst00000392625 sg00000167851 cd300a-204 17 74466658 74484790 + mRNA protein_coding
108851 enst00000310828 sg00000167851 cd300a-201 17 74466675 74484167 + mRNA protein_coding
108851 enst00000361933 sg00000167851 cd300a-203 17 74466675 74484167 + mRNA protein_coding
108852 enst00000582319 sg00000167851 cd300a-206 17 74466676 74484168 + lnc_RNA retained_intron
109038 enst00000577511 sg00000167851 cd300a-205 17 74466862 74484296 + mRNA protein_coding
-113202 enst00000528128 sg00000141540 ttyh2-204 17 74243374 74252288 + mRNA nonsense_mediated_decay
-115776 enst00000534346 sg00000141540 ttyh2-208 17 74240800 74250014 + lnc_RNA processed_transcript
-133932 enst00000578825 sg00000141540 ttyh2-209 17 74222644 74244073 + lnc_RNA retained_intron
-140960 enst00000529107 sg00000141540 ttyh2-206 17 74215616 74260651 + mRNA protein_coding
-143005 enst00000269346 sg00000141540 ttyh2-201 17 74213571 74262020 + mRNA protein_coding
-143234 enst00000532794 sg00000246731 ac100786.1-202 17 74211486 74213342 - lnc_RNA lncrna
-143234 enst00000670574 sg00000246731 ac100786.1-205 17 74210012 74213342 - lnc_RNA lncrna
-143234 enst00000662857 sg00000246731 ac100786.1-204 17 74210012 74213342 - lnc_RNA lncrna
-143255 enst00000499670 sg00000246731 ac100786.1-201 17 74209980 74213321 - lnc_RNA lncrna
-143268 enst00000531617 sg00000246731 ac100786.1-203 17 74212674 74213308 - lnc_RNA lncrna
-152872 enst00000528433 sg00000172809 rpl38-203 17 74203704 74204190 + mRNA protein_coding
-152872 enst00000533498 sg00000172809 rpl38-206 17 74203704 74209896 + mRNA protein_coding
-152882 enst00000534490 sg00000172809 rpl38-207 17 74203694 74209461 + mRNA protein_coding
-152883 enst00000584577 sg00000172809 rpl38-208 17 74203693 74209878 + mRNA protein_coding
-152898 enst00000311111 sg00000172809 rpl38-201 17 74203678 74210655 + mRNA protein_coding
-152901 enst00000529123 sg00000172809 rpl38-204 17 74203675 74204593 + lnc_RNA retained_intron
-152914 enst00000530646 sg00000172809 rpl38-205 17 74203662 74206283 + lnc_RNA retained_intron
-152994 enst00000439590 sg00000172809 rpl38-202 17 74203582 74209880 + mRNA protein_coding
173650 enst00000314401 sg00000178789 cd300lb-201 17 74523153 74531474 - mRNA protein_coding
173651 enst00000392621 sg00000178789 cd300lb-202 17 74521174 74531475 - mRNA protein_coding
188291 enst00000330793 sg00000167850 cd300c-201 17 74541073 74546115 - mRNA protein_coding
194913 enst00000430386 sg00000236770 ac079325.1-201 17 74549399 74552737 - pseudogenic_transcript unprocessed_pseudogene
-202364 enst00000584003 sg00000266357 linc02074-202 17 74064357 74154212 - lnc_RNA lncrna
209519 enst00000641710 sg00000284690 cd300h-202 17 74560701 74567343 - mRNA polymorphic_pseudogene
209519 enst00000651677 sg00000284690 cd300h-203 17 74560701 74567343 - mRNA protein_coding
209519 enst00000641031 sg00000284690 cd300h-201 17 74560781 74567343 - mRNA polymorphic_pseudogene
209519 enst00000651881 sg00000284690 cd300h-204 17 74560781 74567343 - mRNA protein_coding
226855 enst00000524389 sg00000182352 c17orf77-203 17 74584679 74592161 + lnc_RNA lncrna
227094 enst00000392620 sg00000182352 c17orf77-202 17 74584918 74594209 + lnc_RNA lncrna
232678 enst00000328023 sg00000182352 c17orf77-201 17 74590502 74594209 + lnc_RNA lncrna
234459 enst00000375352 sg00000204345 cd300ld-201 17 74579365 74592283 - mRNA protein_coding
242016 enst00000581412 sg00000261222 ac064805.1-201 17 74599840 74604269 + lnc_RNA lncrna
-243674 enst00000653467 sg00000266357 linc02074-203 17 74062113 74112902 - lnc_RNA lncrna
-243674 enst00000668167 sg00000266357 linc02074-206 17 74062111 74112902 - lnc_RNA lncrna
-243674 enst00000654301 sg00000266357 linc02074-204 17 74062111 74112902 - lnc_RNA lncrna
-243674 enst00000666198 sg00000266357 linc02074-205 17 74063894 74112902 - lnc_RNA lncrna
-243677 enst00000581028 sg00000266357 linc02074-201 17 74043452 74112899 - lnc_RNA lncrna
245913 enst00000569279 sg00000261222 ac064805.1-202 17 74603737 74607229 + lnc_RNA lncrna
247157 enst00000577560 sg00000261222 ac064805.1-203 17 74604981 74607229 + lnc_RNA lncrna
261523 enst00000412268 sg00000186407 cd300e-202 17 74617147 74619347 - mRNA protein_coding
265914 enst00000392619 sg00000186407 cd300e-201 17 74609885 74623738 - mRNA protein_coding
312754 enst00000340415 sg00000172794 rab37-201 17 74670578 74747334 + mRNA protein_coding
313317 enst00000402449 sg00000172794 rab37-208 17 74671141 74745874 + mRNA protein_coding
313356 enst00000392617 sg00000172794 rab37-207 17 74671180 74747335 + lnc_RNA retained_intron
319776 enst00000582959 sg00000264659 ac064805.2-203 17 74672712 74677600 - lnc_RNA lncrna
319796 enst00000665064 sg00000264659 ac064805.2-201 17 74670077 74677620 - lnc_RNA lncrna
319800 enst00000663016 sg00000264659 ac064805.2-202 17 74670077 74677624 - lnc_RNA lncrna
347431 enst00000581500 sg00000186074 cd300lf-208 17 74695753 74705255 - mRNA protein_coding
347431 enst00000361254 sg00000186074 cd300lf-204 17 74694311 74705255 - mRNA protein_coding
347431 enst00000343125 sg00000186074 cd300lf-203 17 74694311 74705255 - mRNA protein_coding
347486 enst00000464910 sg00000186074 cd300lf-206 17 74695037 74705310 - mRNA protein_coding
347486 enst00000462044 sg00000186074 cd300lf-205 17 74695037 74705310 - mRNA nonsense_mediated_decay
355099 enst00000326165 sg00000186074 cd300lf-202 17 74694317 74712923 - mRNA protein_coding
355101 enst00000583544 sg00000186074 cd300lf-209 17 74704352 74712925 - lnc_RNA retained_intron
355117 enst00000583937 sg00000186074 cd300lf-210 17 74694814 74712941 - mRNA protein_coding
355130 enst00000301573 sg00000186074 cd300lf-201 17 74694318 74712954 - mRNA protein_coding
355154 enst00000469092 sg00000186074 cd300lf-207 17 74694317 74712978 - mRNA protein_coding
378774 enst00000528438 sg00000172794 rab37-212 17 74736598 74746192 + mRNA protein_coding
378996 enst00000392615 sg00000172794 rab37-206 17 74736820 74747300 + mRNA protein_coding
379093 enst00000392614 sg00000172794 rab37-205 17 74736917 74747335 + mRNA protein_coding
379395 enst00000533530 sg00000172794 rab37-214 17 74737219 74744465 + lnc_RNA retained_intron
379397 enst00000527040 sg00000172794 rab37-211 17 74737221 74744559 + lnc_RNA retained_intron
379397 enst00000577548 sg00000172794 rab37-215 17 74737221 74745028 + lnc_RNA retained_intron
379406 enst00000392612 sg00000172794 rab37-203 17 74737230 74747335 + mRNA protein_coding
379408 enst00000392610 sg00000172794 rab37-202 17 74737232 74747335 + mRNA protein_coding
379432 enst00000392613 sg00000172794 rab37-204 17 74737256 74747335 + mRNA protein_coding
379447 enst00000613645 sg00000172794 rab37-216 17 74737271 74747334 + mRNA protein_coding
379447 enst00000481224 sg00000172794 rab37-209 17 74737271 74747335 + mRNA nonsense_mediated_decay
387017 enst00000488977 sg00000172794 rab37-210 17 74744841 74747334 + lnc_RNA retained_intron
387034 enst00000531420 sg00000172794 rab37-213 17 74744858 74745794 + lnc_RNA retained_intron
390789 enst00000581999 sg00000284186 mir3615-201 17 74748613 74748699 + miRNA mirna
390804 enst00000262613 sg00000109062 slc9a3r1-201 17 74748628 74769353 + mRNA protein_coding
390828 enst00000583369 sg00000109062 slc9a3r1-205 17 74748652 74768582 + mRNA protein_coding
391088 enst00000585285 sg00000266036 ac016888.1-201 17 74747319 74748912 - lnc_RNA lncrna
404179 enst00000413388 sg00000109062 slc9a3r1-202 17 74762003 74769296 + mRNA protein_coding
405206 enst00000578958 sg00000109062 slc9a3r1-203 17 74763030 74768559 + lnc_RNA retained_intron
405604 enst00000581356 sg00000109062 slc9a3r1-204 17 74763428 74768803 + mRNA nonsense_mediated_decay
-406670 enst00000647802 sg00000285648 ac137735.2-201 17 73926421 73949906 - lnc_RNA lncrna
414645 enst00000581762 sg00000109065 nat9-215 17 74771625 74772469 - lnc_RNA retained_intron
416275 enst00000581466 sg00000109065 nat9-214 17 74772272 74774099 - mRNA protein_coding
417883 enst00000580632 sg00000109065 nat9-211 17 74771558 74775707 - mRNA protein_coding
418269 enst00000578947 sg00000109065 nat9-206 17 74772903 74776093 - mRNA protein_coding
418304 enst00000581451 sg00000109065 nat9-213 17 74773609 74776128 - mRNA protein_coding
418474 enst00000578822 sg00000109065 nat9-204 17 74771695 74776298 - mRNA protein_coding
418480 enst00000580216 sg00000109065 nat9-209 17 74772238 74776304 - lnc_RNA processed_transcript
418499 enst00000582870 sg00000109065 nat9-220 17 74771660 74776323 - mRNA protein_coding
418499 enst00000582359 sg00000109065 nat9-218 17 74772673 74776323 - lnc_RNA retained_intron
418499 enst00000583834 sg00000109065 nat9-225 17 74770581 74776323 - lnc_RNA retained_intron
418500 enst00000581136 sg00000109065 nat9-212 17 74771389 74776324 - mRNA protein_coding
418507 enst00000584022 sg00000109065 nat9-227 17 74771691 74776331 - mRNA nonsense_mediated_decay
418507 enst00000579218 sg00000109065 nat9-207 17 74771794 74776331 - mRNA protein_coding
418512 enst00000579837 sg00000109065 nat9-208 17 74775360 74776336 - lnc_RNA retained_intron
418513 enst00000578862 sg00000109065 nat9-205 17 74772175 74776337 - lnc_RNA retained_intron
418513 enst00000583476 sg00000109065 nat9-222 17 74771768 74776337 - mRNA protein_coding
418515 enst00000580301 sg00000109065 nat9-210 17 74770567 74776339 - mRNA protein_coding
418518 enst00000583757 sg00000109065 nat9-224 17 74771728 74776342 - mRNA protein_coding
418521 enst00000357814 sg00000109065 nat9-201 17 74770529 74776345 - mRNA protein_coding
418521 enst00000583989 sg00000109065 nat9-226 17 74772266 74776345 - lnc_RNA processed_transcript
418521 enst00000582118 sg00000109065 nat9-216 17 74773354 74776345 - lnc_RNA retained_intron
418521 enst00000585240 sg00000109065 nat9-229 17 74772442 74776345 - lnc_RNA processed_transcript
418527 enst00000578798 sg00000109065 nat9-203 17 74772031 74776351 - lnc_RNA retained_intron
418527 enst00000582168 sg00000109065 nat9-217 17 74772994 74776351 - lnc_RNA retained_intron
418537 enst00000577428 sg00000109065 nat9-202 17 74772275 74776361 - lnc_RNA processed_transcript
418541 enst00000582524 sg00000109065 nat9-219 17 74771764 74776365 - mRNA protein_coding
418543 enst00000582993 sg00000109065 nat9-221 17 74773311 74776367 - lnc_RNA retained_intron
418543 enst00000583689 sg00000109065 nat9-223 17 74772777 74776367 - lnc_RNA retained_intron
418543 enst00000584409 sg00000109065 nat9-228 17 74772295 74776367 - lnc_RNA processed_transcript
418675 enst00000417024 sg00000109066 tmem104-202 17 74776499 74839752 + mRNA protein_coding
418675 enst00000335464 sg00000109066 tmem104-201 17 74776499 74839753 + mRNA protein_coding
418676 enst00000582773 sg00000109066 tmem104-205 17 74776500 74839751 + mRNA protein_coding
418676 enst00000578764 sg00000109066 tmem104-203 17 74776500 74795589 + mRNA protein_coding
418685 enst00000584246 sg00000109066 tmem104-207 17 74776509 74785680 + lnc_RNA retained_intron
418696 enst00000582330 sg00000109066 tmem104-204 17 74776520 74839750 + mRNA protein_coding
-444386 enst00000659097 sg00000288006 ac137735.3-201 17 73912190 73931436 + lnc_RNA lncrna
-444698 enst00000581911 sg00000266765 ac137735.1-201 17 73894749 73911878 - lnc_RNA lncrna
479275 enst00000584171 sg00000109066 tmem104-206 17 74837099 74837908 + lnc_RNA processed_transcript

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