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
#42 7 989495 990877 1382 3 54 9.90347e-23 2.345e-20
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
-2838 enst00000415893 sg00000073067 cyp2w1-203 7 986657 988804 + mRNA protein_coding
-3081 enst00000468456 sg00000073067 cyp2w1-205 7 986414 987380 + lnc_RNA retained_intron
-3094 enst00000462453 sg00000073067 cyp2w1-204 7 986401 987275 + lnc_RNA retained_intron
-6137 enst00000340150 sg00000073067 cyp2w1-202 7 983358 989640 + mRNA protein_coding
-6314 enst00000308919 sg00000073067 cyp2w1-201 7 983181 989640 + mRNA protein_coding
-13946 enst00000457254 sg00000240230 cox19-202 7 898778 975549 - mRNA nonsense_mediated_decay
-13946 enst00000344111 sg00000240230 cox19-201 7 964852 975549 - mRNA protein_coding
-13946 enst00000466146 sg00000240230 cox19-203 7 972701 975549 - lnc_RNA retained_intron
-14379 enst00000466853 sg00000240230 cox19-204 7 972942 975116 - lnc_RNA retained_intron
32149 enst00000362153 sg00000199023 mir339-201 7 1022933 1023026 - miRNA mirna
-34088 enst00000539900 sg00000105963 adap1-216 7 897901 955407 - mRNA protein_coding
-34089 enst00000435943 sg00000105963 adap1-202 7 904247 955406 - mRNA protein_coding
-34145 enst00000477906 sg00000105963 adap1-210 7 904187 955350 - lnc_RNA processed_transcript
-34798 enst00000649206 sg00000105963 adap1-219 7 897903 954697 - mRNA protein_coding
-34815 enst00000265846 sg00000105963 adap1-201 7 897900 954680 - mRNA protein_coding
37462 enst00000412051 sg00000146540 c7orf50-204 7 997016 1028339 - mRNA protein_coding
37475 enst00000465681 sg00000146540 c7orf50-206 7 1024502 1028352 - lnc_RNA retained_intron
38148 enst00000418941 sg00000225146 ac073957.1-201 7 1029025 1043891 + lnc_RNA lncrna
-43679 enst00000463358 sg00000105963 adap1-209 7 904152 945816 - lnc_RNA processed_transcript
-43679 enst00000611167 sg00000105963 adap1-217 7 897901 945816 - mRNA protein_coding
53669 enst00000444847 sg00000164849 gpr146-203 7 1044546 1059261 + mRNA protein_coding
53728 enst00000481403 sg00000164849 gpr146-205 7 1044605 1045816 + lnc_RNA processed_transcript
-54315 enst00000454383 sg00000105963 adap1-208 7 900142 935180 - mRNA protein_coding
-61981 enst00000453823 sg00000105963 adap1-207 7 900533 927514 - mRNA protein_coding
-62279 enst00000449296 sg00000105963 adap1-205 7 897901 927216 - mRNA protein_coding
-62279 enst00000446141 sg00000105963 adap1-204 7 897909 927216 - mRNA protein_coding
-62440 enst00000495686 sg00000105963 adap1-214 7 919968 927055 - lnc_RNA retained_intron
64402 enst00000474396 sg00000164849 gpr146-204 7 1055279 1056552 + lnc_RNA processed_transcript
64408 enst00000397095 sg00000164849 gpr146-201 7 1055285 1059261 + mRNA protein_coding
64429 enst00000444428 sg00000146540 c7orf50-205 7 997607 1055306 - mRNA protein_coding
65780 enst00000427680 sg00000164849 gpr146-202 7 1056657 1057631 + mRNA protein_coding
-66157 enst00000488527 sg00000105963 adap1-213 7 904247 923338 - lnc_RNA processed_transcript
68384 enst00000549241 sg00000257607 ac073957.2-201 7 1055360 1059261 - lnc_RNA lncrna
-68606 enst00000437486 sg00000105963 adap1-203 7 899465 920889 - mRNA protein_coding
-68606 enst00000617043 sg00000105963 adap1-218 7 897901 920889 - mRNA protein_coding
83573 enst00000449721 sg00000224079 ac091729.1-201 7 1074450 1078036 + lnc_RNA lncrna
-83879 enst00000478000 sg00000105963 adap1-211 7 897910 905616 - lnc_RNA retained_intron
-84357 enst00000481406 sg00000105963 adap1-212 7 903957 905138 - lnc_RNA retained_intron
-84418 enst00000453175 sg00000105963 adap1-206 7 898917 905077 - mRNA protein_coding
-88096 enst00000495809 sg00000105963 adap1-215 7 897945 901399 - lnc_RNA retained_intron
89986 enst00000415656 sg00000226291 ac091729.2-201 7 1080863 1082178 + lnc_RNA lncrna
91331 enst00000401670 sg00000164850 gper1-204 7 1082208 1092881 + mRNA protein_coding
95930 enst00000413368 sg00000164850 gper1-205 7 1086807 1091949 + mRNA protein_coding
95930 enst00000397092 sg00000164850 gper1-203 7 1086807 1093815 + mRNA protein_coding
95999 enst00000297469 sg00000164850 gper1-201 7 1086876 1093815 + mRNA protein_coding
-97195 enst00000464468 sg00000239857 get4-206 7 892300 895658 + lnc_RNA retained_intron
97236 enst00000397088 sg00000164850 gper1-202 7 1088113 1093810 + mRNA protein_coding
100751 enst00000617001 sg00000164850 gper1-206 7 1091628 1093809 + mRNA protein_coding
-102009 enst00000483469 sg00000239857 get4-207 7 887486 892474 + lnc_RNA retained_intron
102061 enst00000619052 sg00000164850 gper1-207 7 1092938 1093741 + mRNA protein_coding
-102462 enst00000426056 sg00000239857 get4-204 7 887033 891054 + mRNA protein_coding
-102948 enst00000609998 sg00000273151 ac073957.3-201 7 879790 886547 - lnc_RNA lncrna
-105471 enst00000441491 sg00000239857 get4-205 7 884024 887519 + mRNA protein_coding
-105952 enst00000407192 sg00000239857 get4-202 7 883543 896436 + mRNA protein_coding
-111590 enst00000412734 sg00000239857 get4-203 7 877905 891066 + mRNA protein_coding
-112941 enst00000265857 sg00000239857 get4-201 7 876554 896436 + mRNA protein_coding
-121021 enst00000497943 sg00000164828 sun1-235 7 868474 874902 + lnc_RNA retained_intron
136511 enst00000488073 sg00000146540 c7orf50-207 7 997494 1127388 - lnc_RNA processed_transcript
-137248 enst00000475971 sg00000164828 sun1-229 7 852247 874902 + lnc_RNA retained_intron
-137303 enst00000459810 sg00000164828 sun1-223 7 852192 852902 + lnc_RNA retained_intron
-137545 enst00000457861 sg00000164828 sun1-222 7 851950 896435 + mRNA nonsense_mediated_decay
-137945 enst00000463848 sg00000164828 sun1-224 7 851550 852773 + lnc_RNA retained_intron
-138328 enst00000488628 sg00000164828 sun1-233 7 851167 852824 + lnc_RNA retained_intron
-139678 enst00000480475 sg00000164828 sun1-231 7 849817 852878 + lnc_RNA retained_intron
-139694 enst00000464442 sg00000164828 sun1-225 7 849801 852907 + lnc_RNA retained_intron
-140887 enst00000433212 sg00000164828 sun1-213 7 848608 874902 + mRNA protein_coding
-146125 enst00000429178 sg00000164828 sun1-212 7 843370 874899 + mRNA protein_coding
-146154 enst00000419312 sg00000164828 sun1-207 7 843341 851481 + mRNA protein_coding
-146574 enst00000471349 sg00000164828 sun1-228 7 842921 848494 + lnc_RNA retained_intron
147370 enst00000397098 sg00000146540 c7orf50-202 7 997006 1138247 - mRNA protein_coding
147380 enst00000357429 sg00000146540 c7orf50-201 7 996986 1138257 - mRNA protein_coding
147380 enst00000397100 sg00000146540 c7orf50-203 7 996987 1138257 - mRNA protein_coding
147383 enst00000491163 sg00000146540 c7orf50-208 7 997633 1138260 - mRNA protein_coding
-147583 enst00000477950 sg00000164828 sun1-230 7 841912 843669 + lnc_RNA retained_intron
-147679 enst00000493681 sg00000164828 sun1-234 7 841816 848421 + lnc_RNA retained_intron
-150699 enst00000450881 sg00000164828 sun1-218 7 838796 852651 + mRNA protein_coding
-156540 enst00000469755 sg00000164828 sun1-227 7 832955 842073 + lnc_RNA processed_transcript
-156988 enst00000483996 sg00000164828 sun1-232 7 832507 839180 + lnc_RNA retained_intron
-156990 enst00000467483 sg00000164828 sun1-226 7 832505 843834 + lnc_RNA retained_intron
-156990 enst00000425407 sg00000164828 sun1-210 7 832505 874920 + mRNA protein_coding
-156992 enst00000403868 sg00000164828 sun1-204 7 832503 843818 + mRNA protein_coding
-156994 enst00000405266 sg00000164828 sun1-205 7 832501 874900 + mRNA protein_coding
-156994 enst00000340926 sg00000164828 sun1-201 7 832501 850767 + lnc_RNA retained_intron
-156994 enst00000413171 sg00000164828 sun1-206 7 832501 874902 + lnc_RNA retained_intron
-157019 enst00000401592 sg00000164828 sun1-203 7 832476 874934 + mRNA protein_coding
-157573 enst00000421580 sg00000164828 sun1-208 7 831922 842019 + mRNA protein_coding
-158565 enst00000457598 sg00000164828 sun1-221 7 830930 842035 + mRNA protein_coding
164800 enst00000471448 sg00000178381 zfand2a-204 7 1152906 1155677 - lnc_RNA retained_intron
166855 enst00000574135 sg00000178381 zfand2a-207 7 1152906 1157732 - mRNA protein_coding
169276 enst00000397083 sg00000178381 zfand2a-202 7 1152906 1160153 - mRNA protein_coding
169301 enst00000401903 sg00000178381 zfand2a-203 7 1152071 1160178 - mRNA protein_coding
169319 enst00000316495 sg00000178381 zfand2a-201 7 1152907 1160196 - mRNA protein_coding
169342 enst00000484977 sg00000178381 zfand2a-206 7 1157023 1160219 - lnc_RNA retained_intron
169497 enst00000423008 sg00000229043 ac091729.3-201 7 1160374 1165580 + lnc_RNA lncrna
169555 enst00000660500 sg00000229043 ac091729.3-202 7 1160432 1165580 + lnc_RNA lncrna
169555 enst00000662926 sg00000229043 ac091729.3-203 7 1160432 1165607 + lnc_RNA lncrna
169617 enst00000422230 sg00000229043 ac091729.3-204 7 1160494 1164575 + lnc_RNA lncrna
169704 enst00000659975 sg00000229043 ac091729.3-205 7 1160581 1165212 + lnc_RNA lncrna
169714 enst00000413706 sg00000229043 ac091729.3-206 7 1160591 1163491 + lnc_RNA lncrna
169719 enst00000655003 sg00000229043 ac091729.3-207 7 1160596 1165607 + lnc_RNA lncrna
169882 enst00000478137 sg00000178381 zfand2a-205 7 1160026 1160759 - lnc_RNA processed_transcript
-172629 enst00000424128 sg00000164828 sun1-209 7 816866 838986 + mRNA protein_coding
-172740 enst00000439679 sg00000164828 sun1-215 7 816755 842086 + mRNA protein_coding
-172852 enst00000440380 sg00000164828 sun1-216 7 816643 838986 + mRNA protein_coding
-172872 enst00000435699 sg00000164828 sun1-214 7 816623 843385 + mRNA protein_coding
-172880 enst00000427969 sg00000164828 sun1-211 7 816615 842568 + lnc_RNA processed_transcript
-172880 enst00000457378 sg00000164828 sun1-220 7 816615 843872 + mRNA protein_coding
-172880 enst00000389574 sg00000164828 sun1-202 7 816615 874902 + mRNA protein_coding
-172880 enst00000452783 sg00000164828 sun1-219 7 816615 874920 + mRNA protein_coding
-172880 enst00000450538 sg00000164828 sun1-217 7 816615 843006 + lnc_RNA processed_transcript
-209591 enst00000461576 sg00000164818 dnaaf5-206 7 779904 785573 + lnc_RNA retained_intron
-211313 enst00000486546 sg00000164818 dnaaf5-207 7 778182 779984 + lnc_RNA processed_transcript
-221020 enst00000403952 sg00000164818 dnaaf5-202 7 768475 786044 + mRNA protein_coding
-225588 enst00000491496 sg00000164818 dnaaf5-208 7 763907 772975 + lnc_RNA retained_intron
241995 enst00000316333 sg00000164853 uncx-201 7 1232872 1237326 + mRNA protein_coding
-261845 enst00000403562 sg00000188191 prkar1b-203 7 549742 727650 - mRNA protein_coding
-262154 enst00000417852 sg00000188191 prkar1b-206 7 607396 727341 - mRNA protein_coding
-262214 enst00000537384 sg00000188191 prkar1b-211 7 549198 727281 - mRNA protein_coding
-262240 enst00000440747 sg00000164818 dnaaf5-205 7 727255 786031 + mRNA protein_coding
-262243 enst00000438961 sg00000164818 dnaaf5-204 7 727252 750953 + lnc_RNA processed_transcript
-262258 enst00000488474 sg00000188191 prkar1b-210 7 696713 727237 - lnc_RNA processed_transcript
-262276 enst00000437419 sg00000164818 dnaaf5-203 7 727219 756792 + mRNA protein_coding
-262518 enst00000478198 sg00000188191 prkar1b-209 7 716619 726977 - lnc_RNA processed_transcript
-262796 enst00000297440 sg00000164818 dnaaf5-201 7 726699 786475 + mRNA protein_coding
-276288 enst00000406797 sg00000188191 prkar1b-204 7 549198 713207 - mRNA protein_coding
-276426 enst00000456696 sg00000188191 prkar1b-208 7 680556 713069 - mRNA protein_coding
276476 enst00000453798 sg00000233082 ac073094.1-201 7 1267353 1269267 + lnc_RNA lncrna
-276555 enst00000544935 sg00000188191 prkar1b-212 7 549197 712940 - mRNA protein_coding
-276555 enst00000430040 sg00000188191 prkar1b-207 7 579256 712940 - mRNA protein_coding
-276923 enst00000360274 sg00000188191 prkar1b-201 7 549750 712572 - mRNA protein_coding
-297701 enst00000414568 sg00000188191 prkar1b-205 7 596180 691794 - mRNA protein_coding
-386310 enst00000429872 sg00000237181 ac147651.4-201 7 603185 608482 + lnc_RNA lncrna
-386812 enst00000400758 sg00000188191 prkar1b-202 7 550270 602683 - mRNA protein_coding
-427537 enst00000453149 sg00000229380 ac147651.2-201 7 561958 565619 + lnc_RNA lncrna
446734 enst00000493998 sg00000164877 micall2-214 7 1428465 1437611 - lnc_RNA retained_intron
447036 enst00000470807 sg00000164877 micall2-206 7 1434366 1437913 - lnc_RNA retained_intron
447588 enst00000460198 sg00000164877 micall2-203 7 1437536 1438465 - lnc_RNA retained_intron
448085 enst00000471899 sg00000164877 micall2-207 7 1434366 1438962 - lnc_RNA processed_transcript
448281 enst00000487187 sg00000164877 micall2-212 7 1436743 1439158 - lnc_RNA retained_intron
448554 enst00000496184 sg00000164877 micall2-215 7 1428479 1439431 - lnc_RNA retained_intron
448994 enst00000479007 sg00000164877 micall2-209 7 1434366 1439871 - lnc_RNA retained_intron
449145 enst00000467783 sg00000164877 micall2-205 7 1434359 1440022 - lnc_RNA retained_intron
449850 enst00000487156 sg00000164877 micall2-211 7 1438925 1440727 - lnc_RNA retained_intron
450647 enst00000467394 sg00000164877 micall2-204 7 1434360 1441524 - lnc_RNA retained_intron
457075 enst00000482839 sg00000164877 micall2-210 7 1445071 1447952 - lnc_RNA retained_intron
457156 enst00000490608 sg00000164877 micall2-213 7 1446657 1448033 - lnc_RNA retained_intron
459659 enst00000413446 sg00000164877 micall2-202 7 1434366 1450536 - mRNA nonsense_mediated_decay
-466922 enst00000656962 sg00000223855 ac147651.1-204 7 522573 525232 + lnc_RNA lncrna
-466941 enst00000662957 sg00000223855 ac147651.1-203 7 522554 525238 + lnc_RNA lncrna
-466953 enst00000663680 sg00000223855 ac147651.1-202 7 522542 525233 + lnc_RNA lncrna
468488 enst00000472100 sg00000164877 micall2-208 7 1428619 1459365 - lnc_RNA retained_intron
468593 enst00000297508 sg00000164877 micall2-201 7 1434359 1459470 - mRNA protein_coding
469060 enst00000445345 sg00000225981 ac102953.1-201 7 1459937 1464008 + lnc_RNA lncrna
-469104 enst00000452622 sg00000223855 ac147651.1-201 7 520391 525232 + lnc_RNA lncrna
-469199 enst00000405692 sg00000197461 pdgfa-204 7 512357 520296 - mRNA protein_coding
-469287 enst00000426681 sg00000197461 pdgfa-205 7 512445 520208 - lnc_RNA processed_transcript
-470086 enst00000402802 sg00000197461 pdgfa-203 7 497258 519409 - mRNA protein_coding
-470101 enst00000354513 sg00000197461 pdgfa-201 7 498309 519394 - mRNA protein_coding
-470987 enst00000400761 sg00000197461 pdgfa-202 7 498493 518508 - mRNA protein_coding
-476028 enst00000482462 sg00000197461 pdgfa-206 7 500778 513467 - lnc_RNA retained_intron
476645 enst00000609755 sg00000273230 ac102953.2-201 7 1464497 1467522 - lnc_RNA lncrna
480884 enst00000479671 sg00000164880 ints1-203 7 1471171 1471761 - lnc_RNA retained_intron
482248 enst00000493446 sg00000164880 ints1-206 7 1470478 1473125 - lnc_RNA processed_transcript
482273 enst00000483196 sg00000164880 ints1-205 7 1471133 1473150 - mRNA protein_coding
485273 enst00000482994 sg00000164880 ints1-204 7 1474200 1476150 - lnc_RNA retained_intron
-493377 enst00000434541 sg00000234471 ac147651.3-201 7 484107 496118 - 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