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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 |
|---|---|---|---|---|---|---|---|---|
| #126 | 13 | 114043702 | 114044738 | 1036 | 3 | 37 | 1.80456e-16 | 1.42432e-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 |
|---|---|---|---|---|---|---|---|---|---|
| -7509 | enst00000542651 | sg00000185989 | rasa3-202 | 13 | 114021409 | 114036193 | - | lnc_RNA | processed_transcript |
| 64082 | enst00000454005 | sg00000232487 | rasa3-it1-201 | 13 | 114107569 | 114108820 | - | lnc_RNA | lncrna |
| -69626 | enst00000636427 | sg00000283199 | c13orf46-201 | 13 | 113953705 | 113974076 | - | mRNA | protein_coding |
| -73293 | enst00000637024 | sg00000283199 | c13orf46-202 | 13 | 113956549 | 113970409 | - | lnc_RNA | processed_transcript |
| 87885 | enst00000334062 | sg00000185989 | rasa3-201 | 13 | 113977783 | 114132623 | - | mRNA | protein_coding |
| 109953 | enst00000643687 | sg00000283361 | cfap97d2-205 | 13 | 114154691 | 114179420 | + | mRNA | protein_coding |
| -114858 | enst00000562710 | sg00000260910 | linc00565-201 | 13 | 113926514 | 113928844 | - | lnc_RNA | lncrna |
| -127761 | enst00000671032 | sg00000229373 | linc00452-203 | 13 | 113915941 | 113920995 | + | lnc_RNA | lncrna |
| 134500 | enst00000635974 | sg00000283361 | cfap97d2-203 | 13 | 114179238 | 114222770 | + | lnc_RNA | processed_transcript |
| 134512 | enst00000635901 | sg00000283361 | cfap97d2-202 | 13 | 114179250 | 114223084 | + | mRNA | protein_coding |
| 134593 | enst00000646158 | sg00000283361 | cfap97d2-206 | 13 | 114179331 | 114222518 | + | mRNA | protein_coding |
| 134593 | enst00000636692 | sg00000283361 | cfap97d2-204 | 13 | 114179331 | 114222776 | + | mRNA | protein_coding |
| -148599 | enst00000426859 | sg00000229373 | linc00452-201 | 13 | 113895103 | 113921317 | + | lnc_RNA | lncrna |
| 154966 | enst00000635874 | sg00000283361 | cfap97d2-201 | 13 | 114199704 | 114222600 | + | lnc_RNA | processed_transcript |
| -155396 | enst00000609661 | sg00000229373 | linc00452-202 | 13 | 113888306 | 113923512 | + | lnc_RNA | lncrna |
| -159965 | enst00000666964 | sg00000274766 | bx072579.2-202 | 13 | 113883737 | 113887142 | + | lnc_RNA | lncrna |
| -159995 | enst00000657154 | sg00000274766 | bx072579.2-203 | 13 | 113883707 | 113887147 | + | lnc_RNA | lncrna |
| -159999 | enst00000655130 | sg00000274766 | bx072579.2-204 | 13 | 113883703 | 113887149 | + | lnc_RNA | lncrna |
| -160035 | enst00000455857 | sg00000274766 | bx072579.2-201 | 13 | 113883667 | 113885335 | + | lnc_RNA | lncrna |
| -160051 | enst00000609861 | sg00000226921 | linc00454-206 | 13 | 113878628 | 113883651 | - | lnc_RNA | lncrna |
| -160053 | enst00000661456 | sg00000226921 | linc00454-208 | 13 | 113878628 | 113883649 | - | lnc_RNA | lncrna |
| -160145 | enst00000430978 | sg00000226921 | linc00454-202 | 13 | 113878489 | 113883557 | - | lnc_RNA | lncrna |
| -160169 | enst00000442500 | sg00000226921 | linc00454-203 | 13 | 113878628 | 113883533 | - | lnc_RNA | lncrna |
| -160224 | enst00000425483 | sg00000226921 | linc00454-201 | 13 | 113880382 | 113883478 | - | lnc_RNA | lncrna |
| -160374 | enst00000609493 | sg00000226921 | linc00454-205 | 13 | 113879004 | 113883328 | - | lnc_RNA | lncrna |
| -161500 | enst00000610194 | sg00000226921 | linc00454-207 | 13 | 113879011 | 113882202 | - | lnc_RNA | lncrna |
| -161772 | enst00000608044 | sg00000226921 | linc00454-204 | 13 | 113879004 | 113881930 | - | lnc_RNA | lncrna |
| -162326 | enst00000671045 | sg00000226921 | linc00454-209 | 13 | 113878630 | 113881376 | - | lnc_RNA | lncrna |
| -165289 | enst00000648342 | sg00000237699 | bx072579.1-202 | 13 | 113878413 | 113879367 | + | lnc_RNA | lncrna |
| -166094 | enst00000449453 | sg00000237699 | bx072579.1-201 | 13 | 113877608 | 113879376 | + | lnc_RNA | lncrna |
| 171097 | enst00000637433 | sg00000283347 | al160396.1-201 | 13 | 114175485 | 114215835 | - | lnc_RNA | lncrna |
| -179534 | enst00000608651 | sg00000272695 | gas6-dt-201 | 13 | 113864168 | 113866833 | + | lnc_RNA | lncrna |
| -179584 | enst00000655351 | sg00000272695 | gas6-dt-202 | 13 | 113864118 | 113866618 | + | lnc_RNA | lncrna |
| -179590 | enst00000669254 | sg00000272695 | gas6-dt-203 | 13 | 113864112 | 113866834 | + | lnc_RNA | lncrna |
| -179626 | enst00000327773 | sg00000183087 | gas6-201 | 13 | 113820549 | 113864076 | - | mRNA | protein_coding |
| -179687 | enst00000476291 | sg00000183087 | gas6-202 | 13 | 113847677 | 113864015 | - | lnc_RNA | processed_transcript |
| 190149 | enst00000628084 | sg00000130177 | cdc16-211 | 13 | 114234887 | 114272675 | + | mRNA | protein_coding |
| 190149 | enst00000360383 | sg00000130177 | cdc16-204 | 13 | 114234887 | 114272675 | + | mRNA | protein_coding |
| 190159 | enst00000356221 | sg00000130177 | cdc16-203 | 13 | 114234897 | 114272723 | + | mRNA | protein_coding |
| 190196 | enst00000650489 | sg00000130177 | cdc16-212 | 13 | 114234934 | 114272657 | + | mRNA | nonsense_mediated_decay |
| 190241 | enst00000375310 | sg00000130177 | cdc16-206 | 13 | 114234979 | 114272675 | + | mRNA | protein_coding |
| 190280 | enst00000494766 | sg00000130177 | cdc16-210 | 13 | 114235018 | 114242675 | + | lnc_RNA | retained_intron |
| 190323 | enst00000252457 | sg00000130177 | cdc16-201 | 13 | 114235061 | 114272675 | + | mRNA | protein_coding |
| 190323 | enst00000375308 | sg00000130177 | cdc16-205 | 13 | 114235061 | 114272675 | + | mRNA | protein_coding |
| 190343 | enst00000252458 | sg00000130177 | cdc16-202 | 13 | 114235081 | 114272723 | + | mRNA | protein_coding |
| 199767 | enst00000582191 | sg00000264539 | mir548ar-201 | 13 | 114244505 | 114244561 | + | miRNA | mirna |
| 199824 | enst00000484907 | sg00000130177 | cdc16-208 | 13 | 114244562 | 114262979 | + | lnc_RNA | retained_intron |
| 201005 | enst00000494581 | sg00000130177 | cdc16-209 | 13 | 114245743 | 114247237 | + | lnc_RNA | processed_transcript |
| -201212 | enst00000611082 | sg00000233695 | gas6-as1-202 | 13 | 113842490 | 113844306 | + | lnc_RNA | lncrna |
| -207658 | enst00000610073 | sg00000183087 | gas6-205 | 13 | 113820552 | 113836044 | - | lnc_RNA | retained_intron |
| -209961 | enst00000480426 | sg00000183087 | gas6-203 | 13 | 113820549 | 113833741 | - | lnc_RNA | retained_intron |
| 219474 | enst00000461716 | sg00000130177 | cdc16-207 | 13 | 114264212 | 114272485 | + | lnc_RNA | processed_transcript |
| -220508 | enst00000608763 | sg00000183087 | gas6-204 | 13 | 113820549 | 113823194 | - | lnc_RNA | retained_intron |
| -228072 | enst00000458001 | sg00000233695 | gas6-as1-201 | 13 | 113815630 | 113845744 | + | lnc_RNA | lncrna |
| 229090 | enst00000580432 | sg00000265450 | mir4502-201 | 13 | 114273828 | 114273908 | + | miRNA | mirna |
| 232585 | enst00000649577 | sg00000285672 | al160396.2-201 | 13 | 114275326 | 114277323 | - | lnc_RNA | lncrna |
| 236863 | enst00000375299 | sg00000169062 | upf3a-202 | 13 | 114281601 | 114305817 | + | mRNA | protein_coding |
| 236865 | enst00000492270 | sg00000169062 | upf3a-209 | 13 | 114281603 | 114282270 | + | mRNA | protein_coding |
| 236890 | enst00000351487 | sg00000169062 | upf3a-201 | 13 | 114281628 | 114305808 | + | mRNA | protein_coding |
| 236899 | enst00000618700 | sg00000169062 | upf3a-211 | 13 | 114281637 | 114283729 | + | lnc_RNA | retained_intron |
| 236907 | enst00000484246 | sg00000169062 | upf3a-208 | 13 | 114281645 | 114291757 | + | lnc_RNA | processed_transcript |
| 236982 | enst00000480362 | sg00000169062 | upf3a-206 | 13 | 114281720 | 114304949 | + | lnc_RNA | processed_transcript |
| 237187 | enst00000474056 | sg00000169062 | upf3a-203 | 13 | 114281925 | 114301792 | + | lnc_RNA | processed_transcript |
| 237215 | enst00000493727 | sg00000169062 | upf3a-210 | 13 | 114281953 | 114301756 | + | lnc_RNA | processed_transcript |
| 240339 | enst00000619079 | sg00000169062 | upf3a-212 | 13 | 114285077 | 114287617 | + | lnc_RNA | retained_intron |
| -240652 | enst00000467169 | sg00000184497 | tmem255b-203 | 13 | 113803050 | 113811953 | + | lnc_RNA | processed_transcript |
| 241237 | enst00000481131 | sg00000169062 | upf3a-207 | 13 | 114285975 | 114291718 | + | lnc_RNA | processed_transcript |
| 241636 | enst00000479712 | sg00000169062 | upf3a-205 | 13 | 114286374 | 114291744 | + | lnc_RNA | processed_transcript |
| 241647 | enst00000475218 | sg00000169062 | upf3a-204 | 13 | 114286385 | 114305808 | + | lnc_RNA | processed_transcript |
| -243814 | enst00000498692 | sg00000184497 | tmem255b-206 | 13 | 113799888 | 113804890 | + | lnc_RNA | processed_transcript |
| 261908 | enst00000392050 | sg00000226158 | clcp2-201 | 13 | 114306646 | 114307066 | + | pseudogenic_transcript | processed_pseudogene |
| 269744 | enst00000646956 | sg00000198824 | champ1-208 | 13 | 114314482 | 114337626 | + | lnc_RNA | processed_transcript |
| 269750 | enst00000463003 | sg00000198824 | champ1-202 | 13 | 114314488 | 114324279 | + | mRNA | protein_coding |
| 269752 | enst00000645174 | sg00000198824 | champ1-206 | 13 | 114314490 | 114324208 | + | mRNA | protein_coding |
| 269765 | enst00000361283 | sg00000198824 | champ1-201 | 13 | 114314503 | 114327322 | + | mRNA | protein_coding |
| 269783 | enst00000646155 | sg00000198824 | champ1-207 | 13 | 114314521 | 114337626 | + | lnc_RNA | processed_transcript |
| 269793 | enst00000478022 | sg00000198824 | champ1-203 | 13 | 114314531 | 114322441 | + | lnc_RNA | processed_transcript |
| 269810 | enst00000644294 | sg00000198824 | champ1-205 | 13 | 114314548 | 114324425 | + | mRNA | protein_coding |
| -275566 | enst00000375348 | sg00000184497 | tmem255b-201 | 13 | 113768136 | 113799857 | + | lnc_RNA | processed_transcript |
| 277462 | enst00000643483 | sg00000198824 | champ1-204 | 13 | 114322200 | 114327321 | + | mRNA | protein_coding |
| -277538 | enst00000483678 | sg00000184497 | tmem255b-204 | 13 | 113766164 | 113769815 | + | lnc_RNA | processed_transcript |
| -284462 | enst00000488362 | sg00000184497 | tmem255b-205 | 13 | 113759240 | 113799660 | + | mRNA | protein_coding |
| -284476 | enst00000375353 | sg00000184497 | tmem255b-202 | 13 | 113759226 | 113816995 | + | mRNA | protein_coding |
| 289210 | enst00000446989 | sg00000229723 | linc01054-201 | 13 | 114329559 | 114333948 | - | lnc_RNA | lncrna |
| -292613 | enst00000625151 | sg00000279770 | linc00552-201 | 13 | 113748511 | 113751089 | - | unconfirmed_transcript | tec |
| 301429 | enst00000568955 | sg00000260615 | rpl23ap97-201 | 13 | 114346167 | 114346637 | + | pseudogenic_transcript | processed_pseudogene |
| -309227 | enst00000606140 | sg00000185974 | grk1-203 | 13 | 113734475 | 113737735 | + | lnc_RNA | retained_intron |
| -317216 | enst00000545304 | sg00000185974 | grk1-202 | 13 | 113726486 | 113735236 | + | lnc_RNA | processed_transcript |
| -376483 | enst00000335678 | sg00000185974 | grk1-201 | 13 | 113667219 | 113737736 | + | mRNA | protein_coding |
| -385504 | enst00000335288 | sg00000186009 | atp4b-201 | 13 | 113648804 | 113658198 | - | mRNA | protein_coding |
| -406551 | enst00000494812 | sg00000198176 | tfdp1-207 | 13 | 113637151 | 113640684 | + | lnc_RNA | processed_transcript |
| -458276 | enst00000453989 | sg00000198176 | tfdp1-203 | 13 | 113585426 | 113633287 | + | mRNA | protein_coding |
| -458369 | enst00000408980 | sg00000198176 | tfdp1-202 | 13 | 113585333 | 113635996 | + | mRNA | protein_coding |
| -458429 | enst00000544902 | sg00000198176 | tfdp1-208 | 13 | 113585273 | 113640310 | + | mRNA | nonsense_mediated_decay |
| -458949 | enst00000375370 | sg00000198176 | tfdp1-201 | 13 | 113584753 | 113641473 | + | mRNA | protein_coding |
| -458959 | enst00000465174 | sg00000198176 | tfdp1-205 | 13 | 113584743 | 113633999 | + | lnc_RNA | processed_transcript |
| -458969 | enst00000464794 | sg00000198176 | tfdp1-204 | 13 | 113584733 | 113586180 | + | lnc_RNA | processed_transcript |
| -458981 | enst00000475254 | sg00000198176 | tfdp1-206 | 13 | 113584721 | 113633285 | + | lnc_RNA | processed_transcript |
| -495369 | enst00000619336 | sg00000150403 | tmco3-209 | 13 | 113548333 | 113552214 | + | mRNA | nonsense_mediated_decay |
| -495399 | enst00000620021 | sg00000150403 | tmco3-210 | 13 | 113548303 | 113554590 | + | mRNA | protein_coding |
| -496553 | enst00000491166 | sg00000150403 | tmco3-208 | 13 | 113547149 | 113549638 | + | lnc_RNA | processed_transcript |
| -497947 | enst00000460039 | sg00000150403 | tmco3-203 | 13 | 113545755 | 113549915 | + | 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