In this section, we investigate overlaps of peaks with the different genomic features.
Let’s look first at those peaks that are lost in TKO with respect of D3.
The total number of peaks is 41215 of which only 393 are lost in TKO when compared to D3 (FDR < 0.05, Log2FC < -1).
A summary barplot is shown below, the categories are somehow selected for:
gencode class | frequency | our class |
---|---|---|
miRNA | 1 | smallRNA |
snoRNA | 1 | smallRNA |
bidirectional_promoter_lncRNA | 2 | lncRNA |
snRNA | 2 | smallRNA |
TEC | 2 | other |
transcribed_unitary_pseudogene | 2 | pseudo |
unprocessed_pseudogene | 2 | pseudo |
transcribed_processed_pseudogene | 3 | pseudo |
sense_overlapping | 4 | other |
misc_RNA | 5 | other |
sense_intronic | 6 | other |
processed_pseudogene | 7 | pseudo |
processed_transcript | 10 | other |
transcribed_unprocessed_pseudogene | 10 | pseudo |
antisense | 22 | other |
lincRNA | 33 | lncRNA |
protein_coding | 238 | coding |
Among the protein coding genes, there are 46 ZNF genes (of a total of 646 annotated in the genome).
Testing for enrichment of ZNFs in peaks.
## ZNF no.ZNF
## yes.peak 46 304
## no.peak 469 19425
We apply Fisher Exact test where the H0 is that the proportion of ZNFs found in peaks is the same as the proportion found in the general pool of genes vs the alternative HA which states that the proportion of ZNFs in peaks is greater than that of the general pool of genes.
##
## Fisher's Exact Test for Count Data
##
## data: contingency.table
## p-value < 2.2e-16
## alternative hypothesis: true odds ratio is greater than 1
## 95 percent confidence interval:
## 4.685079 Inf
## sample estimates:
## odds ratio
## 6.265804
The P-value indicates that we reject the H0 in the favor of HA.
chrom | start | end | gene_id | gene_name |
---|---|---|---|---|
chr3 | 100749156 | 100993515 | ENSG00000154175.16 | ABI3BP |
chr7 | 92131774 | 92245924 | ENSG00000285953.1 | AC000120.3 |
chr19 | 57487718 | 57505381 | ENSG00000268107.5 | AC003005.1 |
chr19 | 57682045 | 57753575 | ENSG00000269026.2 | AC003006.1 |
chr19 | 57437970 | 57477536 | ENSG00000268163.1 | AC004076.1 |
chr12 | 4649101 | 4774184 | ENSG00000255639.3 | AC005833.1 |
chr12 | 4273762 | 4405490 | ENSG00000285901.1 | AC008012.1 |
chr19 | 57876765 | 57916591 | ENSG00000269476.1 | AC010326.2 |
chr19 | 52880663 | 52962768 | ENSG00000283088.1 | AC010487.3 |
chr16 | 71447600 | 71489311 | ENSG00000261611.6 | AC010547.4 |
chr3 | 28349178 | 29767537 | ENSG00000283563.1 | AC098650.1 |
chr3 | 113361901 | 113515151 | ENSG00000285943.1 | AC112128.1 |
chr1 | 75724347 | 75787575 | ENSG00000117054.13 | ACADM |
chr6 | 135283532 | 135497776 | ENSG00000135541.20 | AHI1 |
chr10 | 38094368 | 38360098 | ENSG00000283930.1 | AL117339.5 |
chr9 | 21802636 | 22032986 | ENSG00000264545.1 | AL359922.1 |
chr2 | 73385758 | 73610793 | ENSG00000116127.17 | ALMS1 |
chr2 | 201288271 | 201357398 | ENSG00000155749.12 | ALS2CR12 |
chr5 | 140401814 | 140539856 | ENSG00000131503.20 | ANKHD1 |
chr5 | 140401908 | 140549569 | ENSG00000254996.5 | ANKHD1-EIF4EBP3 |
chr7 | 92246234 | 92401384 | ENSG00000001629.9 | ANKIB1 |
chr18 | 9136228 | 9285985 | ENSG00000101745.16 | ANKRD12 |
chr17 | 60443149 | 60526219 | ENSG00000062725.9 | APPBP2 |
chr12 | 105173296 | 105236238 | ENSG00000136044.11 | APPL2 |
chr4 | 152779937 | 152918463 | ENSG00000164144.15 | ARFIP1 |
chr10 | 50739318 | 50816495 | ENSG00000204147.10 | ASAH2B |
chr1 | 197084128 | 197146694 | ENSG00000066279.17 | ASPM |
chr5 | 81972025 | 82276857 | ENSG00000152348.15 | ATG10 |
chr11 | 108222484 | 108369102 | ENSG00000149311.18 | ATM |
chr3 | 142449235 | 142578826 | ENSG00000175054.14 | ATR |
chr17 | 82942155 | 83051810 | ENSG00000175711.8 | B3GNTL1 |
chr11 | 27654893 | 27722058 | ENSG00000176697.18 | BDNF |
chr13 | 32315474 | 32400266 | ENSG00000139618.14 | BRCA2 |
chr11 | 108308519 | 108467531 | ENSG00000166323.12 | C11orf65 |
chr2 | 27537386 | 27582721 | ENSG00000221843.4 | C2orf16 |
chr2 | 189879609 | 190203484 | ENSG00000187699.10 | C2orf88 |
chr15 | 44288729 | 44415758 | ENSG00000166734.19 | CASC4 |
chr4 | 168863770 | 169010275 | ENSG00000145439.11 | CBR4 |
chr2 | 113437691 | 113496189 | ENSG00000136682.14 | CBWD2 |
chr9 | 68232003 | 68300015 | ENSG00000196873.15 | CBWD3 |
chr2 | 196639554 | 196763490 | ENSG00000144395.17 | CCDC150 |
chr13 | 102729369 | 102759070 | ENSG00000175820.3 | CCDC168 |
chr1 | 93179919 | 93278730 | ENSG00000122483.17 | CCDC18 |
chr1 | 169394870 | 169460669 | ENSG00000117477.12 | CCDC181 |
chr10 | 32446140 | 32882874 | ENSG00000216937.13 | CCDC7 |
chr11 | 96352769 | 96389956 | ENSG00000149231.13 | CCDC82 |
chr5 | 134286350 | 134371047 | ENSG00000006837.11 | CDKL3 |
chr2 | 37201612 | 37231713 | ENSG00000115816.14 | CEBPZ |
chr2 | 37196488 | 37216193 | ENSG00000218739.9 | CEBPZOS |
chr10 | 93496632 | 93529092 | ENSG00000138180.15 | CEP55 |
chr11 | 95789965 | 95832693 | ENSG00000166037.10 | CEP57 |
chr3 | 101723925 | 101770562 | ENSG00000182504.10 | CEP97 |
chr3 | 113286947 | 113441610 | ENSG00000206530.10 | CFAP44 |
chr2 | 86503431 | 86563479 | ENSG00000115561.15 | CHMP3 |
chr11 | 77514936 | 77637805 | ENSG00000074201.8 | CLNS1A |
chr9 | 17134982 | 17503923 | ENSG00000044459.14 | CNTLN |
chr7 | 43608456 | 43729717 | ENSG00000106603.18 | COA1 |
chr13 | 39655627 | 39791665 | ENSG00000133103.16 | COG6 |
chrX | 108439844 | 108697545 | ENSG00000188153.13 | COL4A5 |
chr1 | 175944831 | 176207493 | ENSG00000143207.20 | COP1 |
chr2 | 210477682 | 210679107 | ENSG00000021826.15 | CPS1 |
chr6 | 83859643 | 83967424 | ENSG00000065615.13 | CYB5R4 |
chr3 | 98795941 | 98901689 | ENSG00000057019.15 | DCBLD2 |
chr8 | 90001405 | 90052092 | ENSG00000104325.6 | DECR1 |
chr17 | 21123364 | 21193265 | ENSG00000109016.17 | DHRS7B |
chr11 | 111927144 | 112022584 | ENSG00000150764.13 | DIXDC1 |
chr5 | 119037772 | 119249138 | ENSG00000172869.14 | DMXL1 |
chr2 | 195737703 | 196068812 | ENSG00000118997.13 | DNAH7 |
chr18 | 67506582 | 67516980 | ENSG00000171451.13 | DSEL |
chr1 | 212035553 | 212107400 | ENSG00000143476.17 | DTL |
chr3 | 108589682 | 108694846 | ENSG00000198919.12 | DZIP3 |
chr17 | 47323290 | 47441312 | ENSG00000178852.15 | EFCAB13 |
chr5 | 60873831 | 60945073 | ENSG00000049167.14 | ERCC8 |
chr21 | 38380027 | 38661780 | ENSG00000157554.18 | ERG |
chr19 | 53013921 | 53016122 | ENSG00000269526.1 | ERVV-1 |
chrX | 57286706 | 57489196 | ENSG00000165591.6 | FAAH2 |
chr11 | 59107185 | 59127410 | ENSG00000189057.10 | FAM111B |
chr5 | 80487969 | 80542563 | ENSG00000152380.9 | FAM151B |
chr7 | 102748971 | 102809225 | ENSG00000222011.8 | FAM185A |
chr15 | 49326962 | 49620931 | ENSG00000166262.15 | FAM227B |
chr4 | 112145397 | 112195256 | ENSG00000174749.5 | FAM241A |
chr15 | 59372693 | 59523549 | ENSG00000157470.11 | FAM81A |
chr11 | 72836745 | 73142261 | ENSG00000137478.14 | FCHSD2 |
chr1 | 59296638 | 59810647 | ENSG00000172456.17 | FGGY |
chr9 | 105558130 | 105641118 | ENSG00000106692.14 | FKTN |
chr15 | 49155656 | 49367869 | ENSG00000156958.14 | GALK2 |
chr18 | 35581117 | 35711834 | ENSG00000141429.13 | GALNT1 |
chr14 | 54842008 | 54902852 | ENSG00000131979.18 | GCH1 |
chr5 | 151822513 | 151924842 | ENSG00000145888.10 | GLRA1 |
chr9 | 86026146 | 86100173 | ENSG00000135052.16 | GOLM1 |
chrX | 9725346 | 9786297 | ENSG00000101850.12 | GPR143 |
chr10 | 91409280 | 91514829 | ENSG00000165338.16 | HECTD2 |
chr15 | 28111040 | 28322152 | ENSG00000128731.16 | HERC2 |
chr2 | 190189735 | 190344193 | ENSG00000198130.15 | HIBCH |
chr6 | 12008762 | 12164999 | ENSG00000095951.16 | HIVEP1 |
chrX | 131273506 | 131578899 | ENSG00000147255.18 | IGSF1 |
chr9 | 5123880 | 5185668 | ENSG00000120210.7 | INSL6 |
chr9 | 100099256 | 100301000 | ENSG00000119509.12 | INVS |
chr13 | 101452593 | 101720856 | ENSG00000198542.13 | ITGBL1 |
chr9 | 4984390 | 5128183 | ENSG00000096968.13 | JAK2 |
chr11 | 96389989 | 96507574 | ENSG00000183340.6 | JRKL |
chrX | 53094145 | 53170914 | ENSG00000232593.7 | KANTR |
chr18 | 79863668 | 79900184 | ENSG00000178342.4 | KCNG2 |
chr4 | 20728616 | 21948799 | ENSG00000185774.15 | KCNIP4 |
chr12 | 280129 | 389454 | ENSG00000073614.12 | KDM5A |
chr1 | 35433490 | 35557950 | ENSG00000142687.17 | KIAA0319L |
chr14 | 58427385 | 58551289 | ENSG00000100578.14 | KIAA0586 |
chr5 | 94152966 | 94618597 | ENSG00000185261.14 | KIAA0825 |
chr12 | 31959370 | 31993107 | ENSG00000174718.11 | KIAA1551 |
chr15 | 89608789 | 89655451 | ENSG00000166813.14 | KIF7 |
chr1 | 173714941 | 173786702 | ENSG00000076321.10 | KLHL20 |
chr6 | 116681187 | 116741866 | ENSG00000196911.10 | KPNA5 |
chrX | 46446857 | 46497422 | ENSG00000147121.15 | KRBOX4 |
chr13 | 108207439 | 108218368 | ENSG00000174405.13 | LIG4 |
chr4 | 150264531 | 151015727 | ENSG00000198589.11 | LRBA |
chr1 | 116111755 | 116135240 | ENSG00000173212.4 | MAB21L3 |
chr1 | 113390749 | 113685923 | ENSG00000081026.18 | MAGI3 |
chr2 | 148021011 | 148516971 | ENSG00000204406.13 | MBD5 |
chr6 | 118813442 | 118935162 | ENSG00000111877.17 | MCM9 |
chr12 | 27022546 | 27066343 | ENSG00000152944.8 | MED21 |
chr18 | 21704957 | 21870957 | ENSG00000101752.11 | MIB1 |
chr14 | 37197913 | 37552361 | ENSG00000151338.18 | MIPOL1 |
chr22 | 30925130 | 30968298 | ENSG00000133422.12 | MORC2 |
chr9 | 21802543 | 21937651 | ENSG00000099810.19 | MTAP |
chr8 | 120445400 | 120542133 | ENSG00000172167.7 | MTBP |
chr19 | 8848844 | 8981342 | ENSG00000181143.15 | MUC16 |
chr15 | 71822289 | 72118577 | ENSG00000066933.15 | MYO9A |
chr3 | 174438573 | 175810552 | ENSG00000177694.15 | NAALADL2 |
chr12 | 4649095 | 4694317 | ENSG00000139180.10 | NDUFA9 |
chr4 | 169392857 | 169612629 | ENSG00000137601.16 | NEK1 |
chr2 | 177227595 | 177392697 | ENSG00000116044.15 | NFE2L2 |
chr3 | 173396284 | 174286644 | ENSG00000169760.17 | NLGN1 |
chr4 | 148078762 | 148444698 | ENSG00000151623.14 | NR3C2 |
chr3 | 31657890 | 32077580 | ENSG00000144645.13 | OSBPL10 |
chr5 | 38845858 | 38945596 | ENSG00000145623.12 | OSMR |
chr4 | 20696282 | 20752907 | ENSG00000163138.18 | PACRGL |
chr2 | 61017225 | 61051990 | ENSG00000162928.8 | PEX13 |
chr20 | 8077251 | 8968360 | ENSG00000182621.17 | PLCB1 |
chr5 | 55424854 | 55535050 | ENSG00000067113.16 | PLPP1 |
chr11 | 74171099 | 74254703 | ENSG00000214517.9 | PPME1 |
chr6 | 57314805 | 57646849 | ENSG00000146143.17 | PRIM2 |
chr7 | 549197 | 727650 | ENSG00000188191.14 | PRKAR1B |
chr11 | 112226365 | 112269955 | ENSG00000150787.7 | PTS |
chr12 | 43718993 | 43758817 | ENSG00000129317.14 | PUS7L |
chr12 | 9148840 | 9208370 | ENSG00000126838.9 | PZP |
chr3 | 120686681 | 120742993 | ENSG00000144840.9 | RABL3 |
chr7 | 5045821 | 5069488 | ENSG00000146587.17 | RBAK |
chr7 | 4983718 | 5073221 | ENSG00000272968.5 | RBAK-RBAKDN |
chr2 | 86505668 | 86721122 | ENSG00000249884.8 | RNF103-CHMP3 |
chr1 | 92298965 | 92402056 | ENSG00000122484.8 | RPAP2 |
chr18 | 70003031 | 70205945 | ENSG00000176225.13 | RTTN |
chr3 | 134065303 | 134250744 | ENSG00000163785.12 | RYK |
chr13 | 23328826 | 23433740 | ENSG00000151835.15 | SACS |
chr7 | 93099513 | 93118023 | ENSG00000205413.7 | SAMD9 |
chr4 | 128864921 | 129093607 | ENSG00000151466.11 | SCLT1 |
chr6 | 107867756 | 107958189 | ENSG00000025796.13 | SEC63 |
chr2 | 217730 | 266398 | ENSG00000035115.21 | SH3YL1 |
chr15 | 50182196 | 50236395 | ENSG00000140284.10 | SLC27A2 |
chr10 | 93893973 | 93956062 | ENSG00000176273.14 | SLC35G1 |
chr12 | 46183063 | 46270017 | ENSG00000111371.15 | SLC38A1 |
chr3 | 113442718 | 113515187 | ENSG00000163611.11 | SPICE1 |
chrX | 56818298 | 56995827 | ENSG00000204271.12 | SPIN3 |
chr2 | 9843354 | 9934416 | ENSG00000115750.16 | TAF1B |
chr5 | 141260225 | 141320821 | ENSG00000178913.7 | TAF7 |
chr17 | 82752064 | 82945922 | ENSG00000141556.20 | TBCD |
chr4 | 106041599 | 106321495 | ENSG00000145348.16 | TBCK |
chrX | 9463295 | 9741037 | ENSG00000101849.16 | TBL1X |
chr13 | 113584721 | 113641470 | ENSG00000198176.12 | TFDP1 |
chr3 | 141944428 | 142149544 | ENSG00000114126.17 | TFDP2 |
chr2 | 187464230 | 187565760 | ENSG00000003436.15 | TFPI |
chr2 | 43230836 | 43596046 | ENSG00000115970.18 | THADA |
chr12 | 4307763 | 4354593 | ENSG00000078237.6 | TIGAR |
chr5 | 43444252 | 43483893 | ENSG00000151881.14 | TMEM267 |
chr3 | 119429500 | 119468830 | ENSG00000176142.12 | TMEM39A |
chr3 | 100492619 | 100577444 | ENSG00000181458.10 | TMEM45A |
chr15 | 42210452 | 42273663 | ENSG00000103978.15 | TMEM87A |
chr13 | 100603927 | 100675093 | ENSG00000125247.15 | TMTC4 |
chr21 | 44350163 | 44443081 | ENSG00000142185.16 | TRPM2 |
chr2 | 98997261 | 99154964 | ENSG00000135951.14 | TSGA10 |
chr3 | 23203020 | 23591793 | ENSG00000182247.9 | UBE2E2 |
chr6 | 99432379 | 99521728 | ENSG00000123552.17 | USP45 |
chr7 | 55436056 | 55572988 | ENSG00000154978.12 | VOPP1 |
chr15 | 61852389 | 62060473 | ENSG00000129003.17 | VPS13C |
chr7 | 93232340 | 93361121 | ENSG00000004766.16 | VPS50 |
chr5 | 37379212 | 37753435 | ENSG00000082068.8 | WDR70 |
chr3 | 195068279 | 195271167 | ENSG00000173950.15 | XXYLT1 |
chr3 | 38346760 | 38421348 | ENSG00000093217.10 | XYLB |
chr3 | 114314501 | 115147271 | ENSG00000181722.16 | ZBTB20 |
chr3 | 28349146 | 28538122 | ENSG00000206559.7 | ZCWPW2 |
chr2 | 206274663 | 206314438 | ENSG00000204186.8 | ZDBF2 |
chr11 | 19117099 | 19176422 | ENSG00000177054.13 | ZDHHC13 |
chr10 | 31318495 | 31529814 | ENSG00000148516.21 | ZEB1 |
chr10 | 134465 | 254637 | ENSG00000015171.19 | ZMYND11 |
chr19 | 19668796 | 19683509 | ENSG00000181896.11 | ZNF101 |
chr7 | 64666083 | 64711582 | ENSG00000196247.11 | ZNF107 |
chr19 | 36214602 | 36238774 | ENSG00000167635.11 | ZNF146 |
chr19 | 43967862 | 43998325 | ENSG00000204920.10 | ZNF155 |
chr19 | 53066606 | 53103436 | ENSG00000170949.17 | ZNF160 |
chr9 | 101398873 | 101410660 | ENSG00000136870.10 | ZNF189 |
chr3 | 44584888 | 44648471 | ENSG00000186448.14 | ZNF197 |
chr19 | 57630395 | 57642779 | ENSG00000121417.13 | ZNF211 |
chr19 | 43951223 | 43967709 | ENSG00000159905.14 | ZNF221 |
chr16 | 71447597 | 71463095 | ENSG00000167377.18 | ZNF23 |
chr10 | 43556344 | 43574618 | ENSG00000196793.13 | ZNF239 |
chr8 | 144720907 | 144756417 | ENSG00000198169.8 | ZNF251 |
chr19 | 52797409 | 52857600 | ENSG00000198538.10 | ZNF28 |
chr17 | 18658429 | 18682262 | ENSG00000249459.8 | ZNF286B |
chr19 | 34677639 | 34686397 | ENSG00000089335.20 | ZNF302 |
chr10 | 38094334 | 38150293 | ENSG00000075407.18 | ZNF37A |
chr19 | 57900296 | 57916610 | ENSG00000173480.10 | ZNF417 |
chr19 | 57487711 | 57496097 | ENSG00000105136.20 | ZNF419 |
chr19 | 52031379 | 52095738 | ENSG00000256087.6 | ZNF432 |
chr19 | 19785839 | 19821751 | ENSG00000081665.13 | ZNF506 |
chr19 | 36534774 | 36605276 | ENSG00000186020.12 | ZNF529 |
chr19 | 7069444 | 7087968 | ENSG00000130544.11 | ZNF557 |
chr19 | 36182060 | 36246257 | ENSG00000196357.11 | ZNF565 |
chr17 | 5179536 | 5191883 | ENSG00000180626.9 | ZNF594 |
chr19 | 52012765 | 52030240 | ENSG00000142556.18 | ZNF614 |
chr19 | 21291160 | 21329425 | ENSG00000182141.10 | ZNF708 |
chr16 | 31713229 | 31794869 | ENSG00000197302.10 | ZNF720 |
chrX | 135248920 | 135344087 | ENSG00000186376.14 | ZNF75D |
chr19 | 53431993 | 53458261 | ENSG00000160336.14 | ZNF761 |
chr19 | 53389793 | 53430413 | ENSG00000196417.12 | ZNF765 |
chr19 | 52269571 | 52296046 | ENSG00000196214.10 | ZNF766 |
chr19 | 57466663 | 57477570 | ENSG00000197128.11 | ZNF772 |
chr19 | 57746796 | 57758159 | ENSG00000152443.12 | ZNF776 |
chr19 | 40028260 | 40056209 | ENSG00000128000.15 | ZNF780B |
chrX | 47836902 | 48002561 | ENSG00000197779.13 | ZNF81 |
chr19 | 57848731 | 57889074 | ENSG00000204514.9 | ZNF814 |
chr19 | 52949379 | 52962911 | ENSG00000180257.13 | ZNF816 |
chr19 | 52928475 | 52962823 | ENSG00000221874.4 | ZNF816-ZNF321P |
chr19 | 11721265 | 11739009 | ENSG00000197933.12 | ZNF823 |
chr19 | 53333746 | 53356906 | ENSG00000213799.12 | ZNF845 |
chr3 | 44494847 | 44510636 | ENSG00000178917.16 | ZNF852 |
chr19 | 52904417 | 52923481 | ENSG00000213793.5 | ZNF888 |
chr2 | 135136916 | 135531236 | ENSG00000121988.17 | ZRANB3 |
chr18 | 35251058 | 35290245 | ENSG00000186814.13 | ZSCAN30 |
chr1 | 45016399 | 45306209 | ENSG00000162415.6 | ZSWIM5 |
Bear in mind that one peak can overlap ore than one genomic feature.
chrom | start | end | gene_id | gene_name |
---|---|---|---|---|
chr2 | 97416165 | 97433527 | ENSG00000230606.10 | AC092683.1 |
chr2 | 97421075 | 97434847 | ENSG00000278766.2 | AC092683.2 |
chr2 | 95807118 | 95816215 | ENSG00000232931.5 | LINC00342 |
chr22 | 30969245 | 30979395 | ENSG00000253352.9 | TUG1 |
chr22 | 30976515 | 30978848 | ENSG00000269987.1 | AC004542.2 |
chr22 | 30977516 | 30977858 | ENSG00000269972.1 | AC004542.1 |
chr2 | 97281904 | 97291780 | ENSG00000277701.4 | AC159540.2 |
chr6 | 71295173 | 71417436 | ENSG00000269966.1 | AL136164.2 |
chr6 | 71344344 | 71420769 | ENSG00000233237.6 | LINC00472 |
chr6 | 30234039 | 30326134 | ENSG00000270604.5 | HCG17 |
chr19 | 27684580 | 27793940 | ENSG00000261824.6 | LINC00662 |
chr19 | 27757184 | 27760849 | ENSG00000261770.1 | AC006504.1 |
chr13 | 95648733 | 95676925 | ENSG00000247400.3 | DNAJC3-DT |
chr6 | 2245748 | 2482022 | ENSG00000250903.8 | GMDS-DT |
chr11 | 59130133 | 59143015 | ENSG00000245571.6 | FAM111A-DT |
chr19 | 19761038 | 19821716 | ENSG00000267581.1 | AC011477.4 |
chr18 | 3284145 | 3327292 | ENSG00000266578.1 | AP001025.1 |
chr5 | 43061395 | 43062441 | ENSG00000272144.1 | AC025171.4 |
chr8 | 142981738 | 143018437 | ENSG00000247317.3 | LY6E-DT |
chr12 | 9240003 | 9257960 | ENSG00000237248.5 | LINC00987 |
chr12 | 9240406 | 9261050 | ENSG00000256427.2 | AC010175.1 |
chr1 | 148295895 | 148344636 | ENSG00000224481.2 | AC245100.1 |
chrX | 115917271 | 115969089 | ENSG00000235244.3 | DANT2 |
chr21 | 22008944 | 22098459 | ENSG00000233215.5 | LINC01687 |
chr12 | 79341205 | 79503396 | ENSG00000257894.2 | AC027288.3 |
chr1 | 229258281 | 229271028 | ENSG00000177788.5 | AL162595.1 |
chr2 | 118132128 | 118222250 | ENSG00000226856.6 | THORLNC |
chr10 | 125700436 | 125719566 | ENSG00000224023.10 | FLJ37035 |
chr14 | 28830244 | 28968400 | ENSG00000258038.5 | LINC02327 |
chr9 | 95759231 | 95875977 | ENSG00000175611.11 | LINC00476 |
chr21 | 15928296 | 16645065 | ENSG00000215386.12 | MIR99AHG |
chr21 | 22098617 | 22116528 | ENSG00000184856.6 | LINC00308 |
chr6 | 140575788 | 140898381 | ENSG00000285875.1 | AL035446.2 |
chr19 | 53007512 | 53013180 | ENSG00000267943.1 | AC010328.1 |
chr4 | 134759399 | 134817289 | ENSG00000249000.1 | AC093722.1 |
Families of repeats that overlap with peaks that are loss in TKO with respect to D3:
PieChart showing the proportion of classes of repeats overlapped by TKO/D3 peaks.
TKO/D3 peaks overlap with repetitive elements. Because H3K9me3 regions controlled by TASOR extend over many thousand of bases, most peaks overlap with more than one repeat. Their characteristics are summarised in Figure (pie chart).
This second piechart shows the same information but distributed into different bespoke categories.
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] viridis_0.5.1 viridisLite_0.3.0 edgeR_3.26.8
## [4] limma_3.40.6 ggplot2_3.2.1 GenomicRanges_1.36.1
## [7] GenomeInfoDb_1.20.0 IRanges_2.18.3 S4Vectors_0.22.1
## [10] BiocGenerics_0.30.0 tidyr_1.0.0 kableExtra_1.1.0
## [13] RColorBrewer_1.1-2 knitr_1.25
##
## loaded via a namespace (and not attached):
## [1] locfit_1.5-9.1 Rcpp_1.0.2
## [3] lattice_0.20-38 Rsamtools_2.0.2
## [5] Biostrings_2.52.0 assertthat_0.2.1
## [7] zeallot_0.1.0 digest_0.6.21
## [9] R6_2.4.0 backports_1.1.5
## [11] evaluate_0.14 highr_0.8
## [13] httr_1.4.1 pillar_1.4.2
## [15] zlibbioc_1.30.0 rlang_0.4.0
## [17] lazyeval_0.2.2 rstudioapi_0.10
## [19] Matrix_1.2-17 rmarkdown_1.16
## [21] labeling_0.3 webshot_0.5.1
## [23] BiocParallel_1.18.1 readr_1.3.1
## [25] stringr_1.4.0 RCurl_1.95-4.12
## [27] munsell_0.5.0 DelayedArray_0.10.0
## [29] compiler_3.6.1 rtracklayer_1.44.4
## [31] xfun_0.10 pkgconfig_2.0.3
## [33] htmltools_0.4.0 tidyselect_0.2.5
## [35] SummarizedExperiment_1.14.1 gridExtra_2.3
## [37] tibble_2.1.3 GenomeInfoDbData_1.2.1
## [39] matrixStats_0.55.0 XML_3.98-1.20
## [41] crayon_1.3.4 dplyr_0.8.3
## [43] withr_2.1.2 GenomicAlignments_1.20.1
## [45] bitops_1.0-6 grid_3.6.1
## [47] gtable_0.3.0 lifecycle_0.1.0
## [49] magrittr_1.5 scales_1.0.0
## [51] stringi_1.4.3 XVector_0.24.0
## [53] xml2_1.2.2 vctrs_0.2.0
## [55] tools_3.6.1 Biobase_2.44.0
## [57] glue_1.3.1 purrr_0.3.2
## [59] hms_0.5.1 yaml_2.2.0
## [61] colorspace_1.4-1 rvest_0.3.4